Diff of the two buildlogs: -- --- b1/build.log 2023-05-10 22:59:09.684950084 +0000 +++ b2/build.log 2023-05-10 23:29:14.361829770 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed May 10 10:37:53 -12 2023 -I: pbuilder-time-stamp: 1683758273 +I: Current time: Wed Jun 12 19:22:18 +14 2024 +I: pbuilder-time-stamp: 1718169738 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./spades_3.15.5+dfsg.orig.tar.xz] I: copying [./spades_3.15.5+dfsg-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Oct 23 04:50:26 2022 -12 +gpgv: Signature made Mon Oct 24 06:50:26 2022 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key @@ -44,135 +44,167 @@ dpkg-source: info: applying typos.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3234275/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4106413/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 12 19:23 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/4106413/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4106413/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='3346a85900b14057ad8433ca644ce7d9' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3234275' - PS1='# ' - PS2='> ' + INVOCATION_ID=60c417aa616f4c6887bc583614f068a5 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=4106413 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.bEtEXioH/pbuilderrc_6S2w --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bEtEXioH/b1 --logfile b1/build.log spades_3.15.5+dfsg-2.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.bEtEXioH/pbuilderrc_22Kz --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bEtEXioH/b2 --logfile b2/build.log --extrapackages usrmerge spades_3.15.5+dfsg-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos1-amd64 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more - -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount - -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/3234275/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 2023 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 2023 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 2023 more + -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount + -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 Jun 12 19:23 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 2023 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/4106413/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -401,7 +433,7 @@ Get: 147 http://deb.debian.org/debian bookworm/main amd64 lynx amd64 2.9.0dev.12-1 [637 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get: 149 http://deb.debian.org/debian bookworm/main amd64 python3-joblib all 1.2.0-4 [211 kB] -Fetched 175 MB in 3s (51.9 MB/s) +Fetched 175 MB in 8s (22.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) @@ -1021,8 +1053,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/spades-3.15.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../spades_3.15.5+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/4106413/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/4106413/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/spades-3.15.5+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../spades_3.15.5+dfsg-2_source.changes dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 3.15.5+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -1260,7 +1303,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/spades-3.15.5+dfsg' dh_auto_build -- all debruijn_test include_test - cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" all debruijn_test include_test VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" all debruijn_test include_test VERBOSE=1 make[2]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/spades-3.15.5+dfsg/assembler/src -B/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -1270,74 +1313,88 @@ make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake --color= make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/cppformat /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake --color= make -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/depend make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd 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/build/spades-3.15.5+dfsg/assembler/ext/src/gqf /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake --color= -make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/edlib /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake --color= +make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/depend make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/edlib /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake --color= +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/gfa1 /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1/CMakeFiles/gfa1.dir/DependInfo.cmake --color= make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/build +make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/depend +make[4]: 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ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/build +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Mutation.cpp.o -MF CMakeFiles/ConsensusCore.dir/Mutation.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Mutation.cpp +[ 0%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o -MF CMakeFiles/BamTools.dir/BamAlignment.cpp.o.d -o CMakeFiles/BamTools.dir/BamAlignment.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/BamAlignment.cpp make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o -MF CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o.d -o CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/AffineAlignment.cpp [ 0%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Coverage.cpp.o -[ 0%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Mutation.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Mutation.cpp.o -MF CMakeFiles/ConsensusCore.dir/Mutation.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Mutation.cpp -[ 0%] Building CXX object ext/cppformat/CMakeFiles/format.dir/format.cc.o [ 0%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/cppformat -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wall -Wextra -pedantic -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/cppformat/CMakeFiles/format.dir/format.cc.o -MF CMakeFiles/format.dir/format.cc.o.d -o CMakeFiles/format.dir/format.cc.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/cppformat/format.cc cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Coverage.cpp.o -MF CMakeFiles/ConsensusCore.dir/Coverage.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Coverage.cpp -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include 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-I/build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -MF CMakeFiles/ConsensusCore.dir/Sequence.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Sequence.cpp [ 2%] Building C object ext/gqf/CMakeFiles/gqf.dir/gqf.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/getopt_pp/CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o -MF CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o.d -o CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/getopt_pp/getopt_pp.cpp cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/gqf/CMakeFiles/gqf.dir/gqf.c.o -MF CMakeFiles/gqf.dir/gqf.c.o.d -o CMakeFiles/gqf.dir/gqf.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -MF CMakeFiles/ConsensusCore.dir/Sequence.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Sequence.cpp -[ 2%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o -MF CMakeFiles/ConsensusCore.dir/Utils.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Utils.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Utils.cpp -[ 2%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o [ 2%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o +[ 2%] Building C object ext/gfa1/CMakeFiles/gfa1.dir/gfa.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/gfa1/CMakeFiles/gfa1.dir/gfa.c.o -MF CMakeFiles/gfa1.dir/gfa.c.o.d -o CMakeFiles/gfa1.dir/gfa.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/gfa1/gfa.c +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem 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/build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/easel.c.o -MF CMakeFiles/easel.dir/easel.c.o.d -o CMakeFiles/easel.dir/easel.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/easel.c /build/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c: In function 'qf_dump_block': /build/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c:610:30: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 610 | printf("%02llx ", j); @@ -1386,120 +1443,103 @@ /build/spades-3.15.5+dfsg/assembler/ext/src/gqf/gqf.c:1615:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1615 | fread(qf->blocks, qf->metadata->size, 1, fin); | 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CMakeFiles/gqf.dir/link.txt --verbose=1 /usr/bin/ar qc libgqf.a CMakeFiles/gqf.dir/gqf.c.o /usr/bin/ranlib libgqf.a -[ 2%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o -MF CMakeFiles/BamTools.dir/SamHeader.cpp.o.d -o CMakeFiles/BamTools.dir/SamHeader.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamHeader.cpp make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 2%] Built target gqf -make -f ext/easel/CMakeFiles/easel.dir/build.make ext/easel/CMakeFiles/easel.dir/depend +[ 3%] Built target gqf +make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/easel /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel 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ext/easel/CMakeFiles/easel.dir/easel.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/easel.c.o -MF CMakeFiles/easel.dir/easel.c.o.d -o CMakeFiles/easel.dir/easel.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/easel.c -[ 3%] Building CXX object 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/build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_avx.c.o -MF CMakeFiles/easel.dir/esl_avx.c.o.d -o CMakeFiles/easel.dir/esl_avx.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_avx.c +[ 3%] Building C object ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o -MF CMakeFiles/easel.dir/esl_buffer.c.o.d -o CMakeFiles/easel.dir/esl_buffer.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_buffer.c +[ 3%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o -MF CMakeFiles/BamTools.dir/SamHeader.cpp.o.d -o CMakeFiles/BamTools.dir/SamHeader.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamHeader.cpp +[ 3%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common 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/build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaGraph.cpp +[ 4%] Building C object ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o -MF CMakeFiles/easel.dir/esl_cluster.c.o.d -o CMakeFiles/easel.dir/esl_cluster.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_cluster.c [ 4%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -MF CMakeFiles/BamTools.dir/SamProgramChain.cpp.o.d -o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamProgramChain.cpp -[ 4%] Linking CXX static library libgetopt_pp.a +[ 4%] Building C object ext/easel/CMakeFiles/easel.dir/esl_composition.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_composition.c.o -MF CMakeFiles/easel.dir/esl_composition.c.o.d -o CMakeFiles/easel.dir/esl_composition.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_composition.c +[ 5%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o -MF CMakeFiles/easel.dir/esl_dirichlet.c.o.d -o CMakeFiles/easel.dir/esl_dirichlet.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_dirichlet.c +[ 6%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o -MF CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConfig.cpp +[ 6%] Linking CXX static library libgetopt_pp.a cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/cmake -P CMakeFiles/getopt_pp.dir/cmake_clean_target.cmake cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/getopt_pp && /usr/bin/cmake -E cmake_link_script CMakeFiles/getopt_pp.dir/link.txt --verbose=1 /usr/bin/ar qc libgetopt_pp.a CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o /usr/bin/ranlib libgetopt_pp.a -[ 5%] Linking CXX static library libedlib.a -cd 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ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -MF CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaConsensus.cpp make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 6%] Building C object ext/easel/CMakeFiles/easel.dir/esl_alphabet.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_alphabet.c.o -MF CMakeFiles/easel.dir/esl_alphabet.c.o.d -o CMakeFiles/easel.dir/esl_alphabet.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_alphabet.c [ 6%] Built target getopt_pp -make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest 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-I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -I/build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wall -Wshadow -Werror -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated -O2 -std=c++14 -MD -MT ext/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o -MF CMakeFiles/gtest.dir/src/gtest-all.cc.o.d -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/src/gtest-all.cc -/usr/bin/ranlib libedlib.a -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 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-I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -MF CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o.d -o CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp -[ 6%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o +[ 8%] Building CXX object 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-D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o -MF CMakeFiles/llvm-support.dir/APInt.cpp.o.d -o CMakeFiles/llvm-support.dir/APInt.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/APInt.cpp -[ 6%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -MF CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamReadGroupDictionary.cpp -[ 6%] Building C object ext/easel/CMakeFiles/easel.dir/esl_avx.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_avx.c.o -MF CMakeFiles/easel.dir/esl_avx.c.o.d -o CMakeFiles/easel.dir/esl_avx.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_avx.c -[ 6%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o -MF CMakeFiles/BamTools.dir/SamSequence.cpp.o.d -o CMakeFiles/BamTools.dir/SamSequence.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamSequence.cpp -[ 6%] Building C object ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_buffer.c.o -MF CMakeFiles/easel.dir/esl_buffer.c.o.d -o CMakeFiles/easel.dir/esl_buffer.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_buffer.c -[ 8%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -MF CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamSequenceDictionary.cpp [ 8%] Linking C static library libgfa1.a cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gfa1 && /usr/bin/cmake -P CMakeFiles/gfa1.dir/cmake_clean_target.cmake cd 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/build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamMultiReader_p.cpp make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 8%] Built target gfa1 -make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend +make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend make[4]: Entering directory 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ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build +make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 9%] Building CXX object ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc && /usr/bin/c++ -DMI_MALLOC_OVERRIDE -DMI_MALLOC_OVERRIDE_GLIBC -DMI_SHOW_ERRORS=1 -DMI_XMALLOC=1 -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -fPIC -Wno-deprecated -O2 -Wall -Wextra -Wno-unknown-pragmas -fvisibility=hidden -Wno-invalid-memory-model -ftls-model=initial-exec -std=gnu++17 -MD -MT ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o -MF CMakeFiles/mimalloc-obj.dir/src/static.c.o.d -o CMakeFiles/mimalloc-obj.dir/src/static.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c -[ 9%] Building C object ext/easel/CMakeFiles/easel.dir/esl_cluster.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem 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/build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_composition.c.o -MF CMakeFiles/easel.dir/esl_composition.c.o.d -o CMakeFiles/easel.dir/esl_composition.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_composition.c -[ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dirichlet.c.o -MF CMakeFiles/easel.dir/esl_dirichlet.c.o.d -o CMakeFiles/easel.dir/esl_dirichlet.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_dirichlet.c +[ 9%] Linking CXX static library libedlib.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake +[ 9%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/common/io/binary -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o -MF CMakeFiles/binary_io.dir/graph_pack.cpp.o.d -o CMakeFiles/binary_io.dir/graph_pack.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edlib.dir/link.txt --verbose=1 +/usr/bin/ar qc libedlib.a CMakeFiles/edlib.dir/edlib.cpp.o +/usr/bin/ranlib libedlib.a +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 9%] Built target edlib +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake --color= In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:28: /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/region.c: In function 'void _mi_mem_collect(mi_os_tld_t*)': /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/region.c:466:15: warning: 'void* memset(void*, int, size_t)' clearing an object of type 'mem_region_t' {aka 'struct mem_region_s'} with no trivial copy-assignment; use value-initialization instead [-Wclass-memaccess] @@ -1508,6 +1548,11 @@ /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/region.c:89:16: note: 'mem_region_t' {aka 'struct mem_region_s'} declared here 89 | typedef struct mem_region_s { | ^~~~~~~~~~~~ +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 9%] Building CXX object common/utils/CMakeFiles/version.dir/version.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/version.dir/version.cpp.o -MF CMakeFiles/version.dir/version.cpp.o.d -o CMakeFiles/version.dir/version.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/utils/version.cpp In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:31: /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/heap.c: In function 'mi_heap_t* mi_heap_new()': /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/heap.c:196:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'mi_heap_t' {aka 'struct mi_heap_s'} with no trivial copy-assignment [-Wclass-memaccess] @@ -1620,6 +1665,9 @@ /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/alloc-override.c:196:53: note: in expansion of macro 'MI_FORWARD2' 196 | void* __libc_realloc(void* p, size_t size) MI_FORWARD2(mi_realloc,p,size); | ^~~~~~~~~~~ +[ 10%] Linking CXX static library libversion.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/version.dir/cmake_clean_target.cmake +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/version.dir/link.txt --verbose=1 In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/static.c:38: /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/init.c: In function 'bool _mi_heap_init()': /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/src/init.c:192:11: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'mi_heap_t' {aka 'struct mi_heap_s'} with no trivial copy-assignment [-Wclass-memaccess] @@ -1628,61 +1676,35 @@ /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include/mimalloc-types.h:340:8: note: 'mi_heap_t' {aka 'struct mi_heap_s'} declared here 340 | struct mi_heap_s { | ^~~~~~~~~ -[ 10%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamRandomAccessController_p.cpp -[ 11%] Linking CXX static library libformat.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake -[ 11%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamReader_p.cpp -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat && /usr/bin/cmake -E cmake_link_script CMakeFiles/format.dir/link.txt --verbose=1 -/usr/bin/ar qc libformat.a CMakeFiles/format.dir/format.cc.o CMakeFiles/format.dir/posix.cc.o -/usr/bin/ranlib libformat.a -[ 11%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o +/usr/bin/ar qc libversion.a CMakeFiles/version.dir/version.cpp.o +[ 10%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -MF CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamReadGroupDictionary.cpp +[ 10%] Building C object ext/easel/CMakeFiles/easel.dir/esl_distance.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_distance.c.o -MF CMakeFiles/easel.dir/esl_distance.c.o.d -o CMakeFiles/easel.dir/esl_distance.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_distance.c +/usr/bin/ranlib libversion.a make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 11%] Built target format -make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend +[ 10%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o -MF CMakeFiles/BamTools.dir/SamSequence.cpp.o.d -o CMakeFiles/BamTools.dir/SamSequence.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamSequence.cpp +[ 10%] Built target version +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/io/binary /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake --color= +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/sequence /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 11%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/common/io/binary -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o -MF CMakeFiles/binary_io.dir/graph_pack.cpp.o.d -o CMakeFiles/binary_io.dir/graph_pack.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp -[ 12%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamWriter_p.cpp -/build/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': -/build/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:325:23: warning: conversion from 'size_t' {aka 'long unsigned int'} to '__gnu_cxx::__alloc_traits, double>::value_type' {aka 'double'} may change value [-Wconversion] - 325 | if (converged_ && Valley_ > x[2] && x[2] > 2) { - | ^~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:359:28: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 359 | ErrorThreshold_ = (Valley_ < mean_coverage_ ? - | ^~~~~~~ -[ 12%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamIndexFactory_p.cpp -[ 12%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -cd 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common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o -MF CMakeFiles/sequence.dir/sequence_tools.cpp.o.d -o CMakeFiles/sequence.dir/sequence_tools.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/sequence/sequence_tools.cpp +[ 12%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -MF CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/SamSequenceDictionary.cpp +[ 12%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore -I/build/spades-3.15.5+dfsg/assembler/src/../ext/include/ConsensusCore -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o -MF CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o.d -o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/ConsensusCore/Poa/PoaGraph.cpp [ 12%] Building C object ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_dmatrix.c.o -MF CMakeFiles/easel.dir/esl_dmatrix.c.o.d -o CMakeFiles/easel.dir/esl_dmatrix.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_dmatrix.c -[ 12%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o -MF CMakeFiles/llvm-support.dir/Atomic.cpp.o.d -o CMakeFiles/llvm-support.dir/Atomic.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Atomic.cpp -[ 12%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamToolsIndex_p.cpp -[ 13%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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ext/easel/CMakeFiles/easel.dir/esl_dsqdata.c.o -MF CMakeFiles/easel.dir/esl_dsqdata.c.o.d -o CMakeFiles/easel.dir/esl_dsqdata.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_dsqdata.c -[ 15%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat 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-I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/ByteArray_p.cpp -[ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o +[ 12%] Building C object ext/easel/CMakeFiles/easel.dir/esl_exponential.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG 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ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_fileparser.c.o -MF CMakeFiles/easel.dir/esl_fileparser.c.o.d -o CMakeFiles/easel.dir/esl_fileparser.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c: In function 'esl_fileparser_NextLine': /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:278:21: warning: comparison between pointer and zero character constant [-Wpointer-compare] @@ -1698,116 +1720,93 @@ /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_fileparser.c:359:10: note: did you mean to dereference the pointer? 359 | while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; | ^ -[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools 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CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamHeader_p.cpp +[ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gencode.c.o -MF CMakeFiles/easel.dir/esl_gencode.c.o.d -o CMakeFiles/easel.dir/esl_gencode.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gencode.c -[ 17%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -[ 17%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/SerialBgzfStream_p.cpp -[ 17%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:32: -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c: In function 'bgzf_check_EOF': -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:73:34: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 73 | #define _bgzf_read(fp, buf, len) fread(buf, 1, len, (_bgzf_file_t)fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:578:9: note: in expansion of macro '_bgzf_read' - 578 | _bgzf_read(fp->fp, buf, 28); - | ^~~~~~~~~~ -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c -In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:46: -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'kftp_send_cmd': -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) - | ^~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:236:9: note: in expansion of macro 'netwrite' - 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'khttp_connect_file': -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) - | ^~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:415:9: note: in expansion of macro 'netwrite' - 415 | netwrite(fp->fd, buf, l); - | ^~~~~~~~ -[ 17%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o -MF CMakeFiles/llvm-support.dir/Errno.cpp.o.d -o CMakeFiles/llvm-support.dir/Errno.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Errno.cpp -[ 17%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c +[ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -MF CMakeFiles/easel.dir/esl_getopts.c.o.d -o CMakeFiles/easel.dir/esl_getopts.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_getopts.c +[ 15%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gev.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gev.c.o -MF CMakeFiles/easel.dir/esl_gev.c.o.d -o CMakeFiles/easel.dir/esl_gev.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gev.c +[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o -MF CMakeFiles/easel.dir/esl_gumbel.c.o.d -o CMakeFiles/easel.dir/esl_gumbel.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gumbel.c +[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_heap.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_heap.c.o -MF CMakeFiles/easel.dir/esl_heap.c.o.d -o CMakeFiles/easel.dir/esl_heap.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_heap.c +[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o -MF CMakeFiles/easel.dir/esl_histogram.c.o.d -o CMakeFiles/easel.dir/esl_histogram.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_histogram.c +/build/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': +/build/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:325:23: warning: conversion from 'size_t' {aka 'long unsigned int'} to '__gnu_cxx::__alloc_traits, double>::value_type' {aka 'double'} may change value [-Wconversion] + 325 | if (converged_ && Valley_ > x[2] && x[2] > 2) { + | ^~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model/kmer_coverage_model.cpp:359:28: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 359 | ErrorThreshold_ = (Valley_ < mean_coverage_ ? + | ^~~~~~~ +[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o -MF CMakeFiles/easel.dir/esl_hmm.c.o.d -o CMakeFiles/easel.dir/esl_hmm.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_hmm.c +[ 16%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -MF CMakeFiles/easel.dir/esl_hyperexp.c.o.d -o CMakeFiles/easel.dir/esl_hyperexp.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_hyperexp.c +[ 16%] Linking CXX static library libsequence.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -P CMakeFiles/sequence.dir/cmake_clean_target.cmake +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/sequence.dir/link.txt --verbose=1 +[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamMultiReader_p.cpp +/usr/bin/ar qc libsequence.a CMakeFiles/sequence.dir/sequence_tools.cpp.o +/usr/bin/ranlib libsequence.a +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 16%] Built target sequence +make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/depend +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/io/graph /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 16%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_reader.cpp.o -MF CMakeFiles/graphio.dir/gfa_reader.cpp.o.d -o CMakeFiles/graphio.dir/gfa_reader.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp +[ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamRandomAccessController_p.cpp +[ 17%] Building C object ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o +cd 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ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/bam/BamReader_p.cpp +[ 18%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp 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-ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -MF CMakeFiles/easel.dir/esl_mem.c.o.d -o CMakeFiles/easel.dir/esl_mem.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mem.c +[ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o -MF CMakeFiles/easel.dir/esl_minimizer.c.o.d -o CMakeFiles/easel.dir/esl_minimizer.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_minimizer.c +[ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o -MF CMakeFiles/easel.dir/esl_mixgev.c.o.d -o CMakeFiles/easel.dir/esl_mixgev.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mixgev.c +[ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o -MF CMakeFiles/easel.dir/esl_mpi.c.o.d -o CMakeFiles/easel.dir/esl_mpi.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mpi.c +[ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msa.c.o -MF CMakeFiles/easel.dir/esl_msa.c.o.d -o CMakeFiles/easel.dir/esl_msa.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msa.c +[ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o -MF CMakeFiles/easel.dir/esl_msacluster.c.o.d -o CMakeFiles/easel.dir/esl_msacluster.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msacluster.c +[ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o -MF CMakeFiles/easel.dir/esl_msafile.c.o.d -o CMakeFiles/easel.dir/esl_msafile.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile.c +[ 19%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o -MF CMakeFiles/easel.dir/esl_msafile2.c.o.d -o CMakeFiles/easel.dir/esl_msafile2.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile2.c /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In member function 'virtual bool io::binary::FullPackIO::BinRead(std::istream&, Type&)': /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:363:10: warning: unused variable 'loaded' [-Wunused-variable] 363 | bool loaded = base::BinRead(is, gp); | ^~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:5: -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined - 8 | safe_mutex_unlock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined - 5 | safe_mutex_lock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:4: -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined - 240 | unpackInt16(const uint8_t* buffer); - | ^~~~~~~~~~~ -[ 18%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c -[ 18%] Building C object ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_getopts.c.o -MF CMakeFiles/easel.dir/esl_getopts.c.o.d -o CMakeFiles/easel.dir/esl_getopts.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_getopts.c -In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:12: -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined - 8 | safe_mutex_unlock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined - 5 | safe_mutex_lock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:11: -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined - 240 | unpackInt16(const uint8_t* buffer); - | ^~~~~~~~~~~ -[ 18%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c -[ 18%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c -In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:14: -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined - 8 | safe_mutex_unlock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined - 5 | safe_mutex_lock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:13: -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined - 240 | unpackInt16(const uint8_t* buffer); - | ^~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c: In function 'queue_print_status': -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c:344:62: warning: format '%lld' expects argument of type 'long long int', but argument 8 has type 'int64_t' {aka 'long int'} [-Wformat=] - 344 | fprintf(fp, "mem=%d head=%d tail=%d n=%d length=%d id=%lld ordered=%d num_adders=%d num_getters=%d\n", - | ~~~^ - | | - | long long int - | %ld - 345 | q->mem, q->head, q->tail, q->n, q->length, q->id, q->ordered, q->num_adders, q->num_getters); - | ~~~~~ - | | - | int64_t {aka long int} -In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c:6: -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h: At top level: -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined - 8 | safe_mutex_unlock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined - 5 | safe_mutex_lock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~ -[ 18%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:7: /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': @@ -1820,7 +1819,6 @@ /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] 101 | bool loaded = io.Load(basename, component); | ^~~~~~ -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::Loader::Load() [with T = debruijn_graph::EdgeIndex]': /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:213:34: required from here /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:101:14: warning: unused variable 'loaded' [-Wunused-variable] @@ -1840,221 +1838,36 @@ /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] 130 | auto loaded = io.BinRead(is, component); | ^~~~~~ -[ 18%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::EdgeIndex]': /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:259:34: required from here /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = debruijn_graph::KmerMapper]': /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:262:35: required from here /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.c /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp: In instantiation of 'void io::binary::{anonymous}::BinReader::Read() [with T = omnigraph::FlankingCoverage]': /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:265:41: required from here /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.cpp:130:14: warning: unused variable 'loaded' [-Wunused-variable] -[ 18%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o -MF CMakeFiles/llvm-support.dir/Error.cpp.o.d -o CMakeFiles/llvm-support.dir/Error.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Error.cpp -In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8: -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined - 8 | safe_mutex_unlock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined - 5 | safe_mutex_lock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:7: -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined - 240 | unpackInt16(const uint8_t* buffer); - | ^~~~~~~~~~~ -[ 19%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c -[ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatParser_p.cpp -[ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.cpp -In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11, - from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10: -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined - 8 | safe_mutex_unlock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined - 5 | safe_mutex_lock(pthread_mutex_t *mutex); - | ^~~~~~~~~~~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:7: -/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined - 240 | unpackInt16(const uint8_t* buffer); - | ^~~~~~~~~~~ -[ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp -[ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/utils/BamException_p.cpp -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 19%] Built target mimalloc-obj -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 19%] Building CXX object common/utils/CMakeFiles/version.dir/version.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/version.dir/version.cpp.o -MF CMakeFiles/version.dir/version.cpp.o.d -o CMakeFiles/version.dir/version.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/utils/version.cpp -[ 20%] Linking CXX static library libversion.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/version.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/version.dir/link.txt --verbose=1 -/usr/bin/ar qc libversion.a CMakeFiles/version.dir/version.cpp.o -[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gev.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gev.c.o -MF CMakeFiles/easel.dir/esl_gev.c.o.d -o CMakeFiles/easel.dir/esl_gev.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gev.c -/usr/bin/ranlib libversion.a -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -MF CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d -o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/ErrorHandling.cpp -[ 20%] Built target version -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/sequence /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 22%] Building CXX object common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o -MF CMakeFiles/sequence.dir/sequence_tools.cpp.o.d -o CMakeFiles/sequence.dir/sequence_tools.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/sequence/sequence_tools.cpp -[ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -MF CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d -o CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/FoldingSet.cpp -[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_gumbel.c.o -MF CMakeFiles/easel.dir/esl_gumbel.c.o.d -o CMakeFiles/easel.dir/esl_gumbel.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_gumbel.c -[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_heap.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_heap.c.o -MF CMakeFiles/easel.dir/esl_heap.c.o.d -o CMakeFiles/easel.dir/esl_heap.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_heap.c -[ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -MF CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d -o CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/FormatVariadic.cpp -[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_histogram.c.o -MF CMakeFiles/easel.dir/esl_histogram.c.o.d -o CMakeFiles/easel.dir/esl_histogram.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_histogram.c -[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hmm.c.o -MF CMakeFiles/easel.dir/esl_hmm.c.o.d -o CMakeFiles/easel.dir/esl_hmm.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_hmm.c -[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_hyperexp.c.o -MF CMakeFiles/easel.dir/esl_hyperexp.c.o.d -o CMakeFiles/easel.dir/esl_hyperexp.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_hyperexp.c -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); - | ^~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ -[ 24%] Linking CXX static library libcoverage_model.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -P CMakeFiles/coverage_model.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -E cmake_link_script CMakeFiles/coverage_model.dir/link.txt --verbose=1 -/usr/bin/ar qc libcoverage_model.a CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_keyhash.c.o -MF CMakeFiles/easel.dir/esl_keyhash.c.o.d -o CMakeFiles/easel.dir/esl_keyhash.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_keyhash.c -/usr/bin/ranlib libcoverage_model.a -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 25%] Built target coverage_model -make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/paired_info /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -[ 25%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/distance_estimation.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.cpp -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mem.c.o -MF CMakeFiles/easel.dir/esl_mem.c.o.d -o CMakeFiles/easel.dir/esl_mem.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mem.c -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_minimizer.c.o -MF CMakeFiles/easel.dir/esl_minimizer.c.o.d -o CMakeFiles/easel.dir/esl_minimizer.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_minimizer.c -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mixgev.c.o -MF CMakeFiles/easel.dir/esl_mixgev.c.o.d -o CMakeFiles/easel.dir/esl_mixgev.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mixgev.c -[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_mpi.c.o -MF CMakeFiles/easel.dir/esl_mpi.c.o.d -o CMakeFiles/easel.dir/esl_mpi.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_mpi.c -[ 25%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.cpp -[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msa.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msa.c.o -MF CMakeFiles/easel.dir/esl_msa.c.o.d -o CMakeFiles/easel.dir/esl_msa.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msa.c -[ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o -MF CMakeFiles/llvm-support.dir/Hashing.cpp.o.d -o CMakeFiles/llvm-support.dir/Hashing.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Hashing.cpp -[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msacluster.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp 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-D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile.c.o -MF CMakeFiles/easel.dir/esl_msafile.c.o.d -o CMakeFiles/easel.dir/esl_msafile.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile.c -[ 27%] Linking CXX static library libBamTools.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1 -[ 27%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o -MF CMakeFiles/llvm-support.dir/Host.cpp.o.d -o CMakeFiles/llvm-support.dir/Host.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Host.cpp -[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile2.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem 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CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -[ 27%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG 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directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 27%] Built target BamTools -make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/io/graph /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph/CMakeFiles/graphio.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/io/graph/CMakeFiles/graphio.dir/build.make common/io/graph/CMakeFiles/graphio.dir/build -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 27%] Building CXX object 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/build/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp -[ 29%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o -MF CMakeFiles/llvm-support.dir/LEB128.cpp.o.d -o CMakeFiles/llvm-support.dir/LEB128.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/LEB128.cpp -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o +[ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamIndexFactory_p.cpp +[ 19%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o -MF CMakeFiles/llvm-support.dir/APInt.cpp.o.d -o CMakeFiles/llvm-support.dir/APInt.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/APInt.cpp +[ 19%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamStandardIndex_p.cpp +[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_afa.c.o -MF CMakeFiles/easel.dir/esl_msafile_afa.c.o.d -o CMakeFiles/easel.dir/esl_msafile_afa.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_afa.c -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o -MF CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d -o CMakeFiles/llvm-support.dir/LineIterator.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/LineIterator.cpp -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o -MF CMakeFiles/easel.dir/esl_msafile_clustal.c.o.d -o CMakeFiles/easel.dir/esl_msafile_clustal.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_clustal.c -[ 30%] Linking CXX static library libsequence.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -P CMakeFiles/sequence.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/sequence.dir/link.txt --verbose=1 -/usr/bin/ar qc libsequence.a CMakeFiles/sequence.dir/sequence_tools.cpp.o -/usr/bin/ranlib libsequence.a make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 30%] Built target sequence +[ 20%] Built target mimalloc-obj make -f projects/spaligner/CMakeFiles/mapping_printer.dir/build.make projects/spaligner/CMakeFiles/mapping_printer.dir/depend make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/spaligner /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/mapping_printer.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/spaligner/CMakeFiles/mapping_printer.dir/build.make projects/spaligner/CMakeFiles/mapping_printer.dir/build make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o -MF CMakeFiles/easel.dir/esl_msafile_phylip.c.o.d -o CMakeFiles/easel.dir/esl_msafile_phylip.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_phylip.c -[ 30%] Building CXX object projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o +[ 20%] Building CXX object projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/spaligner -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spaligner/CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o -MF CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o.d -o CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spaligner/mapping_printer.cpp -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -MF CMakeFiles/easel.dir/esl_msafile_psiblast.c.o.d -o CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_psiblast.c -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -MF CMakeFiles/llvm-support.dir/Locale.cpp.o.d -o CMakeFiles/llvm-support.dir/Locale.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Locale.cpp -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -MF CMakeFiles/easel.dir/esl_msafile_selex.c.o.d -o CMakeFiles/easel.dir/esl_msafile_selex.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_selex.c -[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -MF CMakeFiles/easel.dir/esl_msafile_stockholm.c.o.d -o CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_stockholm.c -[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -MF CMakeFiles/llvm-support.dir/MD5.cpp.o.d -o CMakeFiles/llvm-support.dir/MD5.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/MD5.cpp -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o -MF CMakeFiles/easel.dir/esl_msashuffle.c.o.d -o CMakeFiles/easel.dir/esl_msashuffle.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msashuffle.c -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o -MF CMakeFiles/easel.dir/esl_msaweight.c.o.d -o CMakeFiles/easel.dir/esl_msaweight.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msaweight.c -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -MF CMakeFiles/easel.dir/esl_normal.c.o.d -o CMakeFiles/easel.dir/esl_normal.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_normal.c -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_paml.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_paml.c.o -MF CMakeFiles/easel.dir/esl_paml.c.o.d -o CMakeFiles/easel.dir/esl_paml.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_paml.c -[ 31%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -MF CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d -o CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/ManagedStatic.cpp -[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_random.c.o -MF CMakeFiles/easel.dir/esl_random.c.o.d -o CMakeFiles/easel.dir/esl_random.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_random.c -[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o -MF CMakeFiles/easel.dir/esl_randomseq.c.o.d -o CMakeFiles/easel.dir/esl_randomseq.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_randomseq.c -[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o -MF CMakeFiles/easel.dir/esl_ratematrix.c.o.d -o CMakeFiles/easel.dir/esl_ratematrix.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_ratematrix.c -[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o -MF CMakeFiles/easel.dir/esl_recorder.c.o.d -o CMakeFiles/easel.dir/esl_recorder.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_recorder.c -[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o -MF CMakeFiles/easel.dir/esl_regexp.c.o.d -o CMakeFiles/easel.dir/esl_regexp.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_regexp.c -[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -MF CMakeFiles/easel.dir/esl_rootfinder.c.o.d -o CMakeFiles/easel.dir/esl_rootfinder.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_rootfinder.c -[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -MF CMakeFiles/easel.dir/esl_scorematrix.c.o.d -o CMakeFiles/easel.dir/esl_scorematrix.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c +[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.cpp:10: /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp: In instantiation of 'void omnigraph::ConstructionHelper::DeleteLink(VertexId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; VertexId = omnigraph::impl::VertexId; EdgeId = omnigraph::impl::EdgeId]': /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:97:9: required from 'void omnigraph::ConstructionHelper::LinkEdges(EdgeId, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster; EdgeId = omnigraph::impl::EdgeId]' @@ -2062,36 +1875,38 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:102:14: warning: unused variable 'res' [-Wunused-variable] 102 | bool res = graph_.vertex(v).RemoveOutgoingEdge(e); | ^~~ -[ 33%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sq.c.o -MF CMakeFiles/easel.dir/esl_sq.c.o.d -o CMakeFiles/easel.dir/esl_sq.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sq.c -[ 34%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -MF CMakeFiles/llvm-support.dir/MemAlloc.cpp.o.d -o CMakeFiles/llvm-support.dir/MemAlloc.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/MemAlloc.cpp -[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o -MF CMakeFiles/easel.dir/esl_sqio.c.o.d -o CMakeFiles/easel.dir/esl_sqio.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio.c -[ 34%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -MF CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o.d -o CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/MemoryBuffer.cpp -[ 34%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -MF CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o.d -o CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/NativeFormatting.cpp -[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -MF CMakeFiles/easel.dir/esl_sqio_ascii.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ascii.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ascii.c -[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -MF CMakeFiles/easel.dir/esl_sqio_ncbi.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ncbi.c -[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -MF CMakeFiles/easel.dir/esl_sse.c.o.d -o CMakeFiles/easel.dir/esl_sse.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sse.c -[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o -MF CMakeFiles/easel.dir/esl_ssi.c.o.d -o CMakeFiles/easel.dir/esl_ssi.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_ssi.c -[ 36%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o -MF CMakeFiles/llvm-support.dir/Path.cpp.o.d -o CMakeFiles/llvm-support.dir/Path.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Path.cpp -[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stack.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stack.c.o -MF CMakeFiles/easel.dir/esl_stack.c.o.d -o CMakeFiles/easel.dir/esl_stack.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stack.c -[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -MF CMakeFiles/easel.dir/esl_stats.c.o.d -o CMakeFiles/easel.dir/esl_stats.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stats.c -[ 36%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.cpp -[ 36%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o -MF CMakeFiles/llvm-support.dir/Process.cpp.o.d -o CMakeFiles/llvm-support.dir/Process.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp -[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o -MF CMakeFiles/easel.dir/esl_stopwatch.c.o.d -o CMakeFiles/easel.dir/esl_stopwatch.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stopwatch.c +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_clustal.c.o -MF CMakeFiles/easel.dir/esl_msafile_clustal.c.o.d -o CMakeFiles/easel.dir/esl_msafile_clustal.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_clustal.c +[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_phylip.c.o -MF CMakeFiles/easel.dir/esl_msafile_phylip.c.o.d -o CMakeFiles/easel.dir/esl_msafile_phylip.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_phylip.c +[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -MF CMakeFiles/easel.dir/esl_msafile_psiblast.c.o.d -o CMakeFiles/easel.dir/esl_msafile_psiblast.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_psiblast.c +[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_selex.c.o -MF CMakeFiles/easel.dir/esl_msafile_selex.c.o.d -o CMakeFiles/easel.dir/esl_msafile_selex.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_selex.c +[ 20%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/index/BamToolsIndex_p.cpp +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); + | ^~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ +[ 20%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BamDeviceFactory_p.cpp +[ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o -MF CMakeFiles/llvm-support.dir/Atomic.cpp.o.d -o CMakeFiles/llvm-support.dir/Atomic.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Atomic.cpp +[ 20%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -MF CMakeFiles/easel.dir/esl_msafile_stockholm.c.o.d -o CMakeFiles/easel.dir/esl_msafile_stockholm.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msafile_stockholm.c +[ 22%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msashuffle.c.o -MF CMakeFiles/easel.dir/esl_msashuffle.c.o.d -o CMakeFiles/easel.dir/esl_msashuffle.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msashuffle.c +[ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -MF CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d -o CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/CrashRecoveryContext.cpp +[ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_msaweight.c.o -MF CMakeFiles/easel.dir/esl_msaweight.c.o.d -o CMakeFiles/easel.dir/esl_msaweight.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_msaweight.c +[ 23%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.cpp In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, @@ -2110,10 +1925,6 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o -MF CMakeFiles/easel.dir/esl_stretchexp.c.o.d -o CMakeFiles/easel.dir/esl_stretchexp.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stretchexp.c -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_threads.c.o -MF CMakeFiles/easel.dir/esl_threads.c.o.d -o CMakeFiles/easel.dir/esl_threads.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_threads.c In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] @@ -2123,72 +1934,149 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_tree.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_tree.c.o -MF CMakeFiles/easel.dir/esl_tree.c.o.d -o CMakeFiles/easel.dir/esl_tree.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_tree.c -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o -MF CMakeFiles/easel.dir/esl_vectorops.c.o.d -o CMakeFiles/easel.dir/esl_vectorops.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_vectorops.c -[ 37%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o -MF CMakeFiles/easel.dir/esl_vmx.c.o.d -o CMakeFiles/easel.dir/esl_vmx.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_vmx.c -[ 38%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o -MF CMakeFiles/llvm-support.dir/Program.cpp.o.d -o CMakeFiles/llvm-support.dir/Program.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Program.cpp -[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -MF CMakeFiles/easel.dir/esl_weibull.c.o.d -o CMakeFiles/easel.dir/esl_weibull.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_weibull.c -[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -MF CMakeFiles/easel.dir/esl_workqueue.c.o.d -o CMakeFiles/easel.dir/esl_workqueue.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_workqueue.c -[ 39%] Building C object ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o -MF CMakeFiles/easel.dir/esl_wuss.c.o.d -o CMakeFiles/easel.dir/esl_wuss.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_wuss.c -[ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o -MF CMakeFiles/llvm-support.dir/Regex.cpp.o.d -o CMakeFiles/llvm-support.dir/Regex.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Regex.cpp -[ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o -MF CMakeFiles/llvm-support.dir/Signals.cpp.o.d -o CMakeFiles/llvm-support.dir/Signals.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Signals.cpp -In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp:100: -/build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc: In static member function 'static size_t llvm::sys::Process::GetMallocUsage()': -/build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:94:18: warning: 'mallinfo mallinfo()' is deprecated [-Wdeprecated-declarations] - 94 | mi = ::mallinfo(); - | ~~~~~~~~~~^~ -In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:35: -/usr/include/malloc.h:114:24: note: declared here - 114 | extern struct mallinfo mallinfo (void) __THROW __MALLOC_DEPRECATED; - | ^~~~~~~~ -[ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem 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-isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_normal.c.o -MF CMakeFiles/easel.dir/esl_normal.c.o.d -o CMakeFiles/easel.dir/esl_normal.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_normal.c +[ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_paml.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_paml.c.o -MF CMakeFiles/easel.dir/esl_paml.c.o.d -o CMakeFiles/easel.dir/esl_paml.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_paml.c +[ 23%] Building C object ext/easel/CMakeFiles/easel.dir/esl_random.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_random.c.o -MF CMakeFiles/easel.dir/esl_random.c.o.d -o CMakeFiles/easel.dir/esl_random.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_random.c +[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_randomseq.c.o -MF CMakeFiles/easel.dir/esl_randomseq.c.o.d -o CMakeFiles/easel.dir/esl_randomseq.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_randomseq.c +[ 24%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Debug.cpp.o -MF CMakeFiles/llvm-support.dir/Debug.cpp.o.d -o CMakeFiles/llvm-support.dir/Debug.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Debug.cpp +[ 24%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ratematrix.c.o -MF CMakeFiles/easel.dir/esl_ratematrix.c.o.d -o CMakeFiles/easel.dir/esl_ratematrix.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_ratematrix.c +[ 25%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY 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common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o -MF CMakeFiles/graphio.dir/gfa_writer.cpp.o.d -o CMakeFiles/graphio.dir/gfa_writer.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_writer.cpp -[ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -MF CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/SourceMgr.cpp -[ 39%] Linking C static library libeasel.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -P CMakeFiles/easel.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -E cmake_link_script CMakeFiles/easel.dir/link.txt --verbose=1 -/usr/bin/ar qc libeasel.a CMakeFiles/easel.dir/easel.c.o CMakeFiles/easel.dir/esl_alphabet.c.o CMakeFiles/easel.dir/esl_avx.c.o CMakeFiles/easel.dir/esl_buffer.c.o CMakeFiles/easel.dir/esl_cluster.c.o CMakeFiles/easel.dir/esl_composition.c.o CMakeFiles/easel.dir/esl_dirichlet.c.o CMakeFiles/easel.dir/esl_distance.c.o CMakeFiles/easel.dir/esl_dmatrix.c.o CMakeFiles/easel.dir/esl_dsqdata.c.o CMakeFiles/easel.dir/esl_exponential.c.o CMakeFiles/easel.dir/esl_fileparser.c.o CMakeFiles/easel.dir/esl_gamma.c.o CMakeFiles/easel.dir/esl_gencode.c.o CMakeFiles/easel.dir/esl_getopts.c.o CMakeFiles/easel.dir/esl_gev.c.o CMakeFiles/easel.dir/esl_gumbel.c.o CMakeFiles/easel.dir/esl_heap.c.o CMakeFiles/easel.dir/esl_histogram.c.o CMakeFiles/easel.dir/esl_hmm.c.o CMakeFiles/easel.dir/esl_hyperexp.c.o CMakeFiles/easel.dir/esl_keyhash.c.o CMakeFiles/easel.dir/esl_mem.c.o CMakeFiles/easel.dir/esl_minimizer.c.o CMakeFiles/easel.dir/esl_mixgev.c.o CMakeFiles/easel.dir/esl_mpi.c.o CMakeFiles/easel.dir/esl_msa.c.o CMakeFiles/easel.dir/esl_msacluster.c.o CMakeFiles/easel.dir/esl_msafile.c.o CMakeFiles/easel.dir/esl_msafile2.c.o CMakeFiles/easel.dir/esl_msafile_a2m.c.o CMakeFiles/easel.dir/esl_msafile_afa.c.o CMakeFiles/easel.dir/esl_msafile_clustal.c.o CMakeFiles/easel.dir/esl_msafile_phylip.c.o CMakeFiles/easel.dir/esl_msafile_psiblast.c.o CMakeFiles/easel.dir/esl_msafile_selex.c.o CMakeFiles/easel.dir/esl_msafile_stockholm.c.o CMakeFiles/easel.dir/esl_msashuffle.c.o CMakeFiles/easel.dir/esl_msaweight.c.o CMakeFiles/easel.dir/esl_normal.c.o CMakeFiles/easel.dir/esl_paml.c.o CMakeFiles/easel.dir/esl_random.c.o CMakeFiles/easel.dir/esl_randomseq.c.o CMakeFiles/easel.dir/esl_ratematrix.c.o CMakeFiles/easel.dir/esl_recorder.c.o CMakeFiles/easel.dir/esl_regexp.c.o CMakeFiles/easel.dir/esl_rootfinder.c.o CMakeFiles/easel.dir/esl_scorematrix.c.o CMakeFiles/easel.dir/esl_sq.c.o CMakeFiles/easel.dir/esl_sqio.c.o CMakeFiles/easel.dir/esl_sqio_ascii.c.o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o CMakeFiles/easel.dir/esl_sse.c.o CMakeFiles/easel.dir/esl_ssi.c.o CMakeFiles/easel.dir/esl_stack.c.o CMakeFiles/easel.dir/esl_stats.c.o CMakeFiles/easel.dir/esl_stopwatch.c.o CMakeFiles/easel.dir/esl_stretchexp.c.o CMakeFiles/easel.dir/esl_threads.c.o CMakeFiles/easel.dir/esl_tree.c.o CMakeFiles/easel.dir/esl_vectorops.c.o CMakeFiles/easel.dir/esl_vmx.c.o CMakeFiles/easel.dir/esl_weibull.c.o CMakeFiles/easel.dir/esl_workqueue.c.o CMakeFiles/easel.dir/esl_wuss.c.o -/usr/bin/ranlib libeasel.a +[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_recorder.c.o -MF CMakeFiles/easel.dir/esl_recorder.c.o.d -o CMakeFiles/easel.dir/esl_recorder.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_recorder.c +[ 25%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Errno.cpp.o -MF CMakeFiles/llvm-support.dir/Errno.cpp.o.d -o CMakeFiles/llvm-support.dir/Errno.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Errno.cpp +[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_regexp.c.o -MF CMakeFiles/easel.dir/esl_regexp.c.o.d -o CMakeFiles/easel.dir/esl_regexp.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_regexp.c +[ 25%] Building C object ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_rootfinder.c.o -MF CMakeFiles/easel.dir/esl_rootfinder.c.o.d -o CMakeFiles/easel.dir/esl_rootfinder.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_rootfinder.c +[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_scorematrix.c.o -MF CMakeFiles/easel.dir/esl_scorematrix.c.o.d -o CMakeFiles/easel.dir/esl_scorematrix.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_scorematrix.c +[ 26%] Linking CXX static library libcoverage_model.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -P CMakeFiles/coverage_model.dir/cmake_clean_target.cmake +[ 26%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/BgzfStream_p.cpp +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model && /usr/bin/cmake -E cmake_link_script CMakeFiles/coverage_model.dir/link.txt --verbose=1 +/usr/bin/ar qc libcoverage_model.a CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o +/usr/bin/ranlib libcoverage_model.a +[ 26%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && 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make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 39%] Built target easel -make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend +[ 26%] Built target coverage_model +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/samtools /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake --color= +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 39%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kstring.c.o -MF CMakeFiles/samtools.dir/kstring.c.o.d -o CMakeFiles/samtools.dir/kstring.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/kstring.c -[ 39%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o -MF CMakeFiles/samtools.dir/bam_aux.c.o.d -o CMakeFiles/samtools.dir/bam_aux.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_aux.c -[ 40%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o -MF CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d -o CMakeFiles/llvm-support.dir/StringExtras.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringExtras.cpp -[ 40%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o -MF CMakeFiles/llvm-support.dir/StringMap.cpp.o.d -o CMakeFiles/llvm-support.dir/StringMap.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringMap.cpp -[ 40%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o -MF CMakeFiles/llvm-support.dir/StringRef.cpp.o.d -o CMakeFiles/llvm-support.dir/StringRef.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringRef.cpp -[ 40%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam.c.o -MF CMakeFiles/samtools.dir/bam.c.o.d -o CMakeFiles/samtools.dir/bam.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam.c -[ 40%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o -MF CMakeFiles/llvm-support.dir/StringSaver.cpp.o.d -o CMakeFiles/llvm-support.dir/StringSaver.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringSaver.cpp -[ 40%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -MF CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d -o CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/ThreadLocal.cpp -[ 41%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o -MF CMakeFiles/llvm-support.dir/Threading.cpp.o.d -o CMakeFiles/llvm-support.dir/Threading.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Threading.cpp -[ 43%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 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-DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Error.cpp.o -MF CMakeFiles/llvm-support.dir/Error.cpp.o.d -o CMakeFiles/llvm-support.dir/Error.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Error.cpp +[ 26%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -MF CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o.d -o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/ErrorHandling.cpp +[ 26%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sq.c.o +cd 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/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio.c.o -MF CMakeFiles/easel.dir/esl_sqio.c.o.d -o CMakeFiles/easel.dir/esl_sqio.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio.c +[ 26%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -MF 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-I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/RollingBuffer_p.cpp +[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ascii.c.o -MF CMakeFiles/easel.dir/esl_sqio_ascii.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ascii.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ascii.c +[ 27%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -MF CMakeFiles/easel.dir/esl_sqio_ncbi.c.o.d -o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sqio_ncbi.c +[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_sse.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_sse.c.o -MF CMakeFiles/easel.dir/esl_sse.c.o.d -o CMakeFiles/easel.dir/esl_sse.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_sse.c +[ 29%] Building C object ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_ssi.c.o -MF CMakeFiles/easel.dir/esl_ssi.c.o.d -o CMakeFiles/easel.dir/esl_ssi.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_ssi.c +[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -MF CMakeFiles/llvm-support.dir/FoldingSet.cpp.o.d -o CMakeFiles/llvm-support.dir/FoldingSet.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/FoldingSet.cpp +[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -MF CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o.d -o CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/FormatVariadic.cpp +[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stack.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stack.c.o -MF CMakeFiles/easel.dir/esl_stack.c.o.d -o CMakeFiles/easel.dir/esl_stack.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stack.c +[ 30%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -MF CMakeFiles/utils.dir/filesystem/copy_file.cpp.o.d -o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/copy_file.cpp +[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stats.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stats.c.o -MF CMakeFiles/easel.dir/esl_stats.c.o.d -o CMakeFiles/easel.dir/esl_stats.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stats.c +[ 30%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/SerialBgzfStream_p.cpp +[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o -MF CMakeFiles/llvm-support.dir/Hashing.cpp.o.d -o CMakeFiles/llvm-support.dir/Hashing.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Hashing.cpp +[ 30%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c +In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:32: +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c: In function 'bgzf_check_EOF': +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:73:34: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 73 | #define _bgzf_read(fp, buf, len) fread(buf, 1, len, (_bgzf_file_t)fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:578:9: note: in expansion of macro '_bgzf_read' + 578 | _bgzf_read(fp->fp, buf, 28); + | ^~~~~~~~~~ +[ 30%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stopwatch.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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-Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -MF CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d -o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.cpp +[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o -MF CMakeFiles/llvm-support.dir/Host.cpp.o.d -o CMakeFiles/llvm-support.dir/Host.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Host.cpp +[ 30%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o -MF CMakeFiles/llvm-support.dir/JSON.cpp.o.d -o CMakeFiles/llvm-support.dir/JSON.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/JSON.cpp +[ 31%] Building C object ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_stretchexp.c.o -MF CMakeFiles/easel.dir/esl_stretchexp.c.o.d -o CMakeFiles/easel.dir/esl_stretchexp.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_stretchexp.c +[ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o -MF CMakeFiles/llvm-support.dir/LEB128.cpp.o.d -o CMakeFiles/llvm-support.dir/LEB128.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/LEB128.cpp +[ 32%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c +In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:46: +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'kftp_send_cmd': +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) + | ^~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:236:9: note: in expansion of macro 'netwrite' + 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'khttp_connect_file': +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) + | ^~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:415:9: note: in expansion of macro 'netwrite' + 415 | netwrite(fp->fd, buf, l); + | ^~~~~~~~ +[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_threads.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_threads.c.o -MF CMakeFiles/easel.dir/esl_threads.c.o.d -o CMakeFiles/easel.dir/esl_threads.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_threads.c +[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_tree.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_tree.c.o -MF CMakeFiles/easel.dir/esl_tree.c.o.d -o CMakeFiles/easel.dir/esl_tree.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_tree.c +[ 32%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o -MF CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d -o CMakeFiles/llvm-support.dir/LineIterator.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/LineIterator.cpp +[ 32%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c +In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:5: +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined + 8 | safe_mutex_unlock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined + 5 | safe_mutex_lock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/block.c:4: +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined + 240 | unpackInt16(const uint8_t* buffer); + | ^~~~~~~~~~~ +[ 32%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vectorops.c.o -MF CMakeFiles/easel.dir/esl_vectorops.c.o.d -o CMakeFiles/easel.dir/esl_vectorops.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_vectorops.c +[ 33%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, @@ -2207,8 +2095,57 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -MF CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d -o CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/TimeProfiler.cpp +In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:12: +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined + 8 | safe_mutex_unlock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined + 5 | safe_mutex_lock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:11: +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined + 240 | unpackInt16(const uint8_t* buffer); + | ^~~~~~~~~~~ +[ 33%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -MF CMakeFiles/graphio.dir/fastg_writer.cpp.o.d -o CMakeFiles/graphio.dir/fastg_writer.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.cpp +[ 33%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c +[ 33%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o -MF CMakeFiles/llvm-support.dir/Locale.cpp.o.d -o CMakeFiles/llvm-support.dir/Locale.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Locale.cpp +[ 33%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c: In function 'queue_print_status': +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c:344:62: warning: format '%lld' expects argument of type 'long long int', but argument 8 has type 'int64_t' {aka 'long int'} [-Wformat=] + 344 | fprintf(fp, "mem=%d head=%d tail=%d n=%d length=%d id=%lld ordered=%d num_adders=%d num_getters=%d\n", + | ~~~^ + | | + | long long int + | %ld + 345 | q->mem, q->head, q->tail, q->n, q->length, q->id, q->ordered, q->num_adders, q->num_getters); + | ~~~~~ + | | + | int64_t {aka long int} +In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/queue.c:6: +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h: At top level: +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined + 8 | safe_mutex_unlock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined + 5 | safe_mutex_lock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:14: +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined + 8 | safe_mutex_unlock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined + 5 | safe_mutex_lock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:13: +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined + 240 | unpackInt16(const uint8_t* buffer); + | ^~~~~~~~~~~ +[ 33%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -2222,8 +2159,21 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o -MF CMakeFiles/llvm-support.dir/Twine.cpp.o.d -o CMakeFiles/llvm-support.dir/Twine.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Twine.cpp +In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8: +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined + 8 | safe_mutex_unlock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined + 5 | safe_mutex_lock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/reader.c:7: +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined + 240 | unpackInt16(const uint8_t* buffer); + | ^~~~~~~~~~~ +[ 33%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.c +[ 34%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -MF CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o.d -o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -2237,76 +2187,36 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 43%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/sam.c.o -MF CMakeFiles/samtools.dir/sam.c.o.d -o CMakeFiles/samtools.dir/sam.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/sam.c -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o -MF CMakeFiles/llvm-support.dir/Unicode.cpp.o.d -o CMakeFiles/llvm-support.dir/Unicode.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Unicode.cpp -[ 43%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o -MF CMakeFiles/samtools.dir/bam_index.c.o.d -o CMakeFiles/samtools.dir/bam_index.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c -[ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o -MF CMakeFiles/llvm-support.dir/WithColor.cpp.o.d -o CMakeFiles/llvm-support.dir/WithColor.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/WithColor.cpp -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] - 565 | ++vptr; - | ^~ -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_core': -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:178:42: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow] - 178 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_load_core': -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 335 | fread(magic, 1, 4, fp); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 342 | fread(&idx->n, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 355 | fread(&size, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 358 | fread(&key, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 362 | fread(&p->n, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 366 | fread(p->list, 16, p->n, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 376 | fread(&index2->n, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 380 | fread(index2->offset, index2->n, 8, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/YAMLParser.cpp -[ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/YAMLTraits.cpp -[ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/raw_os_ostream.cpp +In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11, + from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10: +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined + 8 | safe_mutex_unlock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined + 5 | safe_mutex_lock(pthread_mutex_t *mutex); + | ^~~~~~~~~~~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/writer.c:7: +/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined + 240 | unpackInt16(const uint8_t* buffer); + | ^~~~~~~~~~~ +[ 34%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatParser_p.cpp +[ 34%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.cpp +[ 34%] Building C object ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_vmx.c.o -MF CMakeFiles/easel.dir/esl_vmx.c.o.d -o CMakeFiles/easel.dir/esl_vmx.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_vmx.c +[ 34%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o -MF CMakeFiles/llvm-support.dir/MD5.cpp.o.d -o CMakeFiles/llvm-support.dir/MD5.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/MD5.cpp +[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_weibull.c.o -MF CMakeFiles/easel.dir/esl_weibull.c.o.d -o CMakeFiles/easel.dir/esl_weibull.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_weibull.c +[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_workqueue.c.o -MF CMakeFiles/easel.dir/esl_workqueue.c.o.d -o CMakeFiles/easel.dir/esl_workqueue.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_workqueue.c +[ 36%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -MF CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d -o CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/ManagedStatic.cpp +[ 36%] Building C object ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/easel/CMakeFiles/easel.dir/esl_wuss.c.o -MF CMakeFiles/easel.dir/esl_wuss.c.o.d -o CMakeFiles/easel.dir/esl_wuss.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/easel/esl_wuss.c +[ 36%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -MF CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d -o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/path_helper.cpp In file included from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -2337,8 +2247,52 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 344 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/raw_ostream.cpp +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 36%] Linking C static library libeasel.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -P CMakeFiles/easel.dir/cmake_clean_target.cmake +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel && /usr/bin/cmake -E cmake_link_script CMakeFiles/easel.dir/link.txt --verbose=1 +/usr/bin/ar qc libeasel.a CMakeFiles/easel.dir/easel.c.o CMakeFiles/easel.dir/esl_alphabet.c.o CMakeFiles/easel.dir/esl_avx.c.o CMakeFiles/easel.dir/esl_buffer.c.o CMakeFiles/easel.dir/esl_cluster.c.o CMakeFiles/easel.dir/esl_composition.c.o CMakeFiles/easel.dir/esl_dirichlet.c.o CMakeFiles/easel.dir/esl_distance.c.o CMakeFiles/easel.dir/esl_dmatrix.c.o CMakeFiles/easel.dir/esl_dsqdata.c.o CMakeFiles/easel.dir/esl_exponential.c.o CMakeFiles/easel.dir/esl_fileparser.c.o CMakeFiles/easel.dir/esl_gamma.c.o CMakeFiles/easel.dir/esl_gencode.c.o CMakeFiles/easel.dir/esl_getopts.c.o CMakeFiles/easel.dir/esl_gev.c.o CMakeFiles/easel.dir/esl_gumbel.c.o CMakeFiles/easel.dir/esl_heap.c.o CMakeFiles/easel.dir/esl_histogram.c.o CMakeFiles/easel.dir/esl_hmm.c.o CMakeFiles/easel.dir/esl_hyperexp.c.o CMakeFiles/easel.dir/esl_keyhash.c.o CMakeFiles/easel.dir/esl_mem.c.o CMakeFiles/easel.dir/esl_minimizer.c.o CMakeFiles/easel.dir/esl_mixgev.c.o CMakeFiles/easel.dir/esl_mpi.c.o CMakeFiles/easel.dir/esl_msa.c.o CMakeFiles/easel.dir/esl_msacluster.c.o CMakeFiles/easel.dir/esl_msafile.c.o CMakeFiles/easel.dir/esl_msafile2.c.o CMakeFiles/easel.dir/esl_msafile_a2m.c.o CMakeFiles/easel.dir/esl_msafile_afa.c.o CMakeFiles/easel.dir/esl_msafile_clustal.c.o CMakeFiles/easel.dir/esl_msafile_phylip.c.o CMakeFiles/easel.dir/esl_msafile_psiblast.c.o CMakeFiles/easel.dir/esl_msafile_selex.c.o CMakeFiles/easel.dir/esl_msafile_stockholm.c.o CMakeFiles/easel.dir/esl_msashuffle.c.o CMakeFiles/easel.dir/esl_msaweight.c.o CMakeFiles/easel.dir/esl_normal.c.o CMakeFiles/easel.dir/esl_paml.c.o CMakeFiles/easel.dir/esl_random.c.o CMakeFiles/easel.dir/esl_randomseq.c.o CMakeFiles/easel.dir/esl_ratematrix.c.o CMakeFiles/easel.dir/esl_recorder.c.o CMakeFiles/easel.dir/esl_regexp.c.o CMakeFiles/easel.dir/esl_rootfinder.c.o CMakeFiles/easel.dir/esl_scorematrix.c.o CMakeFiles/easel.dir/esl_sq.c.o CMakeFiles/easel.dir/esl_sqio.c.o CMakeFiles/easel.dir/esl_sqio_ascii.c.o CMakeFiles/easel.dir/esl_sqio_ncbi.c.o CMakeFiles/easel.dir/esl_sse.c.o CMakeFiles/easel.dir/esl_ssi.c.o CMakeFiles/easel.dir/esl_stack.c.o CMakeFiles/easel.dir/esl_stats.c.o CMakeFiles/easel.dir/esl_stopwatch.c.o CMakeFiles/easel.dir/esl_stretchexp.c.o CMakeFiles/easel.dir/esl_threads.c.o CMakeFiles/easel.dir/esl_tree.c.o CMakeFiles/easel.dir/esl_vectorops.c.o CMakeFiles/easel.dir/esl_vmx.c.o CMakeFiles/easel.dir/esl_weibull.c.o CMakeFiles/easel.dir/esl_workqueue.c.o CMakeFiles/easel.dir/esl_wuss.c.o +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] + 565 | ++vptr; + | ^~ +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ +/usr/bin/ranlib libeasel.a +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 36%] Built target easel +make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/depend +[ 36%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/CMakeFiles/hmmer.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/build +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 37%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/build.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/build.c.o -MF CMakeFiles/hmmer.dir/src/build.c.o.d -o CMakeFiles/hmmer.dir/src/build.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/build.c +[ 38%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o -MF CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d -o CMakeFiles/utils.dir/filesystem/temporary.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/temporary.cpp In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds] @@ -2361,131 +2315,90 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 44%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o -MF CMakeFiles/llvm-support.dir/regcomp.c.o.d -o CMakeFiles/llvm-support.dir/regcomp.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/regcomp.c -[ 44%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o -MF CMakeFiles/samtools.dir/bam_pileup.c.o.d -o CMakeFiles/samtools.dir/bam_pileup.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_pileup.c -[ 44%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -MF CMakeFiles/llvm-support.dir/regerror.c.o.d -o CMakeFiles/llvm-support.dir/regerror.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/regerror.c -[ 44%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/common/io/graph -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o -MF CMakeFiles/graphio.dir/fastg_writer.cpp.o.d -o CMakeFiles/graphio.dir/fastg_writer.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/graph/fastg_writer.cpp -[ 45%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -MF CMakeFiles/llvm-support.dir/regexec.c.o.d -o CMakeFiles/llvm-support.dir/regexec.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/regexec.c -[ 45%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -MF CMakeFiles/samtools.dir/bam_lpileup.c.o.d -o CMakeFiles/samtools.dir/bam_lpileup.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_lpileup.c -[ 45%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o -MF CMakeFiles/llvm-support.dir/regfree.c.o.d -o CMakeFiles/llvm-support.dir/regfree.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/regfree.c -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, - from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.cpp:1: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 45%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -MF CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/regstrlcpy.c -[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o -MF CMakeFiles/samtools.dir/bam_md.c.o.d -o CMakeFiles/samtools.dir/bam_md.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_md.c -[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/razf.c.o -MF CMakeFiles/samtools.dir/razf.c.o.d -o CMakeFiles/samtools.dir/razf.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c -[ 46%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/common/io/binary -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o -MF CMakeFiles/binary_io.dir/genomic_info.cpp.o.d -o CMakeFiles/binary_io.dir/genomic_info.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/genomic_info.cpp -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_flush': -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:234:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function '_razf_write': -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:201:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_close': -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:805:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:808:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:810:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_end_flush': -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:258:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'save_zindex': -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:96:19: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:99:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 99 | write(fd, &v32, sizeof(uint32_t)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:106:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/faidx.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/faidx.c.o -MF CMakeFiles/samtools.dir/faidx.c.o.d -o CMakeFiles/samtools.dir/faidx.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/faidx.c -make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/CMakeFiles/hmmer.dir/DependInfo.cmake --color= +[ 38%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools -I/build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/src -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -MF CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o.d -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api/internal/utils/BamException_p.cpp +[ 38%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o +cd 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ext/hmmer/CMakeFiles/hmmer.dir/src/cachedb.c.o -MF CMakeFiles/hmmer.dir/src/cachedb.c.o.d -o CMakeFiles/hmmer.dir/src/cachedb.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/cachedb.c +[ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT 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/build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o -MF CMakeFiles/llvm-support.dir/Path.cpp.o.d -o CMakeFiles/llvm-support.dir/Path.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Path.cpp +[ 39%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o -MF CMakeFiles/hmmer.dir/src/emit.c.o.d -o CMakeFiles/hmmer.dir/src/emit.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/emit.c +[ 39%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/errors.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/errors.c.o -MF CMakeFiles/hmmer.dir/src/errors.c.o.d -o CMakeFiles/hmmer.dir/src/errors.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/errors.c +[ 39%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o -MF CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d -o CMakeFiles/utils.dir/logger/logger_impl.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger_impl.cpp +[ 39%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/evalues.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/evalues.c.o -MF CMakeFiles/hmmer.dir/src/evalues.c.o.d -o CMakeFiles/hmmer.dir/src/evalues.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/evalues.c +[ 40%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/eweight.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/eweight.c.o -MF CMakeFiles/hmmer.dir/src/eweight.c.o.d -o CMakeFiles/hmmer.dir/src/eweight.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/eweight.c +[ 40%] Linking CXX static library libmapping_printer.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -P CMakeFiles/mapping_printer.dir/cmake_clean_target.cmake +[ 41%] Linking CXX static library libgraphio.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/mapping_printer.dir/link.txt --verbose=1 +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -P CMakeFiles/graphio.dir/cmake_clean_target.cmake +/usr/bin/ar qc libmapping_printer.a CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphio.dir/link.txt --verbose=1 +/usr/bin/ar qc libgraphio.a CMakeFiles/graphio.dir/gfa_reader.cpp.o CMakeFiles/graphio.dir/gfa_writer.cpp.o CMakeFiles/graphio.dir/fastg_writer.cpp.o +[ 41%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Process.cpp.o -MF CMakeFiles/llvm-support.dir/Process.cpp.o.d -o CMakeFiles/llvm-support.dir/Process.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp +/usr/bin/ranlib libmapping_printer.a +/usr/bin/ranlib libgraphio.a make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/hmmer/CMakeFiles/hmmer.dir/build.make ext/hmmer/CMakeFiles/hmmer.dir/build -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 47%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/build.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o -MF CMakeFiles/samtools.dir/bedidx.c.o.d -o CMakeFiles/samtools.dir/bedidx.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bedidx.c -[ 47%] Linking CXX static library libConsensusCore.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1 -[ 47%] Linking CXX static library ../../../lib/libgtest.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest.dir/cmake_clean_target.cmake -/usr/bin/ar qc libConsensusCore.a CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o 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-isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o -MF CMakeFiles/samtools.dir/bam_sort.c.o.d -o CMakeFiles/samtools.dir/bam_sort.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_sort.c -/usr/bin/ar qc ../../../lib/libgtest.a "CMakeFiles/gtest.dir/src/gtest-all.cc.o" -/usr/bin/ranlib libConsensusCore.a -/usr/bin/ranlib ../../../lib/libgtest.a +[ 41%] Built target mapping_printer make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 41%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_decoding.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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/build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback.c.o -MF CMakeFiles/hmmer.dir/src/generic_fwdback.c.o.d -o CMakeFiles/hmmer.dir/src/generic_fwdback.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_fwdback.c +[ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Program.cpp.o -MF CMakeFiles/llvm-support.dir/Program.cpp.o.d -o CMakeFiles/llvm-support.dir/Program.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Program.cpp +[ 44%] Linking CXX static library libBamTools.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1 +[ 44%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && 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CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o +[ 44%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o -MF CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o.d -o CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_fwdback_banded.c +/usr/bin/ranlib libBamTools.a make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 47%] Built target gtest -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend +[ 44%] Built target BamTools +make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= -[ 47%] Built target ConsensusCore +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/samtools /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools 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-g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_null2.c.o -MF CMakeFiles/hmmer.dir/src/generic_null2.c.o.d -o CMakeFiles/hmmer.dir/src/generic_null2.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_null2.c make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build +make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 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CMakeFiles/hmmer.dir/src/cachedb.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/cachedb.c -[ 48%] Linking CXX static library libmapping_printer.a -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +[ 44%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 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ext/hmmer/CMakeFiles/hmmer.dir/src/h2_io.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/heatmap.c.o -MF CMakeFiles/hmmer.dir/src/heatmap.c.o.d -o CMakeFiles/hmmer.dir/src/heatmap.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/heatmap.c +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -2498,12 +2411,29 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -P CMakeFiles/mapping_printer.dir/cmake_clean_target.cmake -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +[ 46%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o -MF CMakeFiles/hmmer.dir/src/hmmlogo.c.o.d -o CMakeFiles/hmmer.dir/src/hmmlogo.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmlogo.c +[ 46%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdmstr.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -MF CMakeFiles/hmmer.dir/src/hmmdmstr.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdmstr.c +In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.cpp:100: +/build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc: In static member function 'static size_t llvm::sys::Process::GetMallocUsage()': +/build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:94:18: warning: 'mallinfo mallinfo()' is deprecated [-Wdeprecated-declarations] + 94 | mi = ::mallinfo(); + | ~~~~~~~~~~^~ +In file included from /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Process.inc:35: +/usr/include/malloc.h:114:24: note: declared here + 114 | extern struct mallinfo mallinfo (void) __THROW __MALLOC_DEPRECATED; + | ^~~~~~~~ +[ 46%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -MF CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdwrkr.c +[ 46%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam.c.o -MF CMakeFiles/samtools.dir/bam.c.o.d -o CMakeFiles/samtools.dir/bam.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam.c +[ 47%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdutils.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdutils.c.o -MF CMakeFiles/hmmer.dir/src/hmmdutils.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdutils.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdutils.c +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/mapping_printer.dir/link.txt --verbose=1 /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ @@ -2513,19 +2443,58 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/usr/bin/ar qc libmapping_printer.a CMakeFiles/mapping_printer.dir/mapping_printer.cpp.o -/usr/bin/ranlib libmapping_printer.a +[ 47%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmer.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmer.c.o -MF CMakeFiles/hmmer.dir/src/hmmer.c.o.d -o CMakeFiles/hmmer.dir/src/hmmer.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmer.c +In file included from /usr/include/string.h:535, + from /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdmstr.c:13: +In function 'memset', + inlined from 'destroy_worker' at /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdmstr.c:1119:5, + inlined from 'update_workers' at /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdmstr.c:287:7: +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: warning: argument 1 null where non-null expected [-Wnonnull] + 59 | return __builtin___memset_chk (__dest, __ch, __len, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 60 | __glibc_objsize0 (__dest)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: note: in a call to built-in function '__builtin_memset' +[ 47%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o -MF CMakeFiles/llvm-support.dir/Regex.cpp.o.d -o CMakeFiles/llvm-support.dir/Regex.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Regex.cpp +[ 47%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o -MF CMakeFiles/hmmer.dir/src/logsum.c.o.d -o CMakeFiles/hmmer.dir/src/logsum.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/logsum.c +[ 47%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o -MF CMakeFiles/hmmer.dir/src/modelconfig.c.o.d -o CMakeFiles/hmmer.dir/src/modelconfig.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/modelconfig.c +[ 47%] Building CXX object common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/common/io/binary -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o -MF CMakeFiles/binary_io.dir/genomic_info.cpp.o.d -o CMakeFiles/binary_io.dir/genomic_info.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/genomic_info.cpp +[ 47%] Linking CXX static library ../../../lib/libgtest.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest.dir/cmake_clean_target.cmake +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 +/usr/bin/ar qc ../../../lib/libgtest.a "CMakeFiles/gtest.dir/src/gtest-all.cc.o" +[ 47%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.o +[ 48%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. 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/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.o -MF CMakeFiles/hmmer.dir/src/modelstats.c.o.d -o CMakeFiles/hmmer.dir/src/modelstats.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/modelstats.c +/usr/bin/ranlib ../../../lib/libgtest.a +[ 48%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -MF CMakeFiles/hmmer.dir/src/seqmodel.c.o.d -o CMakeFiles/hmmer.dir/src/seqmodel.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/seqmodel.c make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -MF CMakeFiles/samtools.dir/bam_reheader.c.o.d -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_reheader.c -[ 48%] Built target mapping_printer -[ 48%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o -MF CMakeFiles/samtools.dir/kprobaln.c.o.d -o CMakeFiles/samtools.dir/kprobaln.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/kprobaln.c -[ 48%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/emit.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o -MF CMakeFiles/samtools.dir/bam_cat.c.o.d -o CMakeFiles/samtools.dir/bam_cat.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_cat.c -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +[ 48%] Built target gtest +make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/depend +[ 48%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o -MF CMakeFiles/hmmer.dir/src/tracealign.c.o.d -o CMakeFiles/hmmer.dir/src/tracealign.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/tracealign.c +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest_main.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/build +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 48%] Building CXX object ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wall -Wshadow -Werror -Wno-error=dangling-else -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated -O2 -std=c++14 -MD -MT ext/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -MF CMakeFiles/gtest_main.dir/src/gtest_main.cc.o.d -o CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/src/gtest_main.cc +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/distance_estimation.hpp:13, + from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/weighted_distance_estimation.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/smoothing_distance_estimation.cpp:1: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -2538,88 +2507,20 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -make -f ext/googletest/googletest/CMakeFiles/gtest_main.dir/build.make ext/googletest/googletest/CMakeFiles/gtest_main.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src 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/build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_msv.c.o -MF CMakeFiles/hmmer.dir/src/generic_msv.c.o.d -o CMakeFiles/hmmer.dir/src/generic_msv.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_msv.c -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -E cmake_link_script CMakeFiles/samtools.dir/link.txt --verbose=1 -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -/usr/bin/ar qc libsamtools.a CMakeFiles/samtools.dir/kstring.c.o CMakeFiles/samtools.dir/bam_aux.c.o CMakeFiles/samtools.dir/bam.c.o CMakeFiles/samtools.dir/bam_import.c.o CMakeFiles/samtools.dir/sam.c.o CMakeFiles/samtools.dir/bam_index.c.o CMakeFiles/samtools.dir/bam_pileup.c.o CMakeFiles/samtools.dir/bam_lpileup.c.o CMakeFiles/samtools.dir/bam_md.c.o CMakeFiles/samtools.dir/razf.c.o CMakeFiles/samtools.dir/faidx.c.o CMakeFiles/samtools.dir/bedidx.c.o CMakeFiles/samtools.dir/bam_sort.c.o CMakeFiles/samtools.dir/sam_header.c.o CMakeFiles/samtools.dir/bam_reheader.c.o CMakeFiles/samtools.dir/kprobaln.c.o CMakeFiles/samtools.dir/bam_cat.c.o -[ 51%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_gtest.cpp -/usr/bin/ranlib libsamtools.a -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 51%] Built target samtools -make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/spades /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/build -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_optacc.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_optacc.c.o -MF CMakeFiles/hmmer.dir/src/generic_optacc.c.o.d -o CMakeFiles/hmmer.dir/src/generic_optacc.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_optacc.c -[ 51%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -MF CMakeFiles/spades-stages.dir/gap_closer.cpp.o.d -o CMakeFiles/spades-stages.dir/gap_closer.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp -[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_stotrace.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_stotrace.c.o -MF CMakeFiles/hmmer.dir/src/generic_stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_stotrace.c -[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_viterbi.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -MF CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o.d -o CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp -[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/generic_vtrace.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/generic_vtrace.c.o -MF CMakeFiles/hmmer.dir/src/generic_vtrace.c.o.d -o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/generic_vtrace.c -[ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/h2_io.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/h2_io.c.o -MF CMakeFiles/hmmer.dir/src/h2_io.c.o.d -o CMakeFiles/hmmer.dir/src/h2_io.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/h2_io.c -[ 52%] Linking CXX static library ../../../lib/libgtest_main.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest_main.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_main.dir/link.txt --verbose=1 -/usr/bin/ar qc ../../../lib/libgtest_main.a CMakeFiles/gtest_main.dir/src/gtest_main.cc.o -/usr/bin/ranlib ../../../lib/libgtest_main.a -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 52%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -MF CMakeFiles/utils.dir/filesystem/copy_file.cpp.o.d -o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/copy_file.cpp -[ 52%] Built target gtest_main -[ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/heatmap.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG 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CMakeFiles/hmmer.dir/src/heatmap.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/heatmap.c -[ 52%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -MF CMakeFiles/utils.dir/filesystem/path_helper.cpp.o.d -o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/path_helper.cpp -[ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmlogo.c.o -MF CMakeFiles/hmmer.dir/src/hmmlogo.c.o.d -o CMakeFiles/hmmer.dir/src/hmmlogo.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmlogo.c -[ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -MF CMakeFiles/hmmer.dir/src/hmmdmstr.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdmstr.c -[ 52%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -MF CMakeFiles/spades-stages.dir/pair_info_count.cpp.o.d -o CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp -[ 53%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o -MF CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d -o CMakeFiles/utils.dir/filesystem/temporary.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/temporary.cpp +[ 48%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -MF CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o.d -o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_alidisplay.c +[ 48%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_bg.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_bg.c.o -MF CMakeFiles/hmmer.dir/src/p7_bg.c.o.d -o CMakeFiles/hmmer.dir/src/p7_bg.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_bg.c +[ 48%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o -MF CMakeFiles/llvm-support.dir/Signals.cpp.o.d -o CMakeFiles/llvm-support.dir/Signals.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Signals.cpp +[ 50%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o -MF CMakeFiles/samtools.dir/bam_import.c.o.d -o CMakeFiles/samtools.dir/bam_import.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_import.c +[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_builder.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_builder.c.o -MF CMakeFiles/hmmer.dir/src/p7_builder.c.o.d -o CMakeFiles/hmmer.dir/src/p7_builder.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_builder.c +[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domaindef.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -MF CMakeFiles/hmmer.dir/src/p7_domaindef.c.o.d -o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_domaindef.c +[ 51%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o -MF CMakeFiles/llvm-support.dir/SmallVector.cpp.o.d -o CMakeFiles/llvm-support.dir/SmallVector.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/SmallVector.cpp In file included from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -2656,19 +2557,14 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -In file included from /usr/include/string.h:535, - from /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdmstr.c:13: -In function 'memset', - inlined from 'destroy_worker' at /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdmstr.c:1119:5, - inlined from 'update_workers' at /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdmstr.c:287:7: -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: warning: argument 1 null where non-null expected [-Wnonnull] - 59 | return __builtin___memset_chk (__dest, __ch, __len, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 60 | __glibc_objsize0 (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/x86_64-linux-gnu/bits/string_fortified.h:59:10: note: in a call to built-in function '__builtin_memset' -[ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -MF CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdwrkr.c +[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gbands.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gbands.c.o -MF CMakeFiles/hmmer.dir/src/p7_gbands.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gbands.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gbands.c +[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmx.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmx.c.o -MF CMakeFiles/hmmer.dir/src/p7_gmx.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmx.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gmx.c +[ 51%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -MF CMakeFiles/llvm-support.dir/SourceMgr.cpp.o.d -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/SourceMgr.cpp +[ 51%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxb.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxb.c.o -MF CMakeFiles/hmmer.dir/src/p7_gmxb.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gmxb.c In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds] @@ -2691,21 +2587,39 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 53%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -MF CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o.d -o CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp -[ 54%] Linking CXX static library libgraphio.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -P CMakeFiles/graphio.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphio.dir/link.txt --verbose=1 -/usr/bin/ar qc libgraphio.a CMakeFiles/graphio.dir/gfa_reader.cpp.o CMakeFiles/graphio.dir/gfa_writer.cpp.o CMakeFiles/graphio.dir/fastg_writer.cpp.o -/usr/bin/ranlib libgraphio.a -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 54%] Built target graphio -[ 54%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/utils.dir/filesystem/glob.cpp.o -MF CMakeFiles/utils.dir/filesystem/glob.cpp.o.d -o CMakeFiles/utils.dir/filesystem/glob.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/utils/filesystem/glob.cpp -[ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdutils.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmdutils.c.o -MF CMakeFiles/hmmer.dir/src/hmmdutils.c.o.d -o CMakeFiles/hmmer.dir/src/hmmdutils.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmdutils.c -[ 55%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_messages.cpp +[ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o -MF CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o.d -o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_gmxchk.c +[ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmm.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmm.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmm.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmm.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_hmm.c +[ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_hmmcache.c +[ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_hmmfile.c +[ 52%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/sam.c.o -MF CMakeFiles/samtools.dir/sam.c.o.d -o CMakeFiles/samtools.dir/sam.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/sam.c +[ 52%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o -MF CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o.d -o CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_hmmwindow.c +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_null3.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_null3.c.o -MF CMakeFiles/hmmer.dir/src/p7_null3.c.o.d -o CMakeFiles/hmmer.dir/src/p7_null3.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_null3.c +[ 53%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o -MF CMakeFiles/samtools.dir/bam_index.c.o.d -o CMakeFiles/samtools.dir/bam_index.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c +[ 53%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_pipeline.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_pipeline.c.o -MF CMakeFiles/hmmer.dir/src/p7_pipeline.c.o.d -o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_pipeline.c +[ 53%] Linking CXX static library ../../../lib/libgtest_main.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -P CMakeFiles/gtest_main.dir/cmake_clean_target.cmake In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds] @@ -2728,16 +2642,54 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 344 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/hmmer.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/hmmer.c.o -MF CMakeFiles/hmmer.dir/src/hmmer.c.o.d -o CMakeFiles/hmmer.dir/src/hmmer.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/hmmer.c -[ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/logsum.c.o -MF CMakeFiles/hmmer.dir/src/logsum.c.o.d -o CMakeFiles/hmmer.dir/src/logsum.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/logsum.c -[ 55%] Building CXX object common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o -MF CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d -o CMakeFiles/utils.dir/logger/logger_impl.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/utils/logger/logger_impl.cpp -[ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/modelconfig.c.o -MF CMakeFiles/hmmer.dir/src/modelconfig.c.o.d -o CMakeFiles/hmmer.dir/src/modelconfig.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/modelconfig.c -[ 55%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/modelstats.c.o -MF CMakeFiles/hmmer.dir/src/modelstats.c.o.d -o CMakeFiles/hmmer.dir/src/modelstats.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/modelstats.c +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_main.dir/link.txt --verbose=1 +/usr/bin/ar qc ../../../lib/libgtest_main.a CMakeFiles/gtest_main.dir/src/gtest_main.cc.o +[ 54%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringExtras.cpp.o -MF CMakeFiles/llvm-support.dir/StringExtras.cpp.o.d -o CMakeFiles/llvm-support.dir/StringExtras.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringExtras.cpp +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_core': +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:178:42: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow] + 178 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c: In function 'bam_index_load_core': +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 335 | fread(magic, 1, 4, fp); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 342 | fread(&idx->n, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 355 | fread(&size, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 358 | fread(&key, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 362 | fread(&p->n, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 366 | fread(p->list, 16, p->n, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 376 | fread(&index2->n, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 380 | fread(index2->offset, index2->n, 8, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/bin/ranlib ../../../lib/libgtest_main.a +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 54%] Built target gtest_main +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build +[ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_prior.c.o +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_prior.c.o -MF CMakeFiles/hmmer.dir/src/p7_prior.c.o.d -o CMakeFiles/hmmer.dir/src/p7_prior.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_prior.c +[ 54%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_gtest.cpp +[ 54%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_profile.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_profile.c.o -MF CMakeFiles/hmmer.dir/src/p7_profile.c.o.d -o CMakeFiles/hmmer.dir/src/p7_profile.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_profile.c In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds] @@ -2760,147 +2712,245 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 55%] Linking CXX static library libllvm-support.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 -/usr/bin/ar qc libllvm-support.a "CMakeFiles/llvm-support.dir/APFloat.cpp.o" "CMakeFiles/llvm-support.dir/APInt.cpp.o" "CMakeFiles/llvm-support.dir/Atomic.cpp.o" "CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o" "CMakeFiles/llvm-support.dir/Debug.cpp.o" "CMakeFiles/llvm-support.dir/Errno.cpp.o" "CMakeFiles/llvm-support.dir/Error.cpp.o" "CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o" "CMakeFiles/llvm-support.dir/FoldingSet.cpp.o" "CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o" "CMakeFiles/llvm-support.dir/Hashing.cpp.o" "CMakeFiles/llvm-support.dir/Host.cpp.o" "CMakeFiles/llvm-support.dir/JSON.cpp.o" "CMakeFiles/llvm-support.dir/LEB128.cpp.o" "CMakeFiles/llvm-support.dir/LineIterator.cpp.o" "CMakeFiles/llvm-support.dir/Locale.cpp.o" "CMakeFiles/llvm-support.dir/MD5.cpp.o" "CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o" "CMakeFiles/llvm-support.dir/MemAlloc.cpp.o" "CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o" "CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o" "CMakeFiles/llvm-support.dir/Path.cpp.o" "CMakeFiles/llvm-support.dir/Process.cpp.o" "CMakeFiles/llvm-support.dir/Program.cpp.o" "CMakeFiles/llvm-support.dir/Regex.cpp.o" "CMakeFiles/llvm-support.dir/Signals.cpp.o" "CMakeFiles/llvm-support.dir/SmallVector.cpp.o" "CMakeFiles/llvm-support.dir/SourceMgr.cpp.o" "CMakeFiles/llvm-support.dir/StringExtras.cpp.o" "CMakeFiles/llvm-support.dir/StringMap.cpp.o" "CMakeFiles/llvm-support.dir/StringRef.cpp.o" "CMakeFiles/llvm-support.dir/StringSaver.cpp.o" "CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o" "CMakeFiles/llvm-support.dir/Threading.cpp.o" "CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o" "CMakeFiles/llvm-support.dir/Twine.cpp.o" "CMakeFiles/llvm-support.dir/Unicode.cpp.o" "CMakeFiles/llvm-support.dir/WithColor.cpp.o" "CMakeFiles/llvm-support.dir/YAMLParser.cpp.o" "CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o" "CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o" "CMakeFiles/llvm-support.dir/raw_ostream.cpp.o" "CMakeFiles/llvm-support.dir/regcomp.c.o" "CMakeFiles/llvm-support.dir/regerror.c.o" "CMakeFiles/llvm-support.dir/regexec.c.o" "CMakeFiles/llvm-support.dir/regfree.c.o" "CMakeFiles/llvm-support.dir/regstrlcpy.c.o" -[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/mpisupport.c.o -MF CMakeFiles/hmmer.dir/src/mpisupport.c.o.d -o CMakeFiles/hmmer.dir/src/mpisupport.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/mpisupport.c -[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/seqmodel.c.o -MF CMakeFiles/hmmer.dir/src/seqmodel.c.o.d -o CMakeFiles/hmmer.dir/src/seqmodel.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/seqmodel.c -[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/tracealign.c.o -MF CMakeFiles/hmmer.dir/src/tracealign.c.o.d -o CMakeFiles/hmmer.dir/src/tracealign.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/tracealign.c -[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -MF CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o.d -o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_alidisplay.c -/usr/bin/ranlib libllvm-support.a -[ 56%] Linking CXX static library libpaired_info.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 -/usr/bin/ar qc libpaired_info.a CMakeFiles/paired_info.dir/distance_estimation.cpp.o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o -/usr/bin/ranlib libpaired_info.a -[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_bg.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_bg.c.o -MF CMakeFiles/hmmer.dir/src/p7_bg.c.o.d -o CMakeFiles/hmmer.dir/src/p7_bg.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_bg.c -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 56%] Built target llvm-support -[ 58%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -MF CMakeFiles/spades-stages.dir/distance_estimation.cpp.o.d -o CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 58%] Built target paired_info -[ 58%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -MF CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o.d -o CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp -[ 58%] Linking CXX static library libteamcity_gtest.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -P CMakeFiles/teamcity_gtest.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/teamcity_gtest.dir/link.txt --verbose=1 -/usr/bin/ar qc libteamcity_gtest.a CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -/usr/bin/ranlib libteamcity_gtest.a -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_builder.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/p7_builder.c.o -MF CMakeFiles/hmmer.dir/src/p7_builder.c.o.d -o CMakeFiles/hmmer.dir/src/p7_builder.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/p7_builder.c -[ 59%] Built target teamcity_gtest -[ 59%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -MF CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o.d -o CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/contig_output_stage.cpp -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp: In member function 'virtual void debruijn_graph::SecondPhaseSetup::run(debruijn_graph::GraphPack&, const char*)': -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:27:9: warning: unused variable 'code' [-Wunused-variable] - 27 | int code = rename(old_pe_contigs_filename.c_str(), new_pe_contigs_filename.c_str()); - | ^~~~ -[ 59%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 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object ext/hmmer/CMakeFiles/hmmer.dir/src/p7_domaindef.c.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/StringSaver.cpp.o -MF CMakeFiles/llvm-support.dir/StringSaver.cpp.o.d -o CMakeFiles/llvm-support.dir/StringSaver.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/StringSaver.cpp +[ 55%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o -MF CMakeFiles/samtools.dir/bam_lpileup.c.o.d -o CMakeFiles/samtools.dir/bam_lpileup.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_lpileup.c +[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_general.c.o -MF CMakeFiles/hmmer.dir/src/fm_general.c.o.d -o CMakeFiles/hmmer.dir/src/fm_general.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_general.c -[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o +[ 56%] Building CXX object ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -MF CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d -o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest/teamcity_messages.cpp +[ 56%] Linking CXX static library libConsensusCore.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1 +/usr/bin/ar qc libConsensusCore.a CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o CMakeFiles/ConsensusCore.dir/Utils.cpp.o CMakeFiles/ConsensusCore.dir/Version.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o +[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_sse.c.o -MF CMakeFiles/hmmer.dir/src/fm_sse.c.o.d -o CMakeFiles/hmmer.dir/src/fm_sse.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_sse.c -[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o +/usr/bin/ranlib libConsensusCore.a +[ 56%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/fm_ssv.c.o -MF CMakeFiles/hmmer.dir/src/fm_ssv.c.o.d -o CMakeFiles/hmmer.dir/src/fm_ssv.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/fm_ssv.c -[ 63%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -MF CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o.d -o CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/chromosome_removal.cpp -[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 56%] Built target ConsensusCore +make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/depend +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/spades /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-stages.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/spades/CMakeFiles/spades-stages.dir/build.make projects/spades/CMakeFiles/spades-stages.dir/build +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 56%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/gap_closer.cpp.o -MF CMakeFiles/spades-stages.dir/gap_closer.cpp.o.d -o CMakeFiles/spades-stages.dir/gap_closer.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp +[ 58%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o -MF CMakeFiles/samtools.dir/bam_md.c.o.d -o CMakeFiles/samtools.dir/bam_md.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_md.c +[ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/decoding.c -[ 63%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o +[ 58%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -MF CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o.d -o CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/ThreadLocal.cpp +[ 58%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/fwdback.c -[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o +[ 58%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/razf.c.o -MF CMakeFiles/samtools.dir/razf.c.o.d -o CMakeFiles/samtools.dir/razf.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_flush': +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:234:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function '_razf_write': +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:201:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_close': +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:805:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:808:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:810:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'razf_end_flush': +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:258:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c: In function 'save_zindex': +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:96:19: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:99:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 99 | write(fd, &v32, sizeof(uint32_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:106:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/ext/src/samtools/razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/io.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/io.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/io.c -[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o +[ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/ssvfilter.c -[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o +[ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/msvfilter.c -[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o +[ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/null2.c -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:9: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:362:64: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] - 140 | bool res = set_.erase(queue_.top()); - | ^~~ -[ 65%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o +[ 59%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/optacc.c -[ 66%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o +[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/stotrace.c -[ 66%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o +[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/vitfilter.c -[ 66%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o +[ 60%] Linking CXX static library libteamcity_gtest.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -P CMakeFiles/teamcity_gtest.dir/cmake_clean_target.cmake +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/teamcity_gtest.dir/link.txt --verbose=1 +[ 60%] Building C object ext/samtools/CMakeFiles/samtools.dir/faidx.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/faidx.c.o -MF CMakeFiles/samtools.dir/faidx.c.o.d -o CMakeFiles/samtools.dir/faidx.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/faidx.c +/usr/bin/ar qc libteamcity_gtest.a CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o +[ 60%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer -I/build/spades-3.15.5+dfsg/assembler/ext/src/hmmer -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src 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CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/p7_oprofile.c -[ 66%] Linking CXX static library libutils.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 -/usr/bin/ar qc libutils.a CMakeFiles/utils.dir/memory_limit.cpp.o CMakeFiles/utils.dir/filesystem/copy_file.cpp.o CMakeFiles/utils.dir/filesystem/path_helper.cpp.o CMakeFiles/utils.dir/filesystem/temporary.cpp.o CMakeFiles/utils.dir/filesystem/glob.cpp.o CMakeFiles/utils.dir/logger/logger_impl.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -/usr/bin/ranlib libutils.a -[ 66%] Building C object ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o +cd 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ext/hmmer/CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -MF CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o.d -o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src/impl_sse/mpi.c +[ 60%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o -MF CMakeFiles/samtools.dir/bam_sort.c.o.d -o CMakeFiles/samtools.dir/bam_sort.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_sort.c +[ 61%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Threading.cpp.o -MF CMakeFiles/llvm-support.dir/Threading.cpp.o.d -o CMakeFiles/llvm-support.dir/Threading.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Threading.cpp +[ 61%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -MF CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o.d -o CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/mismatch_correction.cpp +[ 61%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -MF CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o.d -o CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/TimeProfiler.cpp +[ 61%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -MF CMakeFiles/spades-stages.dir/pair_info_count.cpp.o.d -o CMakeFiles/spades-stages.dir/pair_info_count.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp +[ 61%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o -MF CMakeFiles/llvm-support.dir/Twine.cpp.o.d -o CMakeFiles/llvm-support.dir/Twine.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Twine.cpp +[ 62%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o -MF CMakeFiles/samtools.dir/sam_header.c.o.d -o CMakeFiles/samtools.dir/sam_header.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/sam_header.c +[ 62%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/Unicode.cpp.o -MF CMakeFiles/llvm-support.dir/Unicode.cpp.o.d -o CMakeFiles/llvm-support.dir/Unicode.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/Unicode.cpp +[ 62%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -MF CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o.d -o CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp +[ 62%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o -MF CMakeFiles/samtools.dir/bam_reheader.c.o.d -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_reheader.c +[ 62%] Linking CXX static library libpaired_info.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -P CMakeFiles/paired_info.dir/cmake_clean_target.cmake +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info && /usr/bin/cmake -E cmake_link_script CMakeFiles/paired_info.dir/link.txt --verbose=1 +/usr/bin/ar qc libpaired_info.a CMakeFiles/paired_info.dir/distance_estimation.cpp.o CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o +[ 62%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o -MF CMakeFiles/samtools.dir/kprobaln.c.o.d -o CMakeFiles/samtools.dir/kprobaln.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/kprobaln.c +/usr/bin/ranlib libpaired_info.a +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 62%] Built target paired_info +[ 62%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/WithColor.cpp.o -MF CMakeFiles/llvm-support.dir/WithColor.cpp.o.d -o CMakeFiles/llvm-support.dir/WithColor.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/WithColor.cpp +[ 62%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cc -DMD5SUM_MAIN -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o -MF CMakeFiles/samtools.dir/bam_cat.c.o.d -o CMakeFiles/samtools.dir/bam_cat.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/samtools/bam_cat.c +[ 63%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -MF CMakeFiles/spades-stages.dir/distance_estimation.cpp.o.d -o CMakeFiles/spades-stages.dir/distance_estimation.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp +[ 65%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLParser.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/YAMLParser.cpp +[ 65%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -MF CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o.d -o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/YAMLTraits.cpp +[ 65%] Linking CXX static library libsamtools.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -P CMakeFiles/samtools.dir/cmake_clean_target.cmake +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools && /usr/bin/cmake -E cmake_link_script CMakeFiles/samtools.dir/link.txt --verbose=1 +/usr/bin/ar qc libsamtools.a CMakeFiles/samtools.dir/kstring.c.o CMakeFiles/samtools.dir/bam_aux.c.o CMakeFiles/samtools.dir/bam.c.o CMakeFiles/samtools.dir/bam_import.c.o CMakeFiles/samtools.dir/sam.c.o CMakeFiles/samtools.dir/bam_index.c.o CMakeFiles/samtools.dir/bam_pileup.c.o CMakeFiles/samtools.dir/bam_lpileup.c.o CMakeFiles/samtools.dir/bam_md.c.o CMakeFiles/samtools.dir/razf.c.o CMakeFiles/samtools.dir/faidx.c.o CMakeFiles/samtools.dir/bedidx.c.o CMakeFiles/samtools.dir/bam_sort.c.o CMakeFiles/samtools.dir/sam_header.c.o CMakeFiles/samtools.dir/bam_reheader.c.o CMakeFiles/samtools.dir/kprobaln.c.o CMakeFiles/samtools.dir/bam_cat.c.o +[ 65%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/raw_os_ostream.cpp +/usr/bin/ranlib libsamtools.a +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 65%] Built target samtools +[ 65%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -MF CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o.d -o CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp +[ 65%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -std=gnu++14 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -MF CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d -o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/raw_ostream.cpp +[ 65%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o -MF CMakeFiles/llvm-support.dir/regcomp.c.o.d -o CMakeFiles/llvm-support.dir/regcomp.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/regcomp.c +[ 65%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o -MF CMakeFiles/llvm-support.dir/regerror.c.o.d -o CMakeFiles/llvm-support.dir/regerror.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/regerror.c +[ 66%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o -MF CMakeFiles/llvm-support.dir/regexec.c.o.d -o CMakeFiles/llvm-support.dir/regexec.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/regexec.c +[ 66%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o -MF CMakeFiles/llvm-support.dir/regfree.c.o.d -o CMakeFiles/llvm-support.dir/regfree.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/regfree.c +[ 66%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cc -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/llvm -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -MD -MT ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o -MF CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /build/spades-3.15.5+dfsg/assembler/ext/src/llvm/regstrlcpy.c +[ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -MF CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o.d -o CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/contig_output_stage.cpp +[ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -MF CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o.d -o CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp +[ 66%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -MF CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o.d -o CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/chromosome_removal.cpp +/build/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp: In member function 'virtual void debruijn_graph::SecondPhaseSetup::run(debruijn_graph::GraphPack&, const char*)': +/build/spades-3.15.5+dfsg/assembler/src/projects/spades/second_phase_setup.cpp:27:9: warning: unused variable 'code' [-Wunused-variable] + 27 | int code = rename(old_pe_contigs_filename.c_str(), new_pe_contigs_filename.c_str()); + | ^~~~ [ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/extract_domains.cpp.o -MF CMakeFiles/spades-stages.dir/extract_domains.cpp.o.d -o CMakeFiles/spades-stages.dir/extract_domains.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/extract_domains.cpp +[ 67%] Linking CXX static library libbinary_io.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -P CMakeFiles/binary_io.dir/cmake_clean_target.cmake +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -E cmake_link_script CMakeFiles/binary_io.dir/link.txt --verbose=1 +/usr/bin/ar qc libbinary_io.a CMakeFiles/binary_io.dir/graph_pack.cpp.o CMakeFiles/binary_io.dir/genomic_info.cpp.o +/usr/bin/ranlib libbinary_io.a make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 67%] Built target binary_io +make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/io /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 67%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/reads/parser.cpp.o -MF CMakeFiles/input.dir/reads/parser.cpp.o.d -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/reads/parser.cpp [ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -MF CMakeFiles/spades-stages.dir/domain_matcher.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_matcher.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp +[ 67%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp +/build/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp: In function 'bool debruijn_graph::{anonymous}::CollectLibInformation(const debruijn_graph::GraphPack&, size_t&, size_t, size_t)': +/build/spades-3.15.5+dfsg/assembler/src/projects/spades/pair_info_count.cpp:235:42: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 235 | if (data.median_insert_size < gp.k() + 2) + | ~~~~~~~^~~ +[ 67%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -MF CMakeFiles/input.dir/reads/paired_readers.cpp.o.d -o CMakeFiles/input.dir/reads/paired_readers.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/reads/paired_readers.cpp +[ 68%] Linking C static library libhmmer.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -P CMakeFiles/hmmer.dir/cmake_clean_target.cmake +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmer.dir/link.txt --verbose=1 +/usr/bin/ar qc libhmmer.a CMakeFiles/hmmer.dir/src/build.c.o CMakeFiles/hmmer.dir/src/cachedb.c.o CMakeFiles/hmmer.dir/src/emit.c.o CMakeFiles/hmmer.dir/src/errors.c.o CMakeFiles/hmmer.dir/src/evalues.c.o CMakeFiles/hmmer.dir/src/eweight.c.o CMakeFiles/hmmer.dir/src/generic_decoding.c.o CMakeFiles/hmmer.dir/src/generic_fwdback.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_chk.c.o CMakeFiles/hmmer.dir/src/generic_fwdback_banded.c.o CMakeFiles/hmmer.dir/src/generic_null2.c.o CMakeFiles/hmmer.dir/src/generic_msv.c.o CMakeFiles/hmmer.dir/src/generic_optacc.c.o CMakeFiles/hmmer.dir/src/generic_stotrace.c.o CMakeFiles/hmmer.dir/src/generic_viterbi.c.o CMakeFiles/hmmer.dir/src/generic_vtrace.c.o CMakeFiles/hmmer.dir/src/h2_io.c.o CMakeFiles/hmmer.dir/src/heatmap.c.o CMakeFiles/hmmer.dir/src/hmmlogo.c.o CMakeFiles/hmmer.dir/src/hmmdmstr.c.o CMakeFiles/hmmer.dir/src/hmmdwrkr.c.o CMakeFiles/hmmer.dir/src/hmmdutils.c.o CMakeFiles/hmmer.dir/src/hmmer.c.o CMakeFiles/hmmer.dir/src/logsum.c.o CMakeFiles/hmmer.dir/src/modelconfig.c.o CMakeFiles/hmmer.dir/src/modelstats.c.o CMakeFiles/hmmer.dir/src/mpisupport.c.o CMakeFiles/hmmer.dir/src/seqmodel.c.o CMakeFiles/hmmer.dir/src/tracealign.c.o CMakeFiles/hmmer.dir/src/p7_alidisplay.c.o CMakeFiles/hmmer.dir/src/p7_bg.c.o CMakeFiles/hmmer.dir/src/p7_builder.c.o CMakeFiles/hmmer.dir/src/p7_domaindef.c.o CMakeFiles/hmmer.dir/src/p7_gbands.c.o CMakeFiles/hmmer.dir/src/p7_gmx.c.o CMakeFiles/hmmer.dir/src/p7_gmxb.c.o CMakeFiles/hmmer.dir/src/p7_gmxchk.c.o CMakeFiles/hmmer.dir/src/p7_hmm.c.o CMakeFiles/hmmer.dir/src/p7_hmmcache.c.o CMakeFiles/hmmer.dir/src/p7_hmmfile.c.o CMakeFiles/hmmer.dir/src/p7_hmmwindow.c.o CMakeFiles/hmmer.dir/src/p7_null3.c.o CMakeFiles/hmmer.dir/src/p7_pipeline.c.o CMakeFiles/hmmer.dir/src/p7_prior.c.o CMakeFiles/hmmer.dir/src/p7_profile.c.o CMakeFiles/hmmer.dir/src/p7_spensemble.c.o CMakeFiles/hmmer.dir/src/p7_tophits.c.o CMakeFiles/hmmer.dir/src/p7_trace.c.o CMakeFiles/hmmer.dir/src/p7_scoredata.c.o CMakeFiles/hmmer.dir/src/hmmpgmd2msa.c.o CMakeFiles/hmmer.dir/src/fm_alphabet.c.o CMakeFiles/hmmer.dir/src/fm_general.c.o CMakeFiles/hmmer.dir/src/fm_sse.c.o CMakeFiles/hmmer.dir/src/fm_ssv.c.o CMakeFiles/hmmer.dir/src/impl_sse/decoding.c.o CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o +[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -MF CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o.d -o CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/restricted_edges_filling.cpp In file included from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:17, from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/pair_info_improver.hpp:12, from /build/spades-3.15.5+dfsg/assembler/src/projects/spades/distance_estimation.cpp:10: @@ -2913,21 +2963,55 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/path_utils.hpp:28:20: warning: unused parameter 'min_dist' [-Wunused-parameter] 28 | size_t min_dist, | ~~~~~~~^~~~~~~~ -[ 67%] Built target utils -make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend +[ 68%] Linking CXX static library libllvm-support.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:9: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' +/build/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:362:64: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] + 140 | bool res = set_.erase(queue_.top()); + | ^~~ +/usr/bin/ar qc libllvm-support.a "CMakeFiles/llvm-support.dir/APFloat.cpp.o" "CMakeFiles/llvm-support.dir/APInt.cpp.o" "CMakeFiles/llvm-support.dir/Atomic.cpp.o" "CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o" "CMakeFiles/llvm-support.dir/Debug.cpp.o" "CMakeFiles/llvm-support.dir/Errno.cpp.o" "CMakeFiles/llvm-support.dir/Error.cpp.o" "CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o" "CMakeFiles/llvm-support.dir/FoldingSet.cpp.o" "CMakeFiles/llvm-support.dir/FormatVariadic.cpp.o" "CMakeFiles/llvm-support.dir/Hashing.cpp.o" "CMakeFiles/llvm-support.dir/Host.cpp.o" "CMakeFiles/llvm-support.dir/JSON.cpp.o" "CMakeFiles/llvm-support.dir/LEB128.cpp.o" "CMakeFiles/llvm-support.dir/LineIterator.cpp.o" "CMakeFiles/llvm-support.dir/Locale.cpp.o" "CMakeFiles/llvm-support.dir/MD5.cpp.o" "CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o" "CMakeFiles/llvm-support.dir/MemAlloc.cpp.o" "CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o" "CMakeFiles/llvm-support.dir/NativeFormatting.cpp.o" "CMakeFiles/llvm-support.dir/Path.cpp.o" "CMakeFiles/llvm-support.dir/Process.cpp.o" "CMakeFiles/llvm-support.dir/Program.cpp.o" "CMakeFiles/llvm-support.dir/Regex.cpp.o" "CMakeFiles/llvm-support.dir/Signals.cpp.o" "CMakeFiles/llvm-support.dir/SmallVector.cpp.o" "CMakeFiles/llvm-support.dir/SourceMgr.cpp.o" "CMakeFiles/llvm-support.dir/StringExtras.cpp.o" "CMakeFiles/llvm-support.dir/StringMap.cpp.o" "CMakeFiles/llvm-support.dir/StringRef.cpp.o" "CMakeFiles/llvm-support.dir/StringSaver.cpp.o" "CMakeFiles/llvm-support.dir/ThreadLocal.cpp.o" "CMakeFiles/llvm-support.dir/Threading.cpp.o" "CMakeFiles/llvm-support.dir/TimeProfiler.cpp.o" "CMakeFiles/llvm-support.dir/Twine.cpp.o" "CMakeFiles/llvm-support.dir/Unicode.cpp.o" "CMakeFiles/llvm-support.dir/WithColor.cpp.o" "CMakeFiles/llvm-support.dir/YAMLParser.cpp.o" "CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o" "CMakeFiles/llvm-support.dir/raw_os_ostream.cpp.o" "CMakeFiles/llvm-support.dir/raw_ostream.cpp.o" "CMakeFiles/llvm-support.dir/regcomp.c.o" "CMakeFiles/llvm-support.dir/regerror.c.o" "CMakeFiles/llvm-support.dir/regexec.c.o" "CMakeFiles/llvm-support.dir/regfree.c.o" "CMakeFiles/llvm-support.dir/regstrlcpy.c.o" +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' +/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' +/build/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:394:46: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] +[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o -MF CMakeFiles/spades-stages.dir/load_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/load_graph.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/load_graph.cpp +/usr/bin/ranlib libhmmer.a +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 68%] Built target hmmer +make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake --color= +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/hmm /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm/CMakeFiles/hmmercpp.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build +make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/build make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 67%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -MF CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d -o CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/id_distributor.cpp -[ 68%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -MF CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d -o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.cpp -[ 68%] Linking CXX static library libbinary_io.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -P CMakeFiles/binary_io.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary && /usr/bin/cmake -E cmake_link_script CMakeFiles/binary_io.dir/link.txt --verbose=1 -/usr/bin/ar qc libbinary_io.a CMakeFiles/binary_io.dir/graph_pack.cpp.o CMakeFiles/binary_io.dir/genomic_info.cpp.o +[ 69%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp +[ 69%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmfile.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmfile.cpp +/build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp: In function 'void nrps::MatchContigsInternal(hmmer::HMMMatcher&, const path_extend::BidirectionalPath&, const std::string&, const std::string&, const std::string&, ContigAlnInfo&, io::OFastaReadStream&, size_t, bool)': +/build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp:61:48: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 61 | if (seqpos2.second - seqpos2.first < model_length / 10) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/usr/bin/ranlib libllvm-support.a +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 69%] Built target llvm-support +[ 69%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -MF CMakeFiles/input.dir/reads/binary_converter.cpp.o.d -o CMakeFiles/input.dir/reads/binary_converter.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_converter.cpp +[ 70%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -MF CMakeFiles/input.dir/reads/binary_streams.cpp.o.d -o CMakeFiles/input.dir/reads/binary_streams.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_streams.cpp In file included from /build/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:10: /build/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp: In member function 'void debruijn_graph::gap_closing::MultiGapJoiner::UpdateGap(debruijn_graph::gap_closing::GapDescription&, debruijn_graph::gap_closing::EdgePair, debruijn_graph::gap_closing::EdgePair) const': /build/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:457:14: warning: unused variable 'u1' [-Wunused-variable] @@ -2936,26 +3020,12 @@ /build/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:458:14: warning: unused variable 'u2' [-Wunused-variable] 458 | bool u2 = UpdateRight(gap, split_orig, split_res); | ^~ -/usr/bin/ranlib libbinary_io.a -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' -/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/gap_closer.cpp:394:46: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] /build/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp: In member function 'debruijn_graph::gap_closing::GapDescription debruijn_graph::gap_closing::HybridGapCloser::ConstructConsensus(gap_info_it, gap_info_it) const': /build/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:630:16: warning: unused variable 'cur_len' [-Wunused-variable] 630 | size_t cur_len = end_it - start_it; | ^~~~~~~ -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 68%] Built target binary_io -[ 68%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp -[ 68%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp -[ 68%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp +[ 70%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15: /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': @@ -2977,6 +3047,35 @@ /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'std::pair debruijn_graph::DomainGraphConstructor::FindMappingToPath(const path_extend::BidirectionalPath&, const omnigraph::MappingPath&, std::vector >&) const': +/build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:216:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 216 | for (;index != res.first; ++index) { + | ~~~~~~^~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'void debruijn_graph::DomainGraphConstructor::ConstructStrongEdgesInternal(debruijn_graph::VertexId, const path_extend::BidirectionalPath&, std::map, std::vector > > >, PairComparator> >&)': +/build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:243:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 243 | if (coords.second + 5000 > path.Length()) { + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp: In member function 'P7_PIPELINE* hmmer::HMMMatcher::pipeline_create(const hmmer::hmmer_cfg&, int, int, int, unsigned int)': +/build/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp:161:34: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 161 | pli->Z = pli->domZ = cfg.Z; + | ~~~~^ +[ 70%] Building CXX object common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -MF CMakeFiles/input.dir/reads/io_helper.cpp.o.d -o CMakeFiles/input.dir/reads/io_helper.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/reads/io_helper.cpp +[ 70%] Linking CXX static library libhmmercpp.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -P CMakeFiles/hmmercpp.dir/cmake_clean_target.cmake +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmercpp.dir/link.txt --verbose=1 +/usr/bin/ar qc libhmmercpp.a CMakeFiles/hmmercpp.dir/hmmfile.cpp.o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o +/usr/bin/ranlib libhmmercpp.a +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 70%] Built target hmmercpp +make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 70%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -MF CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d -o CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/id_distributor.cpp In file included from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21, @@ -3015,8 +3114,10 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 504 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp +[ 72%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -MF CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d -o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/components/connected_component.cpp +[ 72%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -MF CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d -o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/read_converter.cpp In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15: /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] @@ -3041,12 +3142,6 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp: In function 'void nrps::MatchContigsInternal(hmmer::HMMMatcher&, const path_extend::BidirectionalPath&, const std::string&, const std::string&, const std::string&, ContigAlnInfo&, io::OFastaReadStream&, size_t, bool)': -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_matcher.cpp:61:48: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 61 | if (seqpos2.second - seqpos2.first < model_length / 10) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -[ 68%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -MF CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o.d -o CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/restricted_edges_filling.cpp In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:12, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_multi_index.hpp:11, @@ -3061,8 +3156,10 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ -[ 68%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp +[ 72%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -MF CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d -o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/dataset_readers.cpp +[ 72%] Building CXX object common/io/CMakeFiles/input.dir/sam/read.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/sam/read.cpp.o -MF CMakeFiles/input.dir/sam/read.cpp.o.d -o CMakeFiles/input.dir/sam/read.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/sam/read.cpp In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_aligning.cpp:13: @@ -3085,6 +3182,62 @@ /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ +[ 73%] Building CXX object common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o -MF CMakeFiles/input.dir/sam/sam_reader.cpp.o.d -o CMakeFiles/input.dir/sam/sam_reader.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/sam/sam_reader.cpp +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 30 | bool loaded = Base::Load(basename, graph); + | ^~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 43 | bool loaded = Base::BinRead(is, graph); + | ^~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); + | ^~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:12, + from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:9, + from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:13, + from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:20: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 73%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.cpp +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, @@ -3102,6 +3255,12 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 73%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp +[ 73%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -MF CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d -o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp +[ 73%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/scaff_supplementary.cpp In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, @@ -3123,23 +3282,8 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 69%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o +[ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -MF CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d -o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp -[ 70%] Linking C static library libhmmer.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -P CMakeFiles/hmmer.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmer.dir/link.txt --verbose=1 -/usr/bin/ar qc libhmmer.a CMakeFiles/hmmer.dir/src/build.c.o CMakeFiles/hmmer.dir/src/cachedb.c.o CMakeFiles/hmmer.dir/src/emit.c.o CMakeFiles/hmmer.dir/src/errors.c.o CMakeFiles/hmmer.dir/src/evalues.c.o CMakeFiles/hmmer.dir/src/eweight.c.o 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CMakeFiles/hmmer.dir/src/impl_sse/fwdback.c.o CMakeFiles/hmmer.dir/src/impl_sse/io.c.o CMakeFiles/hmmer.dir/src/impl_sse/ssvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/msvfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/null2.c.o CMakeFiles/hmmer.dir/src/impl_sse/optacc.c.o CMakeFiles/hmmer.dir/src/impl_sse/stotrace.c.o CMakeFiles/hmmer.dir/src/impl_sse/vitfilter.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_omx.c.o CMakeFiles/hmmer.dir/src/impl_sse/p7_oprofile.c.o CMakeFiles/hmmer.dir/src/impl_sse/mpi.c.o -/usr/bin/ranlib libhmmer.a -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 70%] Built target hmmer -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/io /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 70%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/reads/parser.cpp.o -MF CMakeFiles/input.dir/reads/parser.cpp.o.d -o CMakeFiles/input.dir/reads/parser.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/reads/parser.cpp In file included from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -3173,45 +3317,6 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:12, - from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:9, - from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:13, - from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/split_path_constructor.hpp:20: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/projects/spades/repeat_resolving.cpp:9: -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 30 | bool loaded = Base::Load(basename, graph); - | ^~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 43 | bool loaded = Base::BinRead(is, graph); - | ^~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); - | ^~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds] @@ -3234,50 +3339,7 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:9, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:7: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'std::pair debruijn_graph::DomainGraphConstructor::FindMappingToPath(const path_extend::BidirectionalPath&, const omnigraph::MappingPath&, std::vector >&) const': -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:216:21: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 216 | for (;index != res.first; ++index) { - | ~~~~~~^~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp: In member function 'void debruijn_graph::DomainGraphConstructor::ConstructStrongEdgesInternal(debruijn_graph::VertexId, const path_extend::BidirectionalPath&, std::map, std::vector > > >, PairComparator> >&)': -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:243:34: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 243 | if (coords.second + 5000 > path.Length()) { - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -[ 70%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/load_graph.cpp.o -MF CMakeFiles/spades-stages.dir/load_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/load_graph.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/load_graph.cpp -[ 70%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o +[ 74%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -MF CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o.d -o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, @@ -3292,10 +3354,6 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 580 | value_type tmp(std::forward(args)...); | ^~~ -[ 70%] Building CXX object common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/reads/paired_readers.cpp.o -MF CMakeFiles/input.dir/reads/paired_readers.cpp.o.d -o CMakeFiles/input.dir/reads/paired_readers.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/reads/paired_readers.cpp -[ 70%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/reads/binary_converter.cpp.o -MF CMakeFiles/input.dir/reads/binary_converter.cpp.o.d -o CMakeFiles/input.dir/reads/binary_converter.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_converter.cpp In file included from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_set.h:27, from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:10: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', @@ -3355,18 +3413,36 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 72%] Building CXX object common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/reads/binary_streams.cpp.o -MF CMakeFiles/input.dir/reads/binary_streams.cpp.o.d -o CMakeFiles/input.dir/reads/binary_streams.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/reads/binary_streams.cpp -[ 73%] Building CXX object projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-stages.dir/domain_graph.cpp.o -MF CMakeFiles/spades-stages.dir/domain_graph.cpp.o.d -o CMakeFiles/spades-stages.dir/domain_graph.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp -make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/hmm /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm/CMakeFiles/hmmercpp.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/hmm/CMakeFiles/hmmercpp.dir/build.make common/hmm/CMakeFiles/hmmercpp.dir/build -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 73%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmfile.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmfile.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmfile.cpp +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, + from /build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:8: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:10, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_index_builders.hpp:10, from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index_refiller.cpp:9: @@ -3381,29 +3457,10 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_position_index.hpp:20:14: warning: ignoring packed attribute because of unpacked non-POD field 'omnigraph::impl::EdgeId debruijn_graph::EdgeInfo::edge_id_' 20 | IdHolder edge_id_; | ^~~~~~~~ -[ 73%] Building CXX object common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/reads/io_helper.cpp.o -MF CMakeFiles/input.dir/reads/io_helper.cpp.o.d -o CMakeFiles/input.dir/reads/io_helper.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/reads/io_helper.cpp -[ 73%] Building CXX object common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/hmm/CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -MF CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o.d -o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp -[ 73%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -MF CMakeFiles/input.dir/dataset_support/read_converter.cpp.o.d -o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/read_converter.cpp -/build/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp: In member function 'P7_PIPELINE* hmmer::HMMMatcher::pipeline_create(const hmmer::hmmer_cfg&, int, int, int, unsigned int)': -/build/spades-3.15.5+dfsg/assembler/src/common/hmm/hmmmatcher.cpp:161:34: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 161 | pli->Z = pli->domZ = cfg.Z; - | ~~~~^ -[ 73%] Linking CXX static library libhmmercpp.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -P CMakeFiles/hmmercpp.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/hmm && /usr/bin/cmake -E cmake_link_script CMakeFiles/hmmercpp.dir/link.txt --verbose=1 -/usr/bin/ar qc libhmmercpp.a CMakeFiles/hmmercpp.dir/hmmfile.cpp.o CMakeFiles/hmmercpp.dir/hmmmatcher.cpp.o -/usr/bin/ranlib libhmmercpp.a -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 73%] Built target hmmercpp -[ 73%] Building CXX object common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -MF CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o.d -o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/dataset_support/dataset_readers.cpp -[ 73%] Building CXX object common/io/CMakeFiles/input.dir/sam/read.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/sam/read.cpp.o -MF CMakeFiles/input.dir/sam/read.cpp.o.d -o CMakeFiles/input.dir/sam/read.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/sam/read.cpp -[ 74%] Building CXX object common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o -MF CMakeFiles/input.dir/sam/sam_reader.cpp.o.d -o CMakeFiles/input.dir/sam/sam_reader.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/io/sam/sam_reader.cpp +[ 74%] Linking CXX static library libinput.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 +/usr/bin/ar qc libinput.a CMakeFiles/input.dir/reads/parser.cpp.o CMakeFiles/input.dir/reads/paired_readers.cpp.o CMakeFiles/input.dir/reads/binary_converter.cpp.o CMakeFiles/input.dir/reads/binary_streams.cpp.o CMakeFiles/input.dir/reads/io_helper.cpp.o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o CMakeFiles/input.dir/sam/read.cpp.o CMakeFiles/input.dir/sam/sam_reader.cpp.o In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]', inlined from 'T* adt::SmallPODVector::emplace(const_iterator, ArgTypes&& ...) [with ArgTypes = {const omnigraph::de::PointT&}; T = omnigraph::de::PointT; Container = adt::impl::HybridAllocatedStorage, 3>]' at /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:581:22, inlined from 'std::pair::iterator, bool> adt::flat_set::emplace(First&&, Args&& ...) [with First = const omnigraph::de::PointT&; Args = {}; T = omnigraph::de::PointT; Comp = std::less >; Container = adt::SmallPODVector]' at /build/spades-3.15.5+dfsg/assembler/src/common/adt/flat_set.hpp:136:34, @@ -3438,10 +3495,34 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:580:20: note: at offset 16 into object 'tmp' of size 16 580 | value_type tmp(std::forward(args)...); | ^~~ +/usr/bin/ranlib libinput.a +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 74%] Built target input In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, - from /build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph_construction.cpp:8: + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.hpp:9, + from /build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp:7: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_container.hpp:9, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp:9, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp:7: /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -3455,6 +3536,19 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': @@ -3506,56 +3600,6 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ -[ 74%] Linking CXX static library libassembly_graph.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -P CMakeFiles/assembly_graph.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/assembly_graph.dir/link.txt --verbose=1 -/usr/bin/ar qc libassembly_graph.a CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o -/usr/bin/ranlib libassembly_graph.a -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 74%] Built target assembly_graph -make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend -make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/modules /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -[ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -MF CMakeFiles/path_extend.dir/pe_config_struct.cpp.o.d -o CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_config_struct.cpp -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o -[ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o -MF CMakeFiles/path_extend.dir/loop_detector.cpp.o.d -o CMakeFiles/path_extend.dir/loop_detector.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_detector.cpp -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o -MF CMakeFiles/modules.dir/chromosome_remover.cpp.o.d -o CMakeFiles/modules.dir/chromosome_remover.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -MF CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d -o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp -[ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o -MF CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d -o CMakeFiles/path_extend.dir/loop_traverser.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o -MF CMakeFiles/modules.dir/alignment/gap_info.cpp.o.d -o CMakeFiles/modules.dir/alignment/gap_info.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/gap_info.cpp -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -MF CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d -o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.cpp -[ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -[ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o -MF CMakeFiles/path_extend.dir/path_extenders.cpp.o.d -o CMakeFiles/path_extend.dir/path_extenders.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -MF CMakeFiles/modules.dir/alignment/bwa_index.cpp.o.d -o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp In file included from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -3589,42 +3633,6 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 75%] Linking CXX static library libinput.a -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 -/usr/bin/ar qc libinput.a CMakeFiles/input.dir/reads/parser.cpp.o CMakeFiles/input.dir/reads/paired_readers.cpp.o CMakeFiles/input.dir/reads/binary_converter.cpp.o CMakeFiles/input.dir/reads/binary_streams.cpp.o CMakeFiles/input.dir/reads/io_helper.cpp.o CMakeFiles/input.dir/dataset_support/read_converter.cpp.o CMakeFiles/input.dir/dataset_support/dataset_readers.cpp.o CMakeFiles/input.dir/sam/read.cpp.o CMakeFiles/input.dir/sam/sam_reader.cpp.o -/usr/bin/ranlib libinput.a -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 75%] Built target input -[ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o -MF CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o.d -o CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] - 565 | ++vptr; - | ^~ -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [344]' [-Warray-bounds] @@ -3669,14 +3677,11 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -MF CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o.d -o CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.cpp In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.hpp:9, - from /build/spades-3.15.5+dfsg/assembler/src/projects/spades/domain_graph.cpp:7: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:11: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -3689,14 +3694,78 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] + 565 | ++vptr; + | ^~ +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ +[ 74%] Linking CXX static library libassembly_graph.a +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -P CMakeFiles/assembly_graph.dir/cmake_clean_target.cmake +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph && /usr/bin/cmake -E cmake_link_script CMakeFiles/assembly_graph.dir/link.txt --verbose=1 +/usr/bin/ar qc libassembly_graph.a CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o +/usr/bin/ranlib libassembly_graph.a +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 74%] Built target assembly_graph +make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/depend +make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/depend +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/modules /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend/CMakeFiles/path_extend.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 74%] Building CXX object common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o +[ 74%] Building CXX object common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/chromosome_remover.cpp.o -MF CMakeFiles/modules.dir/chromosome_remover.cpp.o.d -o CMakeFiles/modules.dir/chromosome_remover.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -MF CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d -o CMakeFiles/modules.dir/genome_consistance_checker.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/genome_consistance_checker.cpp +[ 74%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o +[ 75%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/long_read_mapper.cpp.o +[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o -MF CMakeFiles/modules.dir/alignment/gap_info.cpp.o.d -o CMakeFiles/modules.dir/alignment/gap_info.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/gap_info.cpp +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings 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/build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -MF CMakeFiles/path_extend.dir/pe_config_struct.cpp.o.d -o CMakeFiles/path_extend.dir/pe_config_struct.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_config_struct.cpp +[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -MF CMakeFiles/modules.dir/alignment/bwa_index.cpp.o.d -o CMakeFiles/modules.dir/alignment/bwa_index.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_index.cpp +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_detector.cpp.o -MF CMakeFiles/path_extend.dir/loop_detector.cpp.o.d -o CMakeFiles/path_extend.dir/loop_detector.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_detector.cpp +[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/loop_traverser.cpp.o -MF CMakeFiles/path_extend.dir/loop_traverser.cpp.o.d -o CMakeFiles/path_extend.dir/loop_traverser.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/loop_traverser.cpp +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -MF CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o.d -o CMakeFiles/modules.dir/alignment/sequence_mapper.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.cpp +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -MF CMakeFiles/path_extend.dir/gap_analyzer.cpp.o.d -o CMakeFiles/path_extend.dir/gap_analyzer.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/gap_analyzer.cpp +[ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/path_extenders.cpp.o -MF CMakeFiles/path_extend.dir/path_extenders.cpp.o.d -o CMakeFiles/path_extend.dir/path_extenders.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_extenders.cpp [ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o -MF CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o.d -o CMakeFiles/modules.dir/alignment/sequence_mapper_notifier.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.cpp +[ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.cpp +[ 76%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp: In member function 'void debruijn_graph::{anonymous}::GappedPathExtractorForTrustedContigs::RemoveMappingsWithBadTotalLength(omnigraph::MappingPath&) const': /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/long_read_mapper.cpp:277:25: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 277 | if (bad_mapping_pos == -1) | ~~~~~~~~~~~~~~~~^~~~~ -[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o +[ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.cpp +[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pe_resolver.cpp.o -MF CMakeFiles/path_extend.dir/pe_resolver.cpp.o.d -o CMakeFiles/path_extend.dir/pe_resolver.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10: /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -3710,8 +3779,20 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] + 565 | ++vptr; + | ^~ +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ +[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/overlap_remover.cpp.o -MF CMakeFiles/path_extend.dir/overlap_remover.cpp.o.d -o CMakeFiles/path_extend.dir/overlap_remover.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp +[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, @@ -3729,18 +3810,11 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:131:64: required from here /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] -[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launch_support.cpp -[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o +[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/bwa_sequence_mapper.hpp:9, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.hpp:10: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -3753,27 +3827,7 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] - 565 | ++vptr; - | ^~ -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ -[ 77%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_filler.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_filler.cpp -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:14: -/build/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp: In instantiation of 'void omnigraph::de::PairedIndexHandler::HandleMerge(const std::vector&, EdgeId) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': -/build/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:597:18: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:638:53: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'float' may change value [-Wconversion] - 638 | if (paired_index_.graph().length(new_edge) > point.d && new_edge != next) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -[ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -MF CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o.d -o CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp -[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o +[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/index/edge_info_updater.hpp:13: In member function 'const Sequence& Sequence::operator=(const Sequence&)', @@ -3931,23 +3985,6 @@ /usr/include/c++/12/bits/move.h:204:11: note: '*(Sequence*)((char*)&__tmp + offsetof(omnigraph::GapDescription,omnigraph::GapDescription::filling_seq_.boost::optional::.boost::optional_detail::optional_base::m_storage.boost::optional_detail::aligned_storage::dummy_)).Sequence::size_' was declared here 204 | _Tp __tmp = _GLIBCXX_MOVE(__a); | ^~~~~ -[ 79%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/gap_dijkstra.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/gap_dijkstra.cpp -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 79%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp In file included from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -3979,6 +4016,12 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 344 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/modules/chromosome_remover.cpp:14: +/build/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp: In instantiation of 'void omnigraph::de::PairedIndexHandler::HandleMerge(const std::vector&, EdgeId) [with G = debruijn_graph::DeBruijnGraph; Traits = omnigraph::de::PointTraits; Container = omnigraph::de::safe_btree_map; typename Graph::EdgeId = omnigraph::impl::EdgeId; EdgeId = omnigraph::impl::EdgeId]': +/build/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:597:18: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:638:53: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'float' may change value [-Wconversion] + 638 | if (paired_index_.graph().length(new_edge) > point.d && new_edge != next) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds] @@ -4001,6 +4044,12 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp +[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp +[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp: In member function 'path_extend::ExtensionChooser::EdgeContainer path_extend::ExtensionChooser2015::FindNextUniqueEdge(path_extend::EdgeId) const': /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:29:19: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 29 | if (sum < absolute_weight_threshold_) { @@ -4026,14 +4075,15 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 80%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -MF CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o.d -o CMakeFiles/modules.dir/alignment/pacbio/g_aligner.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/pacbio/g_aligner.cpp +[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp +[ 81%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp:7: + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.hpp:9, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp:7: /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -4050,8 +4100,9 @@ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.hpp:9, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/overlap_remover.cpp:7: + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.cpp:7: /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -4065,12 +4116,23 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp -[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp -[ 80%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp +/build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual path_extend::Connections path_extend::LongReadsLibConnectionCondition::ConnectedWith(path_extend::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': +/build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:111:28: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] + 111 | if (iter->second < min_read_count_) { + | ^~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.cpp:5: /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp: In static member function 'static int path_extend::ExtenderTriplet::GetPriority(io::LibraryType)': /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:28:41: warning: this statement may fall through [-Wimplicit-fallthrough=] @@ -4217,76 +4279,6 @@ /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/extenders_logic.hpp:46:13: note: in expansion of macro 'SET_PRIORITY' 46 | SET_PRIORITY(LibraryType::AssemblyGraph); | ^~~~~~~~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:14: -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 30 | bool loaded = Base::Load(basename, graph); - | ^~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 43 | bool loaded = Base::BinRead(is, graph); - | ^~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); - | ^~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ -[ 81%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/path_extend && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -MF CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o.d -o CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function 'virtual path_extend::Connections path_extend::LongReadsLibConnectionCondition::ConnectedWith(path_extend::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const': -/build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:111:28: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] - 111 | if (iter->second < min_read_count_) { - | ^~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_set.h:27, from /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:12: In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', @@ -4317,16 +4309,21 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 344 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] - 565 | ++vptr; - | ^~ -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds] @@ -4349,7 +4346,30 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pipeline/launcher.cpp:14: +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 30 | bool loaded = Base::Load(basename, graph); + | ^~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 43 | bool loaded = Base::BinRead(is, graph); + | ^~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); + | ^~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -4362,11 +4382,55 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] + 565 | ++vptr; + | ^~ +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ [ 81%] Linking CXX static library libspades-stages.a cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -P CMakeFiles/spades-stages.dir/cmake_clean_target.cmake cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-stages.dir/link.txt --verbose=1 /usr/bin/ar qc libspades-stages.a "CMakeFiles/spades-stages.dir/gap_closer.cpp.o" "CMakeFiles/spades-stages.dir/mismatch_correction.cpp.o" "CMakeFiles/spades-stages.dir/pair_info_count.cpp.o" "CMakeFiles/spades-stages.dir/second_phase_setup.cpp.o" "CMakeFiles/spades-stages.dir/distance_estimation.cpp.o" "CMakeFiles/spades-stages.dir/repeat_resolving.cpp.o" "CMakeFiles/spades-stages.dir/contig_output_stage.cpp.o" "CMakeFiles/spades-stages.dir/hybrid_aligning.cpp.o" "CMakeFiles/spades-stages.dir/chromosome_removal.cpp.o" "CMakeFiles/spades-stages.dir/extract_domains.cpp.o" "CMakeFiles/spades-stages.dir/domain_matcher.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph_construction.cpp.o" "CMakeFiles/spades-stages.dir/restricted_edges_filling.cpp.o" "CMakeFiles/spades-stages.dir/load_graph.cpp.o" "CMakeFiles/spades-stages.dir/domain_graph.cpp.o" /usr/bin/ranlib libspades-stages.a +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 81%] Built target spades-stages +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:7: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -4420,27 +4484,6 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 81%] Built target spades-stages -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/scaffolder2015/path_polisher.cpp:7: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/histogram.hpp:12, from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info_buffer.hpp:9, from /build/spades-3.15.5+dfsg/assembler/src/common/paired_info/paired_info.hpp:13, @@ -4481,16 +4524,16 @@ make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 81%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o -MF CMakeFiles/pipeline.dir/config_struct.cpp.o.d -o CMakeFiles/pipeline.dir/config_struct.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/pipeline/config_struct.cpp [ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o -[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/pipeline/CMakeFiles/pipeline.dir/graph_pack.cpp.o -MF CMakeFiles/pipeline.dir/graph_pack.cpp.o.d -o CMakeFiles/pipeline.dir/graph_pack.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/pipeline/graph_pack.cpp -[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o -MF CMakeFiles/pipeline.dir/library_data.cpp.o.d -o CMakeFiles/pipeline.dir/library_data.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/pipeline/library_data.cpp cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o -MF CMakeFiles/pipeline.dir/library.cpp.o.d -o CMakeFiles/pipeline.dir/library.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/pipeline/library.cpp +[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/pipeline/CMakeFiles/pipeline.dir/library_data.cpp.o -MF CMakeFiles/pipeline.dir/library_data.cpp.o.d -o CMakeFiles/pipeline.dir/library_data.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/pipeline/library_data.cpp +[ 82%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o -MF CMakeFiles/pipeline.dir/stage.cpp.o.d -o CMakeFiles/pipeline.dir/stage.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.cpp -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o -MF CMakeFiles/pipeline.dir/config_struct.cpp.o.d -o CMakeFiles/pipeline.dir/config_struct.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/pipeline/config_struct.cpp In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-3.15.5+dfsg/assembler/src/common/pipeline/stage.cpp:9: /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': @@ -4639,9 +4682,9 @@ make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 82%] Built target pipeline make -f common/stages/CMakeFiles/stages.dir/build.make common/stages/CMakeFiles/stages.dir/depend +make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/depend make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/stages /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages/CMakeFiles/stages.dir/DependInfo.cmake --color= -make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/depend make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer/CMakeFiles/spades-ionhammer.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' @@ -4650,36 +4693,54 @@ make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build.make projects/ionhammer/CMakeFiles/spades-ionhammer.dir/build make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o -[ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o [ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o -[ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o -[ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -[ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/stages/CMakeFiles/stages.dir/read_conversion.cpp.o -MF CMakeFiles/stages.dir/read_conversion.cpp.o.d -o CMakeFiles/stages.dir/read_conversion.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/stages/read_conversion.cpp -[ 83%] Building CXX object common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -MF CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/subcluster.cpp -[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o +[ 82%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o +[ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings 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-ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -MF CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/config_struct.cpp cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/stages/CMakeFiles/stages.dir/simplification.cpp.o -MF CMakeFiles/stages.dir/simplification.cpp.o.d -o CMakeFiles/stages.dir/simplification.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -MF CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o.d -o 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projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -MF CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/subcluster.cpp +[ 83%] Building CXX object common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o +[ 83%] Building CXX object common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o +[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/stages/CMakeFiles/stages.dir/ss_edge_split.cpp.o -MF CMakeFiles/stages.dir/ss_edge_split.cpp.o.d -o CMakeFiles/stages.dir/ss_edge_split.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/stages/ss_edge_split.cpp cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/stages && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT common/stages/CMakeFiles/stages.dir/genomic_info_filler.cpp.o -MF CMakeFiles/stages.dir/genomic_info_filler.cpp.o.d -o CMakeFiles/stages.dir/genomic_info_filler.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/common/stages/genomic_info_filler.cpp -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o +[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -MF CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/err_helper_table.cpp -[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -MF CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/config_struct.cpp +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -MF CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_helpers.cpp +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -MF CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -MF CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o -MF CMakeFiles/spades-ionhammer.dir/main.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/main.cpp +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o -MF CMakeFiles/spades-ionhammer.dir/reference.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/reference.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/reference.cpp +[ 84%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/quality_metrics.cpp +[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/quality_thresholds_estimator.cpp +[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -MF CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/hamcluster_1.cpp +/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void BaseHypothesisEvaluator(BamTools::BamAlignment&, const std::string&, const std::string&, float&, float&, int)': +/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:26:56: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] + 26 | if (not GetBamTags(alignment, flow_order_str.length(), measurements, phase_params, start_flow)) + | ~~~~~~~~~~~~~~~~~~~~~^~ +/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:28:34: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] + 28 | num_flows = measurements.size(); + | ~~~~~~~~~~~~~~~~~^~ +/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:46:57: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] + 46 | unsigned int prefix_size = master_read.sequence.size(); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ +/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void RevComplementInPlace(std::string&)': +/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:292:32: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] + 292 | int backward_idx = seq.size()-1; + | ~~~~~~~~~~^~ /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function 'void TreephaserLite::SetModelParameters(double, double, double)': /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp:85:76: warning: conversion from 'double' to '__gnu_cxx::__alloc_traits, float>::value_type' {aka 'float'} may change value [-Wfloat-conversion] 85 | transition_base_[nuc][flow] = nuc_avaliability[nuc] * (1-droop_rate) * (1-incomplete_extension_rate); @@ -4707,28 +4768,10 @@ /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/TreephaserLite.cpp:514:72: warning: conversion from 'double' to 'float' may change value [-Wfloat-conversion] 514 | child->per_flow_metric = (child->path_metric + 0.5 * penalty1) / child->flow; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void BaseHypothesisEvaluator(BamTools::BamAlignment&, const std::string&, const std::string&, float&, float&, int)': -/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:26:56: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] - 26 | if (not GetBamTags(alignment, flow_order_str.length(), measurements, phase_params, start_flow)) - | ~~~~~~~~~~~~~~~~~~~~~^~ -/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:28:34: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] - 28 | num_flows = measurements.size(); - | ~~~~~~~~~~~~~~~~~^~ -/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:46:57: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'unsigned int' may change value [-Wconversion] - 46 | unsigned int prefix_size = master_read.sequence.size(); - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ -/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function 'void RevComplementInPlace(std::string&)': -/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:292:32: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'int' may change value [-Wconversion] - 292 | int backward_idx = seq.size()-1; - | ~~~~~~~~~~^~ -[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -MF CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/quality_thresholds_estimator.cpp -[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -MF CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/hamcluster_1.cpp -[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o [ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/normal_quality_model.cpp cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/gamma_poisson_model.cpp +[ 86%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/ionhammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -MF CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o.d -o CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/normal_quality_model.cpp In file included from /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/hkmer.hpp:13, from /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_data.hpp:16, from /build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/kmer_data.cpp:8: @@ -4750,10 +4793,6 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ -/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/main.cpp: In static member function 'static bool hammer::correction::TKMerDataEstimator::stage(hammer_config::HammerStage, hammer_config::HammerStage)': -/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/main.cpp:90:3: warning: control reaches end of non-void function [-Wreturn-type] - 90 | } - | ^ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:12, from /build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:11: @@ -4771,26 +4810,10 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator; size_t = long unsigned int]' /build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:345:28: required from here /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/main.cpp: In static member function 'static bool hammer::correction::TKMerDataEstimator::stage(hammer_config::HammerStage, hammer_config::HammerStage)': +/build/spades-3.15.5+dfsg/assembler/src/projects/ionhammer/main.cpp:90:3: warning: control reaches end of non-void function [-Wreturn-type] + 90 | } + | ^ /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' @@ -4798,16 +4821,6 @@ /build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' /build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification.cpp:474:24: required from here /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] - 565 | ++vptr; - | ^~ -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' @@ -4881,6 +4894,36 @@ /build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:581:16: warning: unused variable 'total_cnt' [-Wunused-variable] 581 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/edge_index.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:19, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper_notifier.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/stages/ss_edge_split.cpp:9: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] + 565 | ++vptr; + | ^~ +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:19: /build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'bool omnigraph::complex_br::ComponentProjector::SplitComponent() [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:813:14: required from 'bool omnigraph::complex_br::ComponentProjector::ProjectComponent() [with Graph = debruijn_graph::DeBruijnGraph]' @@ -5069,86 +5112,105 @@ make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 86%] Built target common_modules make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/spades /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake --color= make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/depend +make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/depend +make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/depend +make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/depend +make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/depend +make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/depend make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/hammer /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer/CMakeFiles/spades-hammer.dir/DependInfo.cmake --color= -make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/depend +make -f 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projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/kmercount /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/kmercount /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu 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/build/spades-3.15.5+dfsg/assembler/src/projects/spades /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades/CMakeFiles/spades-core.dir/DependInfo.cmake --color= +make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/depend +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/hammer/CMakeFiles/spades-hammer.dir/build.make projects/hammer/CMakeFiles/spades-hammer.dir/build make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/corrector/CMakeFiles/spades-corrector-core.dir/build.make projects/corrector/CMakeFiles/spades-corrector-core.dir/build make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/bin_converter /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/gbuilder /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/build make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/depend +make -f projects/spades/CMakeFiles/spades-core.dir/build.make projects/spades/CMakeFiles/spades-core.dir/build +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build.make projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/build +[ 86%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/build +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o -MF CMakeFiles/spades-hammer.dir/main.cpp.o.d -o CMakeFiles/spades-hammer.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/main.cpp +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/gmapper /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper/CMakeFiles/spades-gmapper.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f projects/kmercount/CMakeFiles/spades-read-filter.dir/build.make projects/kmercount/CMakeFiles/spades-read-filter.dir/build +[ 86%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -MF CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/corrector/positional_read.cpp +[ 86%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o +make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/kmercount /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/DependInfo.cmake --color= +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -MF CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o.d -o CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/hammer_tools.cpp [ 86%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o -make -f projects/kmercount/CMakeFiles/spades-kmercount.dir/build.make projects/kmercount/CMakeFiles/spades-kmercount.dir/build -[ 86%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 86%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o +[ 86%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-core.dir/pipeline.cpp.o -MF CMakeFiles/spades-core.dir/pipeline.cpp.o.d -o CMakeFiles/spades-core.dir/pipeline.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp +[ 86%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o +make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 87%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-core.dir/main.cpp.o -MF CMakeFiles/spades-core.dir/main.cpp.o.d -o CMakeFiles/spades-core.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/main.cpp -[ 87%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -[ 87%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -[ 87%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o -[ 87%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o -MF CMakeFiles/spades-core.dir/series_analysis.cpp.o.d -o CMakeFiles/spades-core.dir/series_analysis.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/series_analysis.cpp -[ 87%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -MF CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/corrector/positional_read.cpp -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o -MF CMakeFiles/spades-hammer.dir/main.cpp.o.d -o CMakeFiles/spades-hammer.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/main.cpp -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o -MF CMakeFiles/spades-kmercount.dir/main.cpp.o.d -o CMakeFiles/spades-kmercount.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp -[ 87%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -MF CMakeFiles/spades-hammer.dir/hamcluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/corrector/interesting_pos_processor.cpp +[ 87%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-core.dir/main.cpp.o -MF CMakeFiles/spades-core.dir/main.cpp.o.d -o CMakeFiles/spades-core.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/main.cpp +make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build [ 87%] Building CXX object projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -[ 87%] Building CXX object projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -[ 87%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -MF CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o.d -o CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction/main.cpp -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -MF CMakeFiles/spades-read-filter.dir/read_filter.cpp.o.d -o CMakeFiles/spades-read-filter.dir/read_filter.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/kmercount/read_filter.cpp -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -MF CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o.d -o CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/mts/contig_abundance.cpp -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -MF CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o.d -o CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/hammer_tools.cpp -[ 88%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -MF CMakeFiles/spades-hammer.dir/hamcluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/hamcluster.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/hamcluster.cpp -[ 89%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -MF CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o.d -o CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/scaffold_correction/main.cpp +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build.make projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/build +make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/build +[ 87%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o -MF CMakeFiles/spades-kmercount.dir/main.cpp.o.d -o CMakeFiles/spades-kmercount.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 90%] Building CXX object projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o +make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build +make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 87%] Building CXX object projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o +[ 88%] Building CXX object projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/kmercount -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/kmercount/CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -MF CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o.d -o CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/kmercount/kmer_estimating.cpp -[ 90%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/corrector/dataset_processor.cpp -/build/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': -/build/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp:357:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] - 357 | for (uint32_t j=0; j::Start(ValueType*, size_t, int) [with ValueType = long unsigned int; int Base = 8; size_t = long unsigned int]': /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:543:13: required from 'static void parallel_radix_sort::PairSort::InitAndSort(PlainType*, ValueType*, size_t, int) [with PlainType = Seq<11, unsigned int>; ValueType = long unsigned int; UnsignedType = Seq<11, unsigned int>; Encoder = EncoderKMer; int Base = 8; size_t = long unsigned int]' @@ -5160,6 +5222,40 @@ /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/parallel_radix_sort.hpp:400:57: warning: unused parameter 'num_threads' [-Wunused-parameter] 400 | void Start(ValueType *original, size_t num_elems, int num_threads) { | ~~~~^~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp: In member function 'size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector >&)': +/build/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_cluster.cpp:357:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] + 357 | for (uint32_t j=0; j::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': +/build/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:197:122: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 488 | graph.ereserve(size_t(2.01*sequences.size())); + | ~~~~~~~~~~~~~~^~ +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] + 504 | graph.vreserve(size_t(2.01*size)); + | ^~~~ +[ 90%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -MF CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/corrector/dataset_processor.cpp /build/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp: In member function 'bool corrector::ContigProcessor::CountPositions(const sam_reader::SingleSamRead&, std::unordered_map&) const': /build/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp:164:65: warning: conversion from 'std::size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 164 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { @@ -5167,47 +5263,76 @@ /build/spades-3.15.5+dfsg/assembler/src/projects/corrector/contig_processor.cpp:164:115: warning: conversion from 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 164 | if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) { | ~~~~~~~~~~~~~~^~ -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp: In function 'void spades::AddPreliminarySimplificationStages(StageManager&)': -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/pipeline.cpp:135:19: warning: unused variable 'mode' [-Wunused-variable] - 135 | pipeline_type mode = cfg::get().mode; - | ^~~~ -[ 90%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -MF CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/corrector/config_struct.cpp -make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/bin_converter /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build.make projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/build -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 90%] Building CXX object projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/bin_converter -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/bin_converter/CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -MF CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o.d -o CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/bin_converter/convert_bin_to_fasta.cpp -[ 90%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o +[ 91%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o -MF CMakeFiles/spades-core.dir/series_analysis.cpp.o.d -o CMakeFiles/spades-core.dir/series_analysis.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spades/series_analysis.cpp +In file included from /build/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:24: +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 30 | bool loaded = Base::Load(basename, graph); + | ^~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 43 | bool loaded = Base::BinRead(is, graph); + | ^~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); + | ^~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, + from /build/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:15: +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 30 | bool loaded = Base::Load(basename, graph); + | ^~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 43 | bool loaded = Base::BinRead(is, graph); + | ^~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); + | ^~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:7: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' +/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' +/build/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:722:28: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] + 140 | bool res = set_.erase(queue_.top()); + | ^~~ +[ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -MF CMakeFiles/spades-hammer.dir/kmer_data.cpp.o.d -o CMakeFiles/spades-hammer.dir/kmer_data.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/kmer_data.cpp -[ 90%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -MF CMakeFiles/spades-corrector-core.dir/main.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/corrector/main.cpp -[ 90%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o +In file included from /build/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:16: +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); + | ^~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ +[ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -MF CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o.d -o CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/config_struct_hammer.cpp -[ 90%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -MF CMakeFiles/spades-hammer.dir/read_corrector.cpp.o.d -o CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp -make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/gbuilder /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder/CMakeFiles/spades-gbuilder.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build.make projects/gbuilder/CMakeFiles/spades-gbuilder.dir/build -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 91%] Building CXX object projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/gbuilder -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o -MF CMakeFiles/spades-gbuilder.dir/main.cpp.o.d -o CMakeFiles/spades-gbuilder.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp -[ 91%] Linking CXX executable ../../bin/spades-truseq-scfcorrection -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-truseq-scfcorrection.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-truseq-scfcorrection ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/gmapper /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper/CMakeFiles/spades-gmapper.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/gmapper/CMakeFiles/spades-gmapper.dir/build.make projects/gmapper/CMakeFiles/spades-gmapper.dir/build -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 91%] Building CXX object projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/gmapper -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/gmapper/CMakeFiles/spades-gmapper.dir/main.cpp.o -MF CMakeFiles/spades-gmapper.dir/main.cpp.o.d -o CMakeFiles/spades-gmapper.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp In file included from /usr/include/string.h:535, from /usr/include/c++/12/cstring:42, from /build/spades-3.15.5+dfsg/assembler/src/common/io/reads/mpmc_bounded.hpp:44, @@ -5323,22 +5448,23 @@ /build/spades-3.15.5+dfsg/assembler/src/projects/kmercount/main.cpp:75:17: note: at offset 40 into object 'kmer' of size 40 75 | RtSeq kmer = seq.start(this->K_) >> 'A'; | ^~~~ -make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/depend -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build.make projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/build -make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 91%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/main.cpp.o -MF CMakeFiles/unitig-coverage.dir/main.cpp.o.d -o CMakeFiles/unitig-coverage.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp +[ 91%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/easel/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/easel -isystem /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/hmmer/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/hmmer/src -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -MF CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o.d -o CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/mts/contig_abundance.cpp +[ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -MF CMakeFiles/spades-hammer.dir/read_corrector.cpp.o.d -o CMakeFiles/spades-hammer.dir/read_corrector.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp +[ 91%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o +cd 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CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/corrector/config_struct.cpp [ 91%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/hammer -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o -MF CMakeFiles/spades-hammer.dir/expander.cpp.o.d -o CMakeFiles/spades-hammer.dir/expander.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/expander.cpp /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp: In member function 'std::string ReadCorrector::CorrectReadRight(const std::string&, const std::string&, size_t)': /build/spades-3.15.5+dfsg/assembler/src/projects/hammer/read_corrector.cpp:72:57: warning: conversion from 'long unsigned int' to 'double' may change value [-Wconversion] 72 | const size_t size_thr = size_t(100 * log2(read_size - right_pos)) + 1; | ~~~~~~~~~~^~~~~~~~~~~ -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 91%] Built target spades-truseq-scfcorrection +[ 91%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/corrector -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o -MF CMakeFiles/spades-corrector-core.dir/main.cpp.o.d -o CMakeFiles/spades-corrector-core.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/corrector/main.cpp +[ 91%] Linking CXX executable ../../bin/spades-truseq-scfcorrection +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/scaffold_correction && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-truseq-scfcorrection.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-truseq-scfcorrection ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make -f projects/spaligner/CMakeFiles/spaligner.dir/build.make projects/spaligner/CMakeFiles/spaligner.dir/depend make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/spaligner /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/spaligner.dir/DependInfo.cmake --color= @@ -5348,52 +5474,26 @@ [ 93%] Building CXX object projects/spaligner/CMakeFiles/spaligner.dir/align_longreads.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/spaligner -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spaligner/CMakeFiles/spaligner.dir/align_longreads.cpp.o -MF CMakeFiles/spaligner.dir/align_longreads.cpp.o.d -o CMakeFiles/spaligner.dir/align_longreads.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp make -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/depend +[ 94%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -MF CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o.d -o CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/spaligner /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner/CMakeFiles/form_truealignments.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/spaligner/CMakeFiles/form_truealignments.dir/build.make projects/spaligner/CMakeFiles/form_truealignments.dir/build make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 93%] Building CXX object projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o +[ 94%] Building CXX object projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/spaligner -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/spaligner/CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o -MF CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o.d -o CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp -[ 93%] Linking CXX executable ../../bin/spades-core -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-core.dir/pipeline.cpp.o" "CMakeFiles/spades-core.dir/main.cpp.o" "CMakeFiles/spades-core.dir/series_analysis.cpp.o" "CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/hmm/libhmmercpp.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so ../../ext/hmmer/libhmmer.a ../../ext/easel/libeasel.a -lm -[ 93%] Linking CXX executable ../../bin/spades-corrector-core -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o" "CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o" "CMakeFiles/spades-corrector-core.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-corrector-core ../../common/io/libinput.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/io/binary/libbinary_io.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 93%] Built target spades-corrector-core +[ 94%] Linking CXX executable ../../bin/spades-kmer-estimating +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmer-estimating.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmer-estimating ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make -f projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build.make projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/depend make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build.make projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/build make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 93%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o +[ 94%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/__/unitig_coverage/profile_storage.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp -In file included from /build/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:29: -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp: In member function 'void debruijn_graph::gap_closing::MultiGapJoiner::UpdateGap(debruijn_graph::gap_closing::GapDescription&, debruijn_graph::gap_closing::EdgePair, debruijn_graph::gap_closing::EdgePair) const': -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:457:14: warning: unused variable 'u1' [-Wunused-variable] - 457 | bool u1 = UpdateLeft(gap, split_orig, split_res); - | ^~ -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:458:14: warning: unused variable 'u2' [-Wunused-variable] - 458 | bool u2 = UpdateRight(gap, split_orig, split_res); - | ^~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:8: -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': -/build/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:197:122: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:488:50: warning: conversion from 'std::vector::size_type' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 488 | graph.ereserve(size_t(2.01*sequences.size())); - | ~~~~~~~~~~~~~~^~ -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] - 504 | graph.vreserve(size_t(2.01*size)); - | ^~~~ -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp: In member function 'debruijn_graph::gap_closing::GapDescription debruijn_graph::gap_closing::HybridGapCloser::ConstructConsensus(gap_info_it, gap_info_it) const': -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:630:16: warning: unused variable 'cur_len' [-Wunused-variable] - 630 | size_t cur_len = end_it - start_it; - | ^~~~~~~ -[ 94%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/main.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp make -f projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/depend make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/DependInfo.cmake --color= @@ -5402,6 +5502,11 @@ make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 94%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -MF CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.cpp +[ 94%] Linking CXX executable ../../bin/spades-convert-bin-to-fasta +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-convert-bin-to-fasta.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-convert-bin-to-fasta ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 94%] Built target spades-kmer-estimating make -f projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/build.make projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/depend make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/DependInfo.cmake --color= @@ -5410,78 +5515,101 @@ make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/cds_subgraphs/CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -MF CMakeFiles/cds-mapping-stats.dir/stats.cpp.o.d -o CMakeFiles/cds-mapping-stats.dir/stats.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp -In file included from /build/spades-3.15.5+dfsg/assembler/src/projects/gbuilder/main.cpp:24: -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 30 | bool loaded = Base::Load(basename, graph); - | ^~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 43 | bool loaded = Base::BinRead(is, graph); - | ^~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); - | ^~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 95%] Built target spades-core +[ 95%] Built target spades-truseq-scfcorrection make -f projects/bin_analysis/CMakeFiles/mag-improve.dir/build.make projects/bin_analysis/CMakeFiles/mag-improve.dir/depend +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis/CMakeFiles/mag-improve.dir/DependInfo.cmake --color= +[ 95%] Built target spades-convert-bin-to-fasta make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f projects/bin_analysis/CMakeFiles/mag-improve.dir/build.make projects/bin_analysis/CMakeFiles/mag-improve.dir/build +[ 95%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -MF CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, - from /build/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:15: -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 30 | bool loaded = Base::Load(basename, graph); - | ^~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 43 | bool loaded = Base::BinRead(is, graph); - | ^~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); - | ^~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ [ 95%] Building CXX object projects/bin_analysis/CMakeFiles/mag-improve.dir/main.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/bin_analysis/CMakeFiles/mag-improve.dir/main.cpp.o -MF CMakeFiles/mag-improve.dir/main.cpp.o.d -o CMakeFiles/mag-improve.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp -[ 95%] Linking CXX executable ../../bin/spades-kmer-estimating -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmer-estimating.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmer-estimating.dir/kmer_estimating.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmer-estimating ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:7: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' -/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/compressor.hpp:123:26: required from 'size_t omnigraph::CompressAllVertices(Graph&, size_t, bool) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]' -/build/spades-3.15.5+dfsg/assembler/src/projects/spades/hybrid_gap_closer.hpp:722:28: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] - 140 | bool res = set_.erase(queue_.top()); - | ^~~ +[ 95%] Linking CXX executable ../../bin/spades-corrector-core +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/corrector && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-corrector-core.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o" "CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o" "CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o" "CMakeFiles/spades-corrector-core.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-corrector-core ../../common/io/libinput.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/io/binary/libbinary_io.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 95%] Built target spades-kmer-estimating -[ 95%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -MF CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/subgraph_extraction.cpp +[ 95%] Built target spades-corrector-core +[ 96%] Building CXX object projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gsimplifier && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/gsimplifier/CMakeFiles/spades-gsimplifier.dir/main.cpp.o -MF CMakeFiles/spades-gsimplifier.dir/main.cpp.o.d -o CMakeFiles/spades-gsimplifier.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp +[ 96%] Linking CXX executable ../../bin/spades-core +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spades && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-core.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-core.dir/pipeline.cpp.o" "CMakeFiles/spades-core.dir/main.cpp.o" "CMakeFiles/spades-core.dir/series_analysis.cpp.o" "CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-core libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/hmm/libhmmercpp.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so ../../ext/hmmer/libhmmer.a ../../ext/easel/libeasel.a -lm +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] + 565 | ++vptr; + | ^~ +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, + from /build/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:8: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, + inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] + 565 | ++vptr; + | ^~ +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 + 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, + | ^~~~~~~~~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:7: +/build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In member function 'bin_refinement::EdgeSet bin_refinement::BoundedRegionsExpander::ProcessComponent(const bin_refinement::VertexSet&, const bin_refinement::EdgeSet&, const bin_refinement::EdgeSet&) const': +/build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:248:47: warning: unused parameter 'reached' [-Wunused-parameter] + 248 | EdgeSet ProcessComponent(const VertexSet &reached, + | ~~~~~~~~~~~~~~~~~^~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::BoundedRegionsExpander::BoundedRegionsExpander(const debruijn_graph::Graph&, const std::set, std::allocator >&, size_t)': +/build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:275:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] + 275 | for (EdgeId e : annotated) { + | ^ +/build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::OnlyAnnotatedReachableExpander::OnlyAnnotatedReachableExpander(const debruijn_graph::Graph&, const bin_refinement::EdgeSet&, size_t, double, double, const std::string&)': +/build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:465:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] + 465 | for (EdgeId e : annotated) { + | ^ +[ 96%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o -MF CMakeFiles/cds-subgraphs.dir/main.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp +[ 96%] Linking CXX executable ../../bin/spades-kmercount +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmercount.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmercount ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so In file included from /build/spades-3.15.5+dfsg/assembler/src/projects/spaligner/align_longreads.cpp:8: /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here @@ -5491,17 +5619,8 @@ /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/projects/gmapper/main.cpp:16: -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); - | ^~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ -[ 95%] Building CXX object projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/cds_subgraphs/CMakeFiles/cds-subgraphs.dir/main.cpp.o -MF CMakeFiles/cds-subgraphs.dir/main.cpp.o.d -o CMakeFiles/cds-subgraphs.dir/main.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 96%] Built target spades-kmercount In file included from /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/sequence_mapper.hpp:18, from /build/spades-3.15.5+dfsg/assembler/src/projects/spaligner/form_truealignments.cpp:20: /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp: In instantiation of 'void debruijn_graph::KmerMapper::HandleGlue(EdgeId, EdgeId, EdgeId) [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]': @@ -5531,26 +5650,6 @@ /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:7: -/build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In member function 'bin_refinement::EdgeSet bin_refinement::BoundedRegionsExpander::ProcessComponent(const bin_refinement::VertexSet&, const bin_refinement::EdgeSet&, const bin_refinement::EdgeSet&) const': -/build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:248:47: warning: unused parameter 'reached' [-Wunused-parameter] - 248 | EdgeSet ProcessComponent(const VertexSet &reached, - | ~~~~~~~~~~~~~~~~~^~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::BoundedRegionsExpander::BoundedRegionsExpander(const debruijn_graph::Graph&, const std::set, std::allocator >&, size_t)': -/build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:275:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] - 275 | for (EdgeId e : annotated) { - | ^ -/build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp: In constructor 'bin_refinement::OnlyAnnotatedReachableExpander::OnlyAnnotatedReachableExpander(const debruijn_graph::Graph&, const bin_refinement::EdgeSet&, size_t, double, double, const std::string&)': -/build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/bin_refinement.hpp:465:21: warning: variable 'e' set but not used [-Wunused-but-set-variable] - 465 | for (EdgeId e : annotated) { - | ^ -[ 96%] Building CXX object projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT projects/unitig_coverage/CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -MF CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o.d -o CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.cpp -In file included from /build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: -/build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp: In function 'void debruijn::simplification::Simplify(debruijn_graph::GraphPack&, const SimplifInfoContainer&, bool, const std::function&)': -/build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:103:16: warning: unused variable 'using_edge_qual' [-Wunused-variable] - 103 | const bool using_edge_qual = edge_qual.IsAttached(); - | ^~~~~~~~~~~~~~~ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stats.cpp:8: @@ -5573,12 +5672,11 @@ /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -[ 96%] Linking CXX executable ../../bin/spades-convert-bin-to-fasta -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_converter && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-convert-bin-to-fasta.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-convert-bin-to-fasta.dir/convert_bin_to_fasta.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-convert-bin-to-fasta ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -[ 97%] Linking CXX executable ../../bin/spades-read-filter -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-read-filter.dir/read_filter.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +In file included from /build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp:8: +/build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp: In function 'void debruijn::simplification::Simplify(debruijn_graph::GraphPack&, const SimplifInfoContainer&, bool, const std::function&)': +/build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:103:16: warning: unused variable 'using_edge_qual' [-Wunused-variable] + 103 | const bool using_edge_qual = edge_qual.IsAttached(); + | ^~~~~~~~~~~~~~~ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/spades-3.15.5+dfsg/assembler/src/projects/bin_analysis/main.cpp:10: @@ -5601,37 +5699,26 @@ /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 97%] Built target spades-convert-bin-to-fasta -[ 98%] Linking CXX executable ../../bin/spades-hammer +[ 96%] Linking CXX executable ../../bin/unitig-coverage +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitig-coverage.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/unitig-coverage.dir/main.cpp.o" "CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/unitig-coverage ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +[ 97%] Linking CXX executable ../../bin/spades-hammer cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/hammer && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-hammer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-hammer.dir/main.cpp.o" "CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o" "CMakeFiles/spades-hammer.dir/hamcluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o" "CMakeFiles/spades-hammer.dir/kmer_data.cpp.o" "CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o" "CMakeFiles/spades-hammer.dir/read_corrector.cpp.o" "CMakeFiles/spades-hammer.dir/expander.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-hammer ../../common/libcommon_modules.a ../../common/io/libinput.a ../../common/utils/libutils.a ../../common/pipeline/libpipeline.a ../../ext/gqf/libgqf.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../ext/gqf/libgqf.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +[ 98%] Linking CXX executable ../../bin/spades-read-filter +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-read-filter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-read-filter.dir/read_filter.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-read-filter ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 98%] Built target spades-hammer +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 98%] Built target unitig-coverage make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 98%] Built target spades-read-filter +[ 98%] Linking CXX executable ../../bin/spades-gmapper +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gmapper.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gmapper.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gmapper ../spades/libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/easel/libeasel.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target spades-hammer -[ 98%] Linking CXX executable ../../bin/spades-kmercount -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/kmercount && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-kmercount.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-kmercount.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-kmercount ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, - from /build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:8: -/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': -/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:83:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' -/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:504:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' -/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:667:49: required from 'boost::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' -/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:720:61: required from 'omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::RelativeCoverageComponentRemover(Graph&, size_t, const omnigraph::FlankingCoverage&, double, size_t, size_t, size_t, double, HandlerF, size_t, std::string) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>; std::string = std::__cxx11::basic_string]' -/usr/include/c++/12/bits/stl_construct.h:119:7: required from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, __cxx11::basic_string, allocator >&}]' -/usr/include/c++/12/bits/alloc_traits.h:635:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/usr/include/c++/12/bits/shared_ptr_base.h:971:16: required from 'std::__shared_count<_Lp>::__shared_count(_Tp*&, std::_Sp_alloc_shared_tag<_Alloc>, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' -/usr/include/c++/12/bits/shared_ptr_base.h:1712:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' -/usr/include/c++/12/bits/shared_ptr.h:464:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' -/usr/include/c++/12/bits/shared_ptr.h:1009:14: required from 'std::shared_ptr >::value), _Tp>::type> std::make_shared(_Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, __cxx11::basic_string, allocator >&}; typename enable_if<(! is_array< >::value), _Tp>::type = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' -/build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:431:49: required from 'omnigraph::AlgoPtr debruijn::simplification::RelativeCoverageComponentRemoverInstance(Graph&, const omnigraph::FlankingCoverage&, const debruijn_graph::config::debruijn_config::simplification::relative_coverage_comp_remover&, const SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' -/build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:157:65: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:53:16: warning: unused variable 'cnt' [-Wunused-variable] - 53 | size_t cnt = border_.erase(v); - | ^~~ +[ 98%] Built target spades-core In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:13: @@ -5654,8 +5741,53 @@ /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], | ^~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:9: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', + inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] + 565 | ++vptr; + | ^~ +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 + 193 | void AddOutgoingEdge(EdgeId e) { + | ~~~~~~~^ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, + from /build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:8: +/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': +/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:83:9: required from 'void omnigraph::simplification::relative_coverage::Component::MakeInner(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]' +/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:504:37: required from 'bool omnigraph::simplification::relative_coverage::component_remover::InnerComponentSearcher::FindComponent() [with Graph = debruijn_graph::DeBruijnGraph]' +/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:667:49: required from 'boost::optional > omnigraph::simplification::relative_coverage::component_remover::RelativeCovComponentFinder::operator()(EdgeId) const [with Graph = debruijn_graph::DeBruijnGraph; EdgeId = omnigraph::impl::EdgeId]' +/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:720:61: required from 'omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover::RelativeCoverageComponentRemover(Graph&, size_t, const omnigraph::FlankingCoverage&, double, size_t, size_t, size_t, double, HandlerF, size_t, std::string) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int; HandlerF = std::function, std::allocator >&)>; std::string = std::__cxx11::basic_string]' +/usr/include/c++/12/bits/stl_construct.h:119:7: required from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, __cxx11::basic_string, allocator >&}]' +/usr/include/c++/12/bits/alloc_traits.h:635:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/usr/include/c++/12/bits/shared_ptr_base.h:971:16: required from 'std::__shared_count<_Lp>::__shared_count(_Tp*&, std::_Sp_alloc_shared_tag<_Alloc>, _Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' +/usr/include/c++/12/bits/shared_ptr_base.h:1712:14: required from 'std::__shared_ptr<_Tp, _Lp>::__shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]' +/usr/include/c++/12/bits/shared_ptr.h:464:59: required from 'std::shared_ptr<_Tp>::shared_ptr(std::_Sp_alloc_shared_tag<_Tp>, _Args&& ...) [with _Alloc = std::allocator; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, std::function, std::allocator >&)>&, const long unsigned int&, std::__cxx11::basic_string, std::allocator >&}; _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' +/usr/include/c++/12/bits/shared_ptr.h:1009:14: required from 'std::shared_ptr >::value), _Tp>::type> std::make_shared(_Args&& ...) [with _Tp = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover; _Args = {debruijn_graph::DeBruijnGraph&, long unsigned int, const omnigraph::FlankingCoverage&, const double&, long unsigned int, long unsigned int, long unsigned int&, double&, function, allocator >&)>&, const long unsigned int&, __cxx11::basic_string, allocator >&}; typename enable_if<(! is_array< >::value), _Tp>::type = omnigraph::simplification::relative_coverage::RelativeCoverageComponentRemover]' +/build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:431:49: required from 'omnigraph::AlgoPtr debruijn::simplification::RelativeCoverageComponentRemoverInstance(Graph&, const omnigraph::FlankingCoverage&, const debruijn_graph::config::debruijn_config::simplification::relative_coverage_comp_remover&, const SimplifInfoContainer&, typename omnigraph::ComponentRemover::HandlerF) [with Graph = debruijn_graph::DeBruijnGraph; omnigraph::AlgoPtr = std::shared_ptr >; typename omnigraph::ComponentRemover::HandlerF = std::function, std::allocator >&)>]' +/build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/simplification.hpp:157:65: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp:53:16: warning: unused variable 'cnt' [-Wunused-variable] + 53 | size_t cnt = border_.erase(v); + | ^~~ make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target spades-kmercount +[ 98%] Built target spades-gmapper In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, from /build/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:9, from /build/spades-3.15.5+dfsg/assembler/src/projects/gsimplifier/main.cpp:12: @@ -5712,59 +5844,6 @@ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/profile_storage.hpp:8, - from /build/spades-3.15.5+dfsg/assembler/src/projects/unitig_coverage/main.cpp:8: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] - 565 | ++vptr; - | ^~ -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, - inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] - 565 | ++vptr; - | ^~ -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 - 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, - | ^~~~~~~~~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:11: /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] @@ -5816,30 +5895,19 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ -[ 98%] Linking CXX executable ../../bin/unitig-coverage -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/unitig_coverage && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitig-coverage.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/unitig-coverage.dir/main.cpp.o" "CMakeFiles/unitig-coverage.dir/profile_storage.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/unitig-coverage ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -[ 98%] Linking CXX executable ../../bin/spaligner -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/spaligner.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/spaligner.dir/align_longreads.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spaligner libmapping_printer.a ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target unitig-coverage -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target spaligner -[ 98%] Linking CXX executable ../../bin/spades-gmapper -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gmapper && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gmapper.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gmapper.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gmapper ../spades/libspades-stages.a ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/ConsensusCore/libConsensusCore.a ../../ext/easel/libeasel.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target spades-gmapper +[ 98%] Linking CXX executable ../../bin/spades-gbuilder +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gbuilder.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gbuilder.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gbuilder ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so [ 98%] Linking CXX executable ../../bin/form_truealignments cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/form_truealignments.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/form_truealignments.dir/form_truealignments.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/form_truealignments ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 98%] Built target form_truealignments +[ 98%] Built target spades-gbuilder In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:9: + from /build/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, + from /build/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:8: /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -5856,8 +5924,8 @@ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/io/graph/gfa_reader.hpp:8, - from /build/spades-3.15.5+dfsg/assembler/src/common/toolchain/utils.hpp:8: + from /build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:8: /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -5882,33 +5950,6 @@ 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', - inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] - 565 | ++vptr; - | ^~ -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp: In member function 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]': -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 - 193 | void AddOutgoingEdge(EdgeId e) { - | ~~~~~~~^ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/stop_condon_finder.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/projects/cds_subgraphs/main.cpp:8: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:565:13: warning: array subscript 1 is outside array bounds of 'omnigraph::PairedVertex::EdgeId [1]' {aka 'omnigraph::impl::EdgeId [1]'} [-Warray-bounds] @@ -5918,6 +5959,14 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 98%] Built target form_truealignments +[ 98%] Linking CXX executable ../../bin/spaligner +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/spaligner && /usr/bin/cmake -E cmake_link_script CMakeFiles/spaligner.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/spaligner.dir/align_longreads.cpp.o "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spaligner libmapping_printer.a ../../common/libcommon_modules.a -lbwa ../../ext/edlib/libedlib.a ../../common/io/graph/libgraphio.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a -lbwa ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a ../../ext/gfa1/libgfa1.a /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 98%] Built target spaligner +[100%] Linking CXX executable ../../bin/cds-subgraphs In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, @@ -5936,6 +5985,8 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-subgraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o" "CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o" "CMakeFiles/cds-subgraphs.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/cds-subgraphs ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: @@ -5946,9 +5997,6 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ -[100%] Linking CXX executable ../../bin/cds-subgraphs -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/cds_subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/cds-subgraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/cds-subgraphs.dir/stop_condon_finder.cpp.o" "CMakeFiles/cds-subgraphs.dir/subgraph_extraction.cpp.o" "CMakeFiles/cds-subgraphs.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/cds-subgraphs ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [100%] Built target cds-subgraphs [100%] Linking CXX executable ../../bin/cds-mapping-stats @@ -5981,11 +6029,6 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ -[100%] Linking CXX executable ../../bin/spades-gbuilder -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/gbuilder && /usr/bin/cmake -E cmake_link_script CMakeFiles/spades-gbuilder.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/spades-gbuilder.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/spades-gbuilder ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[100%] Built target spades-gbuilder [100%] Linking CXX executable ../../bin/mag-improve cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/projects/bin_analysis && /usr/bin/cmake -E cmake_link_script CMakeFiles/mag-improve.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now "CMakeFiles/mag-improve.dir/main.cpp.o" "../../ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o" -o ../../bin/mag-improve ../../common/io/graph/libgraphio.a ../../common/libcommon_modules.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/gfa1/libgfa1.a ../../common/paired_info/libpaired_info.a ../../common/stages/libstages.a ../../common/pipeline/libpipeline.a ../../common/io/libinput.a ../../ext/samtools/libsamtools.a ../../ext/bamtools/api/libBamTools.a ../../common/modules/path_extend/libpath_extend.a -lssw ../../common/io/binary/libbinary_io.a ../../common/modules/coverage_model/libcoverage_model.a -lnlopt ../../ext/gqf/libgqf.a ../../common/modules/libmodules.a ../../common/assembly_graph/libassembly_graph.a ../../common/utils/libutils.a ../../common/utils/libversion.a ../../ext/cppformat/libformat.a ../../ext/llvm/libllvm-support.a /usr/lib/x86_64-linux-gnu/libdl.a /usr/lib/llvm-14/lib/libLLVMSupport.a -lrt -ldl -lm /usr/lib/x86_64-linux-gnu/libz3.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libtinfo.so /usr/lib/llvm-14/lib/libLLVMDemangle.a ../../common/sequence/libsequence.a ../../ext/edlib/libedlib.a -lbwa /usr/lib/x86_64-linux-gnu/libz.so @@ -6005,356 +6048,356 @@ make -f CMakeFiles/Makefile2 test/debruijn/CMakeFiles/debruijn_test.dir/all make[4]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake --color= make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake --color= make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/depend make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake --color= +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake --color= make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend -make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/cppformat /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake --color= -Dependencies file "common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/compiler_depend.internal". +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake --color= +make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend +Dependencies file "ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/compiler_depend.internal". +make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/llvm /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake --color= +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/cppformat /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake --color= make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/gqf /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake --color= -Consolidate compiler generated dependencies of target coverage_model -make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -Dependencies file "ext/mimalloc/CMakeFiles/mimalloc-obj.dir/src/static.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/compiler_depend.internal". +make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend +make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/edlib /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake --color= +make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/bamtools/api /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/DependInfo.cmake --color= +make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/llvm /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake --color= +make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend +Dependencies file "common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/compiler_depend.internal". +Dependencies file "ext/gqf/CMakeFiles/gqf.dir/gqf.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target mimalloc-obj +Consolidate compiler generated dependencies of target gqf make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/edlib /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake --color= -make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake --color= +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build +make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build +Dependencies file "ext/cppformat/CMakeFiles/format.dir/format.cc.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". +make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +Dependencies file "ext/cppformat/CMakeFiles/format.dir/posix.cc.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". +Dependencies file "ext/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/depend -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/compiler_depend.internal". make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build'. +make[5]: Nothing to be done for 'ext/gqf/CMakeFiles/gqf.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -Dependencies file "ext/cppformat/CMakeFiles/format.dir/format.cc.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/cppformat/CMakeFiles/format.dir/posix.cc.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/cppformat/CMakeFiles/format.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o.d" is newer than depends file 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Consolidate compiler generated dependencies of target format make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake --color= -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/io/binary /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake --color= +Consolidate compiler generated dependencies of target gtest make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build +make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/cppformat/CMakeFiles/format.dir/build'. +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +Consolidate compiler generated dependencies of target edlib Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/APFloat.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". -Dependencies file "ext/gqf/CMakeFiles/gqf.dir/gqf.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/gqf/CMakeFiles/gqf.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/APInt.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". +make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/googletest/googletest/CMakeFiles/gtest.dir/build'. +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +[ 2%] Built target mimalloc-obj Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/CrashRecoveryContext.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target gqf -Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". 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Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Host.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build +[ 4%] Built target gqf Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/JSON.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +[ 7%] Built target format Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/LEB128.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Locale.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MD5.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/ManagedStatic.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +[ 7%] Built target gtest Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MemAlloc.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -Dependencies file "ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/edlib/CMakeFiles/edlib.dir/compiler_depend.internal". 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Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". +make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/bamtools/api/CMakeFiles/BamTools.dir/compiler_depend.internal". +Dependencies file "ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o.d" is newer than depends file 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Dependencies file "ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/llvm/CMakeFiles/llvm-support.dir/compiler_depend.internal". -[ 2%] Built target mimalloc-obj -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/edlib/CMakeFiles/edlib.dir/build'. -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/googletest/googletest/CMakeFiles/gtest.dir/build.make ext/googletest/googletest/CMakeFiles/gtest.dir/build +Dependencies file "common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target BamTools +Dependencies file "common/utils/CMakeFiles/utils.dir/logger/logger_impl.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/googletest/googletest/CMakeFiles/gtest.dir/build'. -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 2%] Built target coverage_model make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/build -Consolidate compiler generated dependencies of target llvm-support -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build -[ 4%] Built target format +Dependencies file "common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/compiler_depend.internal". make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/bamtools/api/CMakeFiles/BamTools.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 7%] Built target gqf -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. +Consolidate compiler generated dependencies of target utils +[ 33%] Built target BamTools make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend -[ 7%] Built target gtest -[ 9%] Built target edlib -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/io/binary /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake --color= -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake --color= -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend -[ 28%] Built target BamTools -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/sequence /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake --color= -make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/paired_info /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake --color= +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend -Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/genomic_info.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". -Dependencies file "common/io/binary/CMakeFiles/binary_io.dir/graph_pack.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/compiler_depend.internal". -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/samtools /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake --color= -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend -[ 50%] Built target llvm-support -Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake --color= -Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". -Dependencies file "common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target binary_io -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -Dependencies file "common/utils/CMakeFiles/version.dir/version.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target version -make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target paired_info -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build +Consolidate compiler generated dependencies of target llvm-support make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. +make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build -Dependencies file "common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/compiler_depend.internal". +[ 35%] Built target utils make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/samtools /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake --color= +make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/llvm/CMakeFiles/llvm-support.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 57%] Built target llvm-support Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". +Consolidate compiler generated dependencies of target coverage_model Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". +make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". +make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake --color= +make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target sequence Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/faidx.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". +make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/modules/coverage_model/CMakeFiles/coverage_model.dir/build'. +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Dependencies file "ext/samtools/CMakeFiles/samtools.dir/kstring.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/__/modules/alignment/edge_index_refiller.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/razf.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". Dependencies file "ext/samtools/CMakeFiles/samtools.dir/sam.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/core/id_distributor.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". +[ 57%] Built target coverage_model Dependencies file "ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/compiler_depend.internal". -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/coverage_uniformity_analyzer.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target samtools -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build -Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_gtest.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". -Dependencies file "ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/teamcity_messages.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/compiler_depend.internal". -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -Consolidate compiler generated dependencies of target teamcity_gtest -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 50%] Built target binary_io -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build -[ 52%] Built target version -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 54%] Built target sequence -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend -[ 61%] Built target samtools +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". +Dependencies file "common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/compiler_depend.internal". +[ 64%] Built target samtools make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake 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Dependencies file "common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o.d" is newer than depends file "/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/CMakeFiles/modules.dir/compiler_depend.internal". -Consolidate compiler generated dependencies of target modules +make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build +[ 73%] Built target input +Consolidate compiler generated dependencies of target modules Consolidate compiler generated dependencies of target path_extend make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/path_extend/CMakeFiles/path_extend.dir/build.make common/modules/path_extend/CMakeFiles/path_extend.dir/build +make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' @@ -6411,42 +6454,31 @@ make -f test/debruijn/CMakeFiles/debruijn_test.dir/build.make test/debruijn/CMakeFiles/debruijn_test.dir/build make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_core_test.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/histogram_test.cpp.o -[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o cd 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test/debruijn/CMakeFiles/debruijn_test.dir/test_utils.cpp.o -[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/construction_test.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o -MF CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/overlap_analysis_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_analysis_test.cpp +[ 95%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -MF CMakeFiles/debruijn_test.dir/simplification_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/simplification_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test_utils.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/test_utils.cpp.o -MF CMakeFiles/debruijn_test.dir/test_utils.cpp.o.d -o CMakeFiles/debruijn_test.dir/test_utils.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/test_utils.cpp +[ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/construction_test.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/construction_test.cpp.o -MF CMakeFiles/debruijn_test.dir/construction_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/construction_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o -MF CMakeFiles/debruijn_test.dir/io_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/io_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/io_test.cpp.o -MF CMakeFiles/debruijn_test.dir/io_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/io_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o -MF CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/path_extend_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/path_extend_test.cpp [ 97%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o -[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o -[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graphio.cpp.o -MF CMakeFiles/debruijn_test.dir/graphio.cpp.o.d -o CMakeFiles/debruijn_test.dir/graphio.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp +[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o -MF CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/overlap_removal_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp +[100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -MF CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o.d -o CMakeFiles/debruijn_test.dir/graph_alignment_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp [100%] Building CXX object test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/debruijn && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/debruijn/CMakeFiles/debruijn_test.dir/test.cpp.o -MF CMakeFiles/debruijn_test.dir/test.cpp.o.d -o CMakeFiles/debruijn_test.dir/test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/test.cpp -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:7: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' -/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:84:57: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] - 140 | bool res = set_.erase(queue_.top()); - | ^~~ /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp: In function 'void debruijn_graph::DeserializePoint(FILE*, size_t&, size_t&, omnigraph::de::RawPoint&)': /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:24:12: warning: unused variable 'read_count' [-Wunused-variable] 24 | size_t read_count = fscanf(file, "%zu %zu %f %f %f .\n", &e1, &e2, @@ -6469,6 +6501,17 @@ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:7: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' +/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_core_test.cpp:84:57: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] + 140 | bool res = set_.erase(queue_.top()); + | ^~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/random_graph.hpp:10, from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:8: /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': @@ -6478,12 +6521,30 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ +/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_TrivialTest_Test::TestBody()': +/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:104:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] + 104 | gap_cfg.penalty_ratio = 0.1; + | ^~~ +/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:115:30: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] + 115 | ends_cfg.penalty_ratio = 0.1; + | ^~~ /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:33:9: required from 'void CompareGraphIterators(I, I) [with I = omnigraph::SmartEdgeIterator, adt::identity>]' /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:63:26: required from here /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] +/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraOneEdgeTest_Test::TestBody()': +/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:153:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 153 | if (g.int_id(*it) == eid_int){ + | ~~~~~~~~~~~~~~^~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraGrowEndsTest_Test::TestBody()': +/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:183:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 183 | if (g.int_id(*it) == eid_int){ + | ~~~~~~~~~~~~~~^~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:191:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] + 191 | gap_cfg.penalty_ratio = 0.1; + | ^~~ In file included from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/io_test.cpp:10: /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here @@ -6499,24 +6560,6 @@ /build/spades-3.15.5+dfsg/assembler/src/common/modules/alignment/kmer_mapper.hpp:147:28: warning: unused parameter 'new_edge' [-Wunused-parameter] 147 | void HandleGlue(EdgeId new_edge, EdgeId edge1, EdgeId edge2) override { | ~~~~~~~^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_TrivialTest_Test::TestBody()': -/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:104:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] - 104 | gap_cfg.penalty_ratio = 0.1; - | ^~~ -/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:115:30: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] - 115 | ends_cfg.penalty_ratio = 0.1; - | ^~~ -/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraOneEdgeTest_Test::TestBody()': -/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:153:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 153 | if (g.int_id(*it) == eid_int){ - | ~~~~~~~~~~~~~~^~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp: In member function 'virtual void GraphAligner_DijkstraGrowEndsTest_Test::TestBody()': -/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:183:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] - 183 | if (g.int_id(*it) == eid_int){ - | ~~~~~~~~~~~~~~^~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:191:29: warning: conversion from 'double' to 'float' changes value from '1.0000000000000001e-1' to '1.00000001e-1f' [-Wfloat-conversion] - 191 | gap_cfg.penalty_ratio = 0.1; - | ^~~ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, @@ -6567,21 +6610,6 @@ 140 | bool res = set_.erase(queue_.top()); | ^~~ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/construction_helper.hpp:9, from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graphio.cpp:9: @@ -6608,6 +6636,19 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' +/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:275:16: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] + 140 | bool res = set_.erase(queue_.top()); + | ^~~ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/modules/graph_construction.hpp:13: /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp: In instantiation of 'void debruijn_graph::FastGraphFromSequencesConstructor::ConstructGraph(Graph&, const std::vector&) const [with Graph = debruijn_graph::DeBruijnGraph]': /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:547:85: required from 'void debruijn_graph::DeBruijnGraphExtentionConstructor::ConstructGraph(bool) [with Graph = debruijn_graph::DeBruijnGraph]' @@ -6620,6 +6661,29 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/construction/debruijn_graph_constructor.hpp:504:36: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] 504 | graph.vreserve(size_t(2.01*size)); | ^~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' +/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:59:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' +/build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:38:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' +/build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:56:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' +/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:222:72: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'T* adt::SmallPODVector::insert(const_iterator, const T&) [with T = omnigraph::impl::EdgeId; Container = adt::impl::HybridAllocatedStorage]', inlined from 'void omnigraph::PairedVertex::AddOutgoingEdge(EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:194:31, inlined from 'omnigraph::GraphCore::EdgeId omnigraph::GraphCore::AddSingleEdge(VertexId, VertexId, const EdgeData&, EdgeId) [with DataMaster = debruijn_graph::DeBruijnDataMaster]' at /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:586:39: @@ -6630,50 +6694,6 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:580:12: note: at offset 8 into object 'e' of size 8 580 | EdgeId AddSingleEdge(VertexId v1, VertexId v2, | ^~~~~~~~~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:12, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:8: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::VertexId; Priority = adt::identity]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::VertexId; Queue = adt::erasable_priority_queue_key_dirty_heap]' -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity]' -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/parallel_processing.hpp:377:30: required from 'size_t omnigraph::PersistentProcessingAlgorithm::Run(bool, double) [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::VertexId; Priority = adt::identity; size_t = long unsigned int]' -/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:275:16: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] - 140 | bool res = set_.erase(queue_.top()); - | ^~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = omnigraph::ObservableGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::LengthComparator]' -/build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp:59:87: required from 'bool omnigraph::EdgeProcessingAlgorithm::Run(const Priority&, ProceedConditionT) [with Priority = omnigraph::LengthComparator; Graph = debruijn_graph::DeBruijnGraph; ProceedConditionT = func::TypedPredicate]' -/build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:38:38: required from 'bool debruijn::simplification::RemoveErroneousEdgesInLengthOrder(Graph&, func::TypedPredicate, size_t, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId; size_t = long unsigned int; typename Graph::EdgeId = omnigraph::impl::EdgeId]' -/build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/single_cell_simplification.hpp:56:45: required from 'bool debruijn::simplification::TopologyRemoveErroneousEdges(Graph&, const debruijn_graph::config::debruijn_config::simplification::topology_based_ec_remover&, std::function) [with Graph = debruijn_graph::DeBruijnGraph; typename Graph::EdgeId = omnigraph::impl::EdgeId]' -/build/spades-3.15.5+dfsg/assembler/src/test/debruijn/simplification_test.cpp:222:72: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12, - from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/path_extend_test.cpp:8: -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 30 | bool loaded = Base::Load(basename, graph); - | ^~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] - 43 | bool loaded = Base::BinRead(is, graph); - | ^~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); - | ^~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] - 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], - | ^~~~~~ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/graph_support/chimera_stats.hpp:12, from /build/spades-3.15.5+dfsg/assembler/src/common/stages/simplification_pipeline/graph_simplification.hpp:11: /build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/relative_coverage_remover.hpp: In instantiation of 'void omnigraph::simplification::relative_coverage::Component::RemoveFromBorder(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': @@ -6699,6 +6719,23 @@ /build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/bulge_remover.hpp:581:16: warning: unused variable 'total_cnt' [-Wunused-variable] 581 | size_t total_cnt = bulges.size(); | ^~~~~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:1: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap >]' /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = omnigraph::CoverageComparator]' @@ -6736,23 +6773,6 @@ /build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:793:16: warning: unused variable 'end_height' [-Wunused-variable] 793 | size_t end_height = component_.avg_distance(g_.EdgeEnd(e)); | ^~~~~~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/graph_alignment_test.cpp:1: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp: In instantiation of 'void adt::erasable_priority_queue_key_dirty_heap::pop() [with T = omnigraph::impl::EdgeId; Priority = adt::identity]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:506:23: required from 'void adt::DynamicQueueIteratorBase::operator++() [with T = omnigraph::impl::EdgeId; Queue = adt::erasable_priority_queue_key_dirty_heap]' /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_iterators.hpp:251:9: required from 'void omnigraph::SmartIterator::operator++() [with Graph = debruijn_graph::DeBruijnGraph; ElementId = omnigraph::impl::EdgeId; Priority = adt::identity]' @@ -6764,25 +6784,6 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/queue_iterator.hpp:140:14: warning: unused variable 'res' [-Wunused-variable] 140 | bool res = set_.erase(queue_.top()); | ^~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp:8: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp: In instantiation of 'void omnigraph::complex_br::SkeletonTree::HandleDelete(VertexId) [with Graph = debruijn_graph::DeBruijnGraph; VertexId = omnigraph::impl::VertexId]': /build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:309:10: required from here /build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:309:32: warning: unused parameter 'v' [-Wunused-parameter] @@ -6803,9 +6804,36 @@ /build/spades-3.15.5+dfsg/assembler/src/common/modules/simplification/complex_bulge_remover.hpp:244:18: warning: variable 'end' set but not used [-Wunused-but-set-variable] 244 | VertexId end = g_.EdgeEnd(old_edge); | ^~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph_pack.hpp:9, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/stats/picture_dump.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/path_visualizer.hpp:12, + from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/path_extend_test.cpp:8: +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::Load(const std::string&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::string = std::__cxx11::basic_string]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:29:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:30:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 30 | bool loaded = Base::Load(basename, graph); + | ^~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp: In instantiation of 'bool io::binary::BasicGraphIO::BinRead(std::istream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph; std::istream = std::basic_istream]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:42:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:43:14: warning: variable 'loaded' set but not used [-Wunused-but-set-variable] + 43 | bool loaded = Base::BinRead(is, graph); + | ^~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/io/binary/basic.hpp:9: +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp: In instantiation of 'void io::binary::GraphIO::LoadImpl(io::binary::impl::BinIStream&, Graph&) [with Graph = debruijn_graph::DeBruijnGraph]': +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:46:10: required from here +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:60:18: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 60 | auto new_id = graph.AddVertex(typename Graph::VertexData(), ids[0], ids[1]); + | ^~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/io/binary/graph.hpp:82:22: warning: variable 'new_id' set but not used [-Wunused-but-set-variable] + 82 | auto new_id = graph.AddEdge(start_ids[0], end_ids[0], + | ^~~~~~ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/paths/bidirectional_path.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/common/modules/path_extend/pe_resolver.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/overlap_removal_test.cpp:8: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = path_extend::PathListener*; unsigned int PreAllocated = 2]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -6818,7 +6846,9 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -6886,21 +6916,6 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds] @@ -6923,7 +6938,7 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -6936,7 +6951,9 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -6949,7 +6966,7 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -6962,11 +6979,20 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, - from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:7: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::PointT; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; | ^~~~~~~~ @@ -6979,6 +7005,10 @@ /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' 327 | new_data = realloc(data, N * sizeof(T)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, + from /build/spades-3.15.5+dfsg/assembler/src/test/debruijn/construction_test.cpp:7: /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': /build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] 316 | delete v; @@ -7001,6 +7031,19 @@ /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:193:33: note: at offset 8 into object 'e' of size 8 193 | void AddOutgoingEdge(EdgeId e) { | ~~~~~~~^ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph.hpp:10, @@ -7083,6 +7126,19 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 504 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256>]' at /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >, std::less, std::allocator > >, std::less, std::allocator > > > >, 256> > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [408]' [-Warray-bounds] @@ -7105,19 +7161,6 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 408 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::impl::EdgeId; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [504]' [-Warray-bounds] @@ -7162,6 +7205,21 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ +In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, + from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] + 316 | delete v; + | ^~~~~~~~ +/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' + 327 | new_data = realloc(data, N * sizeof(T)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In member function 'void btree::btree_node::set_child(int, btree::btree_node*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]', inlined from 'void btree::btree::rebalance_or_split(iterator*) [with Params = btree::btree_map_params > >, std::less, std::allocator > > > >, 256>]' at /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:2151:24: /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree.h:577:23: warning: array subscript 'btree::btree_node > >, std::less, std::allocator > > > >, 256> >[0]' is partly outside array bounds of 'unsigned char [384]' [-Warray-bounds] @@ -7184,21 +7242,6 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: object of size 384 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -In file included from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:15, - from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/observable_graph.hpp:11: -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp: In member function 'void adt::impl::HybridAllocatedStorage::grow(typename adt::impl::SmallPODVectorData::size_type) [with T = omnigraph::de::RawPointT; unsigned int PreAllocated = 3]': -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:316:17: warning: 'void operator delete(void*, std::size_t)' called on a pointer passed to mismatched reallocation function 'void* realloc(void*, size_t)' [-Wmismatched-dealloc] - 316 | delete v; - | ^~~~~~~~ -/build/spades-3.15.5+dfsg/assembler/src/common/adt/small_pod_vector.hpp:327:35: note: call to 'void* realloc(void*, size_t)' - 327 | new_data = realloc(data, N * sizeof(T)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/btree_container.h:21, from /build/spades-3.15.5+dfsg/assembler/ext/include/btree/safe_btree_set.h:36, from /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph/core/graph_core.hpp:21: @@ -7317,152 +7360,152 @@ make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make -f ext/mimalloc/CMakeFiles/mimalloc-obj.dir/build.make ext/mimalloc/CMakeFiles/mimalloc-obj.dir/depend make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/depend cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/mimalloc/CMakeFiles/mimalloc-obj.dir/DependInfo.cmake --color= +make -f ext/bamtools/api/CMakeFiles/BamTools.dir/build.make ext/bamtools/api/CMakeFiles/BamTools.dir/depend make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/modules/coverage_model /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake --color= make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/cppformat 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make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/depend [ 29%] Built target edlib make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/depend make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake --color= -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/io/binary /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/binary/CMakeFiles/binary_io.dir/DependInfo.cmake --color= -make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend [ 51%] Built target llvm-support +make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/version.dir/DependInfo.cmake --color= +make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/depend [ 51%] Built target gtest make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/depend make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/sequence /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/sequence/CMakeFiles/sequence.dir/DependInfo.cmake --color= -make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/paired_info /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/paired_info/CMakeFiles/paired_info.dir/DependInfo.cmake --color= -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/samtools /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake --color= -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake --color= -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/io/binary/CMakeFiles/binary_io.dir/build.make common/io/binary/CMakeFiles/binary_io.dir/build make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/utils/CMakeFiles/version.dir/build.make common/utils/CMakeFiles/version.dir/build +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/sequence/CMakeFiles/sequence.dir/build.make common/sequence/CMakeFiles/sequence.dir/build make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/utils/CMakeFiles/version.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/io/binary/CMakeFiles/binary_io.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/sequence/CMakeFiles/sequence.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 53%] Built target version make -f common/paired_info/CMakeFiles/paired_info.dir/build.make common/paired_info/CMakeFiles/paired_info.dir/build +[ 51%] Built target binary_io +make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend +[ 53%] Built target version +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/depend make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. -make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 53%] Built target binary_io +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/samtools /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake --color= +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/paired_info/CMakeFiles/paired_info.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/depend +make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/ext/src/teamcity_gtest /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/DependInfo.cmake --color= [ 56%] Built target sequence +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build.make ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= -[ 63%] Built target samtools -[ 63%] Built target teamcity_gtest -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend -[ 63%] Built target paired_info make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/io /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake --color= +make[5]: Nothing to be done for 'ext/teamcity_gtest/CMakeFiles/teamcity_gtest.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +[ 56%] Built target paired_info +make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'ext/samtools/CMakeFiles/samtools.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build -make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. +[ 56%] Built target teamcity_gtest make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/utils/CMakeFiles/utils.dir/build.make common/utils/CMakeFiles/utils.dir/build +[ 63%] Built target samtools +make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. +make[5]: Nothing to be done for 'common/utils/CMakeFiles/utils.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/io /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/io/CMakeFiles/input.dir/DependInfo.cmake --color= [ 65%] Built target utils make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/depend -[ 70%] Built target input make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/assembly_graph /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/assembly_graph/CMakeFiles/assembly_graph.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build +make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Nothing to be done for 'common/io/CMakeFiles/input.dir/build'. +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' +make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/assembly_graph/CMakeFiles/assembly_graph.dir/build.make common/assembly_graph/CMakeFiles/assembly_graph.dir/build +[ 70%] Built target input make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'common/assembly_graph/CMakeFiles/assembly_graph.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' @@ -7478,14 +7521,14 @@ make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make -f common/modules/CMakeFiles/modules.dir/build.make common/modules/CMakeFiles/modules.dir/build make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. +make[5]: Nothing to be done for 'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -make[5]: Nothing to be done for 'common/modules/path_extend/CMakeFiles/path_extend.dir/build'. +make[5]: Nothing to be done for 'common/modules/CMakeFiles/modules.dir/build'. make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' -[ 80%] Built target modules -[ 90%] Built target path_extend +[ 85%] Built target path_extend make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend +[ 90%] Built target modules make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/spades-3.15.5+dfsg/assembler/src /build/spades-3.15.5+dfsg/assembler/src/common/pipeline /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake --color= make[5]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' @@ -7519,21 +7562,21 @@ make -f test/include_test/CMakeFiles/include_test.dir/build.make test/include_test/CMakeFiles/include_test.dir/build make[5]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' [ 95%] Building CXX object test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o -[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/seq_test.cpp.o -MF CMakeFiles/include_test.dir/seq_test.cpp.o.d -o CMakeFiles/include_test.dir/seq_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp -[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/sequence_test.cpp.o -MF CMakeFiles/include_test.dir/sequence_test.cpp.o.d -o CMakeFiles/include_test.dir/sequence_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/include_test/sequence_test.cpp -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o -MF CMakeFiles/include_test.dir/rtseq_test.cpp.o.d -o CMakeFiles/include_test.dir/rtseq_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/rtseq_test.cpp.o -MF CMakeFiles/include_test.dir/rtseq_test.cpp.o.d -o CMakeFiles/include_test.dir/rtseq_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/include_test/rtseq_test.cpp cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/quality_test.cpp.o -MF CMakeFiles/include_test.dir/quality_test.cpp.o.d -o CMakeFiles/include_test.dir/quality_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/include_test/quality_test.cpp [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/nucl_test.cpp.o -MF CMakeFiles/include_test.dir/nucl_test.cpp.o.d -o CMakeFiles/include_test.dir/nucl_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/include_test/nucl_test.cpp [ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -MF CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o.d -o CMakeFiles/include_test.dir/cyclic_hash_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/include_test/cyclic_hash_test.cpp +[ 97%] Building CXX object test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o +cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o -MF CMakeFiles/include_test.dir/binary_test.cpp.o.d -o CMakeFiles/include_test.dir/binary_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/include_test/binary_test.cpp [100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/test.cpp.o cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/test.cpp.o -MF CMakeFiles/include_test.dir/test.cpp.o.d -o CMakeFiles/include_test.dir/test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/include_test/test.cpp -[100%] Building CXX object test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o -cd /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/test/include_test && /usr/bin/c++ -DNDEBUG -DUSE_GLIBCXX_PARALLEL=1 -I/build/spades-3.15.5+dfsg/assembler/src/include -I/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/include -I/build/spades-3.15.5+dfsg/assembler/src -I/build/spades-3.15.5+dfsg/assembler/src/common -I/build/spades-3.15.5+dfsg/assembler/ext/src/mimalloc/include -isystem /build/spades-3.15.5+dfsg/assembler/src/../ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest/include -isystem /build/spades-3.15.5+dfsg/assembler/ext/src/googletest/googletest -g -O2 -ffile-prefix-map=/build/spades-3.15.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wno-deprecated -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -std=gnu++14 -MD -MT test/include_test/CMakeFiles/include_test.dir/binary_test.cpp.o -MF CMakeFiles/include_test.dir/binary_test.cpp.o.d -o CMakeFiles/include_test.dir/binary_test.cpp.o -c /build/spades-3.15.5+dfsg/assembler/src/test/include_test/binary_test.cpp In file included from /build/spades-3.15.5+dfsg/assembler/src/test/include_test/seq_test.cpp:7: In member function 'char Seq::operator[](size_t) const [with long unsigned int size_ = 7; T = long unsigned int]', inlined from 'char Seq::first() const [with long unsigned int size_ = 7; T = long unsigned int]' at /build/spades-3.15.5+dfsg/assembler/src/common/sequence/seq.hpp:461:26, @@ -7736,10 +7779,10 @@ make[2]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/spades-3.15.5+dfsg' dh_auto_test -O--sourcedirectory=assembler/src -O--buildsystem=cmake - cd obj-x86_64-linux-gnu && make -j15 test ARGS\+=--verbose ARGS\+=-j15 + cd obj-x86_64-linux-gnu && make -j16 test ARGS\+=--verbose ARGS\+=-j16 make[1]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j15 +/usr/bin/ctest --force-new-ctest-process --verbose -j16 UpdateCTestConfiguration from :/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu @@ -7766,7 +7809,7 @@ 1: [----------] Global test environment set-up. 1: [----------] 20 tests from Seq 1: [ RUN ] Seq.Selector -1: [ OK ] Seq.Selector (0 ms) +1: [ OK ] Seq.Selector (1 ms) 1: [ RUN ] Seq.ShiftLeft 1: [ OK ] Seq.ShiftLeft (0 ms) 1: [ RUN ] Seq.ShiftRight @@ -7805,7 +7848,7 @@ 1: [ OK ] Seq.Test16_2 (0 ms) 1: [ RUN ] Seq.TestFirstLast 1: [ OK ] Seq.TestFirstLast (0 ms) -1: [----------] 20 tests from Seq (0 ms total) +1: [----------] 20 tests from Seq (1 ms total) 1: 1: [----------] 6 tests from Sequence 1: [ RUN ] Sequence.Selector @@ -7896,44 +7939,44 @@ 1: [ RUN ] Binary.Simple 1: [ OK ] Binary.Simple (0 ms) 1: [ RUN ] Binary.Containers -1: [ OK ] Binary.Containers (1 ms) +1: [ OK ] Binary.Containers (0 ms) 1: [ RUN ] Binary.Variadic 1: [ OK ] Binary.Variadic (0 ms) -1: [----------] 3 tests from Binary (1 ms total) +1: [----------] 3 tests from Binary (0 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 58 tests from 7 test suites ran. (1 ms total) 1: [ PASSED ] 58 tests. -1/2 Test #1: include_test ..................... Passed 0.01 sec +1/2 Test #1: include_test ..................... Passed 0.06 sec 2: Running main() from gtest_main.cpp 2: [==========] Running 98 tests from 10 test suites. 2: [----------] Global test environment set-up. 2: [----------] 6 tests from GraphCore 2: [ RUN ] GraphCore.Empty -2: 0:00:00.000 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.011 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] GraphCore.Empty (12 ms) +2: 0:00:00.010 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.046 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] GraphCore.Empty (40 ms) 2: [ RUN ] GraphCore.OneVertex -2: 0:00:00.011 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.011 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.050 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.050 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneVertex (0 ms) 2: [ RUN ] GraphCore.OneEdge -2: 0:00:00.011 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.011 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.050 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.050 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.OneEdge (0 ms) 2: [ RUN ] GraphCore.VertexMethods -2: 0:00:00.011 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.011 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.050 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.050 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.VertexMethods (0 ms) 2: [ RUN ] GraphCore.SmartIterator -2: 0:00:00.011 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.011 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.050 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.050 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SmartIterator (0 ms) 2: [ RUN ] GraphCore.SelfRCEdgeMerge -2: 0:00:00.011 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.011 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.050 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.050 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 2: [ OK ] GraphCore.SelfRCEdgeMerge (0 ms) -2: [----------] 6 tests from GraphCore (12 ms total) +2: [----------] 6 tests from GraphCore (40 ms total) 2: 2: [----------] 1 test from Histogram 2: [ RUN ] Histogram.StrongWeakPtrBasic @@ -7954,7 +7997,7 @@ 2: [ RUN ] PairedInfo.Prune 2: [ OK ] PairedInfo.Prune (0 ms) 2: [ RUN ] PairedInfo.Neighbours -2: [ OK ] PairedInfo.Neighbours (0 ms) +2: [ OK ] PairedInfo.Neighbours (1 ms) 2: [ RUN ] PairedInfo.DoubledInfo 2: [ OK ] PairedInfo.DoubledInfo (0 ms) 2: [ RUN ] PairedInfo.HalfNeighbours @@ -7966,10 +8009,10 @@ 2: [ RUN ] PairedInfo.PairTraverse 2: [ OK ] PairedInfo.PairTraverse (0 ms) 2: [ RUN ] PairedInfo.RandomSymmetry -2: 0:00:00.012 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.012 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] PairedInfo.RandomSymmetry (98 ms) -2: [----------] 13 tests from PairedInfo (103 ms total) +2: 0:00:00.050 1M / 6M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.050 1M / 6M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] PairedInfo.RandomSymmetry (158 ms) +2: [----------] 13 tests from PairedInfo (159 ms total) 2: 2: [----------] 13 tests from OverlapAnalysis 2: [ RUN ] OverlapAnalysis.Trivial @@ -8012,854 +8055,854 @@ 2: 2: [----------] 17 tests from Simplification 2: [ RUN ] Simplification.SimpleTipClipperTest -2: 0:00:00.115 1M / 8M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.119 1M / 8M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.119 1M / 8M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp -2: 0:00:00.119 1M / 8M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started -2: 0:00:00.122 1M / 12M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip -2: [ OK ] Simplification.SimpleTipClipperTest (7 ms) +2: 0:00:00.209 1M / 7M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.214 1M / 7M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.222 1M / 7M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip.grp +2: 0:00:00.230 1M / 7M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip started +2: 0:00:00.274 1M / 11M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_tip/simpliest_tip +2: [ OK ] Simplification.SimpleTipClipperTest (89 ms) 2: [ RUN ] Simplification.SimpleBulgeRemovalTest -2: 0:00:00.122 1M / 12M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.122 1M / 12M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.122 1M / 12M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp -2: 0:00:00.122 1M / 12M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started -2: 0:00:00.128 1M / 12M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge -2: 0:00:00.135 1M / 12M INFO General (graph_simplification.hpp : 645) Creating br instance -2: [ OK ] Simplification.SimpleBulgeRemovalTest (29 ms) +2: 0:00:00.298 1M / 11M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.298 1M / 11M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.298 1M / 11M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp +2: 0:00:00.298 1M / 11M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started +2: 0:00:00.314 1M / 11M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge +2: 0:00:00.318 1M / 11M INFO General (graph_simplification.hpp : 645) Creating br instance +2: [ OK ] Simplification.SimpleBulgeRemovalTest (52 ms) 2: [ RUN ] Simplification.TipobulgeTest -2: 0:00:00.152 1M / 12M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.152 1M / 12M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.152 1M / 12M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp -2: 0:00:00.152 1M / 12M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started -2: 0:00:00.152 1M / 12M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:00.152 1M / 12M INFO General (graph_simplification.hpp : 645) Creating br instance -2: [ OK ] Simplification.TipobulgeTest (1 ms) +2: 0:00:00.350 1M / 11M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.366 1M / 11M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.382 1M / 11M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp +2: 0:00:00.398 1M / 11M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started +2: 0:00:00.414 1M / 11M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:00.446 1M / 11M INFO General (graph_simplification.hpp : 645) Creating br instance +2: [ OK ] Simplification.TipobulgeTest (128 ms) 2: [ RUN ] Simplification.SimpleECTest -2: 0:00:00.152 1M / 12M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.152 1M / 12M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.152 1M / 12M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:00.152 1M / 12M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.231 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.SimpleECTest (139 ms) +2: 0:00:00.478 1M / 11M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.494 1M / 11M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.510 1M / 11M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.526 1M / 11M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.621 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.SimpleECTest (208 ms) 2: [ RUN ] Simplification.SimpleIterECTest -2: 0:00:00.292 1M / 58M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.299 1M / 58M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.311 1M / 58M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:00.323 1M / 58M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.398 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.SimpleIterECTest (165 ms) +2: 0:00:00.690 1M / 57M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.702 1M / 57M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.714 1M / 57M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.726 1M / 57M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.809 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.SimpleIterECTest (163 ms) 2: [ RUN ] Simplification.IterECTest -2: 0:00:00.457 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.463 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.475 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:00.491 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.563 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: [ OK ] Simplification.IterECTest (168 ms) +2: 0:00:00.852 1M / 59M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.852 1M / 59M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.853 1M / 59M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.853 1M / 59M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.889 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: [ OK ] Simplification.IterECTest (68 ms) 2: [ RUN ] Simplification.IterUniquePath -2: 0:00:00.625 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.631 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.639 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp -2: 0:00:00.651 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started -2: 0:00:00.720 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path -2: 0:00:00.727 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology -2: 0:00:00.758 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology -2: [ OK ] Simplification.IterUniquePath (192 ms) +2: 0:00:00.921 1M / 59M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:00.922 1M / 59M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:00.922 1M / 59M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path.grp +2: 0:00:00.922 1M / 59M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path started +2: 0:00:00.952 623M / 623M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/iter_unique_path +2: 0:00:00.954 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology +2: 0:00:00.968 623M / 623M INFO General (single_cell_simplification: 49) Removing connections based on topology +2: [ OK ] Simplification.IterUniquePath (76 ms) 2: [ RUN ] Simplification.MFUniquePath -2: 0:00:00.817 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.819 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.819 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path.grp -2: 0:00:00.819 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started -2: 0:00:00.861 607M / 607M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path -2: 0:00:00.863 607M / 607M INFO General (single_cell_simplification: 126) Removing connections based on max flow strategy -2: [ OK ] Simplification.MFUniquePath (126 ms) +2: 0:00:00.997 1M / 59M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.002 1M / 59M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.002 1M / 59M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path.grp +2: 0:00:01.002 1M / 59M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/topology_ec/unique_path started +2: 0:00:01.025 607M / 607M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/topology_ec/unique_path +2: 0:00:01.030 607M / 607M INFO General (single_cell_simplification: 126) Removing connections based on max flow strategy +2: [ OK ] Simplification.MFUniquePath (122 ms) 2: [ RUN ] Simplification.ComplexBulgeRemoverOnSimpleBulge -2: 0:00:00.943 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.947 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.960 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp -2: 0:00:00.975 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started -2: 0:00:00.988 1M / 60M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge -2: 0:00:00.996 1M / 60M INFO General (simplification_test.cpp : 276) Done -2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (52 ms) +2: 0:00:01.119 1M / 59M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.126 1M / 59M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.126 1M / 59M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge.grp +2: 0:00:01.126 1M / 59M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge started +2: 0:00:01.127 1M / 59M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/simpliest_bulge/simpliest_bulge +2: 0:00:01.127 1M / 59M INFO General (simplification_test.cpp : 276) Done +2: [ OK ] Simplification.ComplexBulgeRemoverOnSimpleBulge (8 ms) 2: [ RUN ] Simplification.ComplexBulge -2: 0:00:00.996 1M / 60M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:00.996 1M / 60M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:00.996 1M / 60M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:00.996 1M / 60M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp -2: 0:00:00.996 1M / 60M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:01.042 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:01.043 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) -2: 0:00:01.098 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:01.235 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). -2: 0:00:01.235 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:01.319 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:01.319 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: [ OK ] Simplification.ComplexBulge (419 ms) +2: 0:00:01.127 1M / 59M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.127 1M / 59M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.127 1M / 59M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:01.127 1M / 59M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp +2: 0:00:01.127 1M / 59M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:01.176 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:01.195 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) +2: 0:00:01.251 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:01.412 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). +2: 0:00:01.414 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:01.466 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:01.470 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: [ OK ] Simplification.ComplexBulge (414 ms) 2: [ RUN ] Simplification.BigComplexBulge -2: 0:00:01.414 1M / 62M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:01.419 1M / 62M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:01.427 1M / 62M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:01.427 1M / 62M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.grp -2: 0:00:01.427 1M / 62M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started -2: 0:00:01.784 1161M / 1161M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge -2: 0:00:01.795 1161M / 1161M INFO General (edge_index.hpp : 156) Using small index (max_id = 21667994) -2: 0:00:01.873 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.031 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 65575 kmers, 48120 bytes occupied (5.87053 bits per kmer). -2: 0:00:02.032 1161M / 1161M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:02.138 1161M / 1161M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started -2: 0:00:02.139 1161M / 1161M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge -2: [ OK ] Simplification.BigComplexBulge (823 ms) +2: 0:00:01.541 1M / 61M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:01.547 1M / 61M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:01.547 1M / 61M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:01.547 1M / 61M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge.grp +2: 0:00:01.547 1M / 61M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started +2: 0:00:01.806 1161M / 1161M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge +2: 0:00:01.814 1161M / 1161M INFO General (edge_index.hpp : 156) Using small index (max_id = 21667994) +2: 0:00:01.886 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:01.982 1161M / 1161M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 65575 kmers, 48120 bytes occupied (5.87053 bits per kmer). +2: 0:00:01.982 1161M / 1161M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:02.063 1161M / 1161M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge started +2: 0:00:02.074 1161M / 1161M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/big_complex_bulge/big_complex_bulge +2: [ OK ] Simplification.BigComplexBulge (650 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover -2: 0:00:02.237 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.243 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.251 1M / 153M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:02.263 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.grp -2: 0:00:02.271 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started -2: 0:00:02.278 1M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph -2: 0:00:02.278 1M / 153M INFO General (edge_index.hpp : 156) Using small index (max_id = 3036) -2: 0:00:02.299 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:02.426 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 100126 kmers, 73064 bytes occupied (5.83776 bits per kmer). -2: 0:00:02.427 2M / 153M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:02.499 2M / 153M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started -2: 0:00:02.507 2M / 153M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph -2: 0:00:02.519 2M / 153M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover (487 ms) +2: 0:00:02.191 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.194 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.194 1M / 151M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:02.194 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph.grp +2: 0:00:02.194 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started +2: 0:00:02.354 1M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph +2: 0:00:02.358 1M / 151M INFO General (edge_index.hpp : 156) Using small index (max_id = 3036) +2: 0:00:02.370 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:02.494 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 100126 kmers, 73064 bytes occupied (5.83776 bits per kmer). +2: 0:00:02.502 2M / 151M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:02.551 2M / 151M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph started +2: 0:00:02.558 2M / 151M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/rel_cov_ec/constructed_graph +2: 0:00:02.558 2M / 151M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover (536 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover1 -2: 0:00:02.724 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:02.727 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:02.727 1M / 153M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:02.727 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp -2: 0:00:02.727 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:02.795 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:02.803 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) -2: 0:00:02.904 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:03.126 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). -2: 0:00:03.127 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:03.234 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started -2: 0:00:03.235 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge -2: 0:00:03.235 1173M / 1173M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover1 (644 ms) +2: 0:00:02.727 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:02.734 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:02.742 1M / 151M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:02.750 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge.grp +2: 0:00:02.766 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:02.829 1173M / 1173M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:02.830 1173M / 1173M INFO General (edge_index.hpp : 156) Using small index (max_id = 21626308) +2: 0:00:02.891 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:03.003 1173M / 1173M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 16969 kmers, 13008 bytes occupied (6.13259 bits per kmer). +2: 0:00:03.006 1173M / 1173M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:03.061 1173M / 1173M INFO General (graphio.cpp : 190) Reading edges positions, ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge started +2: 0:00:03.074 1173M / 1173M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge/complex_bulge +2: 0:00:03.090 1173M / 1173M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover1 (434 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover2 -2: 0:00:03.368 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.379 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.391 1M / 153M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:03.403 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp -2: 0:00:03.419 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started -2: 0:00:03.431 3M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph -2: 0:00:03.443 3M / 153M INFO General (edge_index.hpp : 156) Using small index (max_id = 35260) -2: 0:00:03.451 3M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:03.455 3M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5034 kmers, 4400 bytes occupied (6.99245 bits per kmer). -2: 0:00:03.471 3M / 153M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:03.499 3M / 153M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:03.515 3M / 153M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph -2: 0:00:03.523 3M / 153M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover2 (203 ms) +2: 0:00:03.161 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:03.166 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:03.182 1M / 151M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:03.198 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph.grp +2: 0:00:03.214 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph started +2: 0:00:03.231 3M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph +2: 0:00:03.246 3M / 151M INFO General (edge_index.hpp : 156) Using small index (max_id = 35260) +2: 0:00:03.278 3M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:03.310 3M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5034 kmers, 4400 bytes occupied (6.99245 bits per kmer). +2: 0:00:03.326 3M / 151M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:03.358 3M / 151M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:03.374 3M / 151M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/complex_bulge_2/graph +2: 0:00:03.390 3M / 151M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover2 (274 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover3 -2: 0:00:03.572 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.579 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.587 1M / 153M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:03.599 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp -2: 0:00:03.611 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started -2: 0:00:03.623 1M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:03.635 1M / 153M INFO General (edge_index.hpp : 156) Using small index (max_id = 12354) -2: 0:00:03.635 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:03.636 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1318 kmers, 1728 bytes occupied (10.4886 bits per kmer). -2: 0:00:03.636 1M / 153M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:03.637 1M / 153M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:03.637 1M / 153M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge -2: 0:00:03.637 1M / 153M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover3 (75 ms) +2: 0:00:03.435 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:03.438 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:03.454 1M / 151M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:03.470 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge.grp +2: 0:00:03.486 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge started +2: 0:00:03.502 1M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:03.518 1M / 151M INFO General (edge_index.hpp : 156) Using small index (max_id = 12354) +2: 0:00:03.550 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:03.574 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 1318 kmers, 1728 bytes occupied (10.4886 bits per kmer). +2: 0:00:03.590 1M / 151M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:03.622 1M / 151M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:03.638 1M / 151M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge/tipobulge +2: 0:00:03.654 1M / 151M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover3 (253 ms) 2: [ RUN ] Simplification.RelativeCoverageRemover4 -2: 0:00:03.647 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.647 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.647 1M / 153M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:03.647 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph.grp -2: 0:00:03.647 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started -2: 0:00:03.648 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph -2: 0:00:03.648 4M / 153M INFO General (edge_index.hpp : 156) Using small index (max_id = 36400) -2: 0:00:03.649 4M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:03.668 4M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 14278 kmers, 11072 bytes occupied (6.20367 bits per kmer). -2: 0:00:03.683 4M / 153M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:03.707 4M / 153M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:03.723 4M / 153M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph -2: 0:00:03.731 4M / 153M INFO General (simplification_test.cpp : 308) Relative coverage component removal: -2: [ OK ] Simplification.RelativeCoverageRemover4 (157 ms) +2: 0:00:03.687 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:03.702 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:03.718 1M / 151M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:03.734 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph.grp +2: 0:00:03.750 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/tipobulge_2/graph started +2: 0:00:03.767 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph +2: 0:00:03.782 4M / 151M INFO General (edge_index.hpp : 156) Using small index (max_id = 36400) +2: 0:00:03.814 4M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:03.846 4M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 14278 kmers, 11072 bytes occupied (6.20367 bits per kmer). +2: 0:00:03.862 4M / 151M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:03.894 4M / 151M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:03.910 4M / 151M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/tipobulge_2/graph +2: 0:00:03.926 4M / 151M INFO General (simplification_test.cpp : 308) Relative coverage component removal: +2: [ OK ] Simplification.RelativeCoverageRemover4 (291 ms) 2: [ RUN ] Simplification.CompressorTest -2: 0:00:03.805 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.811 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.819 1M / 153M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:03.831 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp -2: 0:00:03.843 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started -2: 0:00:03.859 2M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph -2: 0:00:03.872 2M / 153M INFO General (edge_index.hpp : 156) Using small index (max_id = 5512) -2: 0:00:03.872 2M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:03.873 2M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 295 kmers, 992 bytes occupied (26.9017 bits per kmer). -2: 0:00:03.873 2M / 153M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:03.873 2M / 153M INFO General (graphio.cpp : 185) No positions were saved -2: 0:00:03.873 2M / 153M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph -2: [ OK ] Simplification.CompressorTest (70 ms) -2: [----------] 17 tests from Simplification (3759 ms total) +2: 0:00:03.979 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:03.982 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:03.998 1M / 151M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:04.014 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph.grp +2: 0:00:04.030 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/compression/graph started +2: 0:00:04.051 2M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/compression/graph +2: 0:00:04.062 2M / 151M INFO General (edge_index.hpp : 156) Using small index (max_id = 5512) +2: 0:00:04.094 2M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.126 2M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 295 kmers, 992 bytes occupied (26.9017 bits per kmer). +2: 0:00:04.142 2M / 151M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:04.174 2M / 151M INFO General (graphio.cpp : 185) No positions were saved +2: 0:00:04.190 2M / 151M INFO General (graphio.cpp : 156) Reading flanking coverage from ./src/test/debruijn/graph_fragments/compression/graph +2: [ OK ] Simplification.CompressorTest (260 ms) +2: [----------] 17 tests from Simplification (4030 ms total) 2: 2: [----------] 9 tests from GraphConstruction 2: [ RUN ] GraphConstruction.SimpleThread -2: 0:00:03.874 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:03.874 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:03.874 1M / 153M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:03.874 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.874 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:03.874 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.874 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:03.899 1M / 153M INFO General (kmer_splitters.hpp : 131) Used 2 reads -2: 0:00:03.899 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:03.900 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. -2: 0:00:03.901 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:03.901 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:03.901 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:03.901 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:03.901 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:03.923 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 6 kmers. -2: 0:00:03.939 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:03.945 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 7 kmers in total. -2: 0:00:03.945 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:03.946 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 7 kmers, 4800 bytes occupied (5485.71 bits per kmer). -2: 0:00:03.946 1M / 153M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:03.946 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:03.947 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:03.947 1M / 153M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:03.947 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:03.959 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted -2: 0:00:03.987 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:04.007 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:04.023 1M / 153M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create -2: 0:00:04.031 1M / 153M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:04.051 1M / 153M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:04.059 1M / 153M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:04.067 1M / 153M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create -2: 0:00:04.079 1M / 153M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SimpleThread (205 ms) +2: 0:00:04.238 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.242 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.242 1M / 151M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:04.243 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.243 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.243 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.243 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.254 1M / 151M INFO General (kmer_splitters.hpp : 131) Used 2 reads +2: 0:00:04.258 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.260 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. +2: 0:00:04.260 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:04.260 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.260 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.260 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.260 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.270 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 6 kmers. +2: 0:00:04.274 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.275 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 7 kmers in total. +2: 0:00:04.275 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.276 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 7 kmers, 4800 bytes occupied (5485.71 bits per kmer). +2: 0:00:04.276 1M / 151M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:04.277 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:04.277 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:04.277 1M / 151M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:04.277 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:04.277 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted +2: 0:00:04.277 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:04.277 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:04.277 1M / 151M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create +2: 0:00:04.277 1M / 151M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:04.277 1M / 151M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:04.277 1M / 151M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:04.277 1M / 151M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create +2: 0:00:04.277 1M / 151M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SimpleThread (39 ms) 2: [ RUN ] GraphConstruction.SimpleThread2 -2: 0:00:04.079 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.079 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:04.079 1M / 153M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:04.079 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.079 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.080 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.080 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.103 1M / 153M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:04.103 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.104 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 8 kmers in total. -2: 0:00:04.105 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:04.105 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.105 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.105 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.105 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.127 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 8 kmers. -2: 0:00:04.131 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.144 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 9 kmers in total. -2: 0:00:04.155 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:04.156 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 9 kmers, 6400 bytes occupied (5688.89 bits per kmer). -2: 0:00:04.156 1M / 153M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:04.157 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:04.157 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:04.157 1M / 153M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:04.158 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:04.158 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted -2: 0:00:04.158 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:04.158 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:04.158 1M / 153M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create -2: 0:00:04.158 1M / 153M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:04.158 1M / 153M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:04.158 1M / 153M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:04.158 1M / 153M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create -2: 0:00:04.158 1M / 153M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SimpleThread2 (79 ms) +2: 0:00:04.279 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.286 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.290 1M / 151M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:04.290 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.291 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.291 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.291 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.302 1M / 151M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:04.307 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.308 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 8 kmers in total. +2: 0:00:04.308 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:04.308 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.308 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.308 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.308 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.318 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 8 kmers. +2: 0:00:04.322 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.323 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 9 kmers in total. +2: 0:00:04.323 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.324 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 9 kmers, 6400 bytes occupied (5688.89 bits per kmer). +2: 0:00:04.324 1M / 151M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:04.325 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:04.325 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:04.325 1M / 151M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:04.325 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:04.325 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 1 sequences extracted +2: 0:00:04.325 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:04.326 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:04.326 1M / 151M INFO General (debruijn_graph_constructor: 487) Total 2 edges to create +2: 0:00:04.326 1M / 151M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:04.326 1M / 151M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:04.326 1M / 151M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:04.327 1M / 151M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create +2: 0:00:04.338 1M / 151M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SimpleThread2 (60 ms) 2: [ RUN ] GraphConstruction.SplitThread -2: 0:00:04.158 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.158 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:04.158 1M / 153M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:04.158 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.158 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.158 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.158 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.179 1M / 153M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:04.195 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.208 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. -2: 0:00:04.215 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:04.227 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.227 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.227 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.227 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.251 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. -2: 0:00:04.259 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.268 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. -2: 0:00:04.275 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:04.276 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). -2: 0:00:04.276 1M / 153M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:04.276 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:04.277 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:04.277 1M / 153M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:04.277 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:04.277 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:04.277 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:04.277 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:04.277 1M / 153M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:04.277 1M / 153M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:04.277 1M / 153M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:04.277 1M / 153M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:04.277 1M / 153M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create -2: 0:00:04.277 1M / 153M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SplitThread (119 ms) +2: 0:00:04.338 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.338 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.338 1M / 151M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:04.338 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.338 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.338 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.338 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.350 1M / 151M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:04.354 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.355 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. +2: 0:00:04.355 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:04.355 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.355 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.355 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.355 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.366 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. +2: 0:00:04.370 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.372 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. +2: 0:00:04.372 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.373 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). +2: 0:00:04.373 1M / 151M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:04.373 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:04.374 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:04.374 1M / 151M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:04.382 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:04.387 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:04.387 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:04.387 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:04.387 1M / 151M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:04.387 1M / 151M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:04.387 1M / 151M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:04.387 1M / 151M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:04.387 1M / 151M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create +2: 0:00:04.387 1M / 151M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SplitThread (49 ms) 2: [ RUN ] GraphConstruction.SplitThread2 -2: 0:00:04.278 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.278 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:04.278 1M / 153M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:04.278 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.278 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.278 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.278 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.303 1M / 153M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:04.315 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.328 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. -2: 0:00:04.328 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:04.328 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.328 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.328 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.328 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.343 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. -2: 0:00:04.355 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.357 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. -2: 0:00:04.357 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:04.358 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 11 kmers, 5600 bytes occupied (4072.73 bits per kmer). -2: 0:00:04.358 1M / 153M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:04.358 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:04.358 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:04.359 1M / 153M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:04.359 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:04.359 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 4 sequences extracted -2: 0:00:04.367 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:04.387 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:04.395 1M / 153M INFO General (debruijn_graph_constructor: 487) Total 8 edges to create -2: 0:00:04.411 1M / 153M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:04.419 1M / 153M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:04.419 1M / 153M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:04.419 1M / 153M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create -2: 0:00:04.419 1M / 153M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.SplitThread2 (142 ms) +2: 0:00:04.387 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.387 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.387 1M / 151M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:04.387 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.387 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.387 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.387 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.398 1M / 151M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:04.402 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.403 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. +2: 0:00:04.403 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:04.403 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.403 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.403 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.403 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.414 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 11 kmers. +2: 0:00:04.418 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.419 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 11 kmers in total. +2: 0:00:04.419 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.420 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 11 kmers, 5600 bytes occupied (4072.73 bits per kmer). +2: 0:00:04.420 1M / 151M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:04.421 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:04.421 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:04.421 1M / 151M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:04.421 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:04.421 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 4 sequences extracted +2: 0:00:04.421 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:04.421 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:04.421 1M / 151M INFO General (debruijn_graph_constructor: 487) Total 8 edges to create +2: 0:00:04.421 1M / 151M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:04.421 1M / 151M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:04.421 1M / 151M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:04.421 1M / 151M INFO General (debruijn_graph_constructor: 503) Total 4 vertices to create +2: 0:00:04.421 1M / 151M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.SplitThread2 (35 ms) 2: [ RUN ] GraphConstruction.Buldge -2: 0:00:04.419 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.419 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:04.420 1M / 153M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:04.420 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.420 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.420 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.420 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.439 1M / 153M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:04.439 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.441 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. -2: 0:00:04.441 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:04.441 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.441 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.441 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.441 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.463 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 12 kmers. -2: 0:00:04.471 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.495 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. -2: 0:00:04.511 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:04.543 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). -2: 0:00:04.578 1M / 153M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:04.603 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:04.604 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:04.604 1M / 153M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:04.604 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:04.604 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2 sequences extracted -2: 0:00:04.604 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:04.604 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:04.604 1M / 153M INFO General (debruijn_graph_constructor: 487) Total 4 edges to create -2: 0:00:04.604 1M / 153M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:04.604 1M / 153M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:04.604 1M / 153M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:04.604 1M / 153M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create -2: 0:00:04.604 1M / 153M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.Buldge (185 ms) +2: 0:00:04.422 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.422 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.422 1M / 151M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:04.430 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.434 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.434 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.434 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.446 1M / 151M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:04.450 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.452 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. +2: 0:00:04.452 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:04.452 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.452 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.452 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.452 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.462 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 12 kmers. +2: 0:00:04.466 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.467 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 12 kmers in total. +2: 0:00:04.467 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.468 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 12 kmers, 5600 bytes occupied (3733.33 bits per kmer). +2: 0:00:04.468 1M / 151M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:04.469 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:04.469 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:04.469 1M / 151M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:04.469 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:04.469 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2 sequences extracted +2: 0:00:04.469 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:04.469 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:04.469 1M / 151M INFO General (debruijn_graph_constructor: 487) Total 4 edges to create +2: 0:00:04.469 1M / 151M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:04.469 1M / 151M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:04.469 1M / 151M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:04.469 1M / 151M INFO General (debruijn_graph_constructor: 503) Total 2 vertices to create +2: 0:00:04.469 1M / 151M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.Buldge (48 ms) 2: [ RUN ] GraphConstruction.CondenseSimple -2: 0:00:04.605 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.605 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:04.605 1M / 153M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:04.605 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.605 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.605 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.605 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.621 1M / 153M INFO General (kmer_splitters.hpp : 131) Used 8 reads -2: 0:00:04.623 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.624 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:04.625 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:04.625 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.625 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.625 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.625 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.641 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. -2: 0:00:04.641 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.642 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:04.642 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:04.653 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). -2: 0:00:04.653 1M / 153M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:04.659 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:04.671 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:04.675 1M / 153M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:04.675 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:04.675 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:04.675 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:04.676 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:04.676 1M / 153M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:04.676 1M / 153M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:04.676 1M / 153M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:04.676 1M / 153M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:04.676 1M / 153M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create -2: 0:00:04.676 1M / 153M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: [ OK ] GraphConstruction.CondenseSimple (72 ms) +2: 0:00:04.469 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.470 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.470 1M / 151M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:04.470 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.470 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.470 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.478 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.495 1M / 151M INFO General (kmer_splitters.hpp : 131) Used 8 reads +2: 0:00:04.498 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.499 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:04.499 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:04.499 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.499 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.499 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.500 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.511 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. +2: 0:00:04.514 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.515 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:04.516 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.516 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:04.516 1M / 151M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:04.517 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:04.517 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:04.517 1M / 151M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:04.517 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:04.517 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:04.517 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:04.517 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:04.517 1M / 151M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:04.517 1M / 151M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:04.517 1M / 151M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:04.517 1M / 151M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:04.517 1M / 151M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create +2: 0:00:04.517 1M / 151M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: [ OK ] GraphConstruction.CondenseSimple (48 ms) 2: [ RUN ] GraphConstruction.TestKmerStoringIndex -2: 0:00:04.676 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.676 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:04.676 1M / 153M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:04.676 1M / 153M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:04.676 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.676 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.676 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.676 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.699 1M / 153M INFO General (kmer_splitters.hpp : 131) Used 8 reads -2: 0:00:04.715 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.716 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:04.716 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:04.716 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.716 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.716 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.716 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.730 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. -2: 0:00:04.735 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.744 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:04.747 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:04.756 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). -2: 0:00:04.756 1M / 153M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:04.756 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:04.757 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:04.757 1M / 153M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:04.757 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:04.757 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:04.757 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:04.757 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:04.757 1M / 153M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:04.757 1M / 153M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:04.757 1M / 153M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:04.757 1M / 153M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:04.757 1M / 153M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create -2: 0:00:04.757 1M / 153M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: 0:00:04.757 1M / 153M INFO General (graph_construction.hpp : 79) Building index with from graph -2: 0:00:04.757 1M / 153M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) -2: 0:00:04.757 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:04.757 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). -2: 0:00:04.758 1M / 153M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: [ OK ] GraphConstruction.TestKmerStoringIndex (81 ms) +2: 0:00:04.518 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.526 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.530 1M / 151M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:04.530 1M / 151M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:04.530 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.530 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.530 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.530 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.542 1M / 151M INFO General (kmer_splitters.hpp : 131) Used 8 reads +2: 0:00:04.546 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.547 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:04.547 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:04.547 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.548 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.548 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.548 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.562 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. +2: 0:00:04.562 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.563 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:04.563 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.564 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:04.564 1M / 151M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:04.565 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:04.565 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:04.565 1M / 151M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:04.565 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:04.565 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:04.565 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:04.565 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:04.565 1M / 151M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:04.565 1M / 151M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:04.565 1M / 151M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:04.565 1M / 151M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:04.565 1M / 151M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create +2: 0:00:04.565 1M / 151M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: 0:00:04.566 1M / 151M INFO General (graph_construction.hpp : 79) Building index with from graph +2: 0:00:04.566 1M / 151M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) +2: 0:00:04.566 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.566 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). +2: 0:00:04.574 1M / 151M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: [ OK ] GraphConstruction.TestKmerStoringIndex (72 ms) 2: [ RUN ] GraphConstruction.TestKmerFreeIndex -2: 0:00:04.758 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.758 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:04.758 1M / 153M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:04.758 1M / 153M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 -2: 0:00:04.758 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.758 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.758 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.758 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.779 1M / 153M INFO General (kmer_splitters.hpp : 131) Used 8 reads -2: 0:00:04.779 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.781 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:04.781 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:04.781 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.781 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.781 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.781 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.797 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. -2: 0:00:04.797 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.798 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. -2: 0:00:04.798 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:04.803 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). -2: 0:00:04.807 1M / 153M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:04.819 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:04.831 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:04.843 1M / 153M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:04.851 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:04.875 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted -2: 0:00:04.891 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:04.919 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:04.923 1M / 153M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create -2: 0:00:04.923 1M / 153M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:04.923 1M / 153M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:04.923 1M / 153M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:04.923 1M / 153M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create -2: 0:00:04.923 1M / 153M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: 0:00:04.923 1M / 153M INFO General (graph_construction.hpp : 79) Building index with from graph -2: 0:00:04.923 1M / 153M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) -2: 0:00:04.923 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:04.923 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). -2: 0:00:04.923 1M / 153M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: [ OK ] GraphConstruction.TestKmerFreeIndex (166 ms) +2: 0:00:04.590 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.594 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.594 1M / 151M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:04.594 1M / 151M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=5 +2: 0:00:04.594 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.594 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.594 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.594 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.606 1M / 151M INFO General (kmer_splitters.hpp : 131) Used 8 reads +2: 0:00:04.610 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.611 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:04.611 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:04.611 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.612 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.612 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.612 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.626 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 13 kmers. +2: 0:00:04.626 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.627 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 13 kmers in total. +2: 0:00:04.627 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.628 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 5600 bytes occupied (3446.15 bits per kmer). +2: 0:00:04.628 1M / 151M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:04.629 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:04.629 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:04.629 1M / 151M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:04.629 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:04.629 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 3 sequences extracted +2: 0:00:04.629 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:04.629 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:04.629 1M / 151M INFO General (debruijn_graph_constructor: 487) Total 6 edges to create +2: 0:00:04.629 1M / 151M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:04.629 1M / 151M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:04.629 1M / 151M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:04.629 1M / 151M INFO General (debruijn_graph_constructor: 503) Total 3 vertices to create +2: 0:00:04.629 1M / 151M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: 0:00:04.630 1M / 151M INFO General (graph_construction.hpp : 79) Building index with from graph +2: 0:00:04.630 1M / 151M INFO General (edge_index.hpp : 156) Using small index (max_id = 9) +2: 0:00:04.630 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.631 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 13 kmers, 800 bytes occupied (492.308 bits per kmer). +2: 0:00:04.638 1M / 151M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: [ OK ] GraphConstruction.TestKmerFreeIndex (53 ms) 2: [ RUN ] GraphConstruction.SimpleTestEarlyPairedInfo -2: 0:00:04.924 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:04.924 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:04.924 1M / 153M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 -2: 0:00:04.924 1M / 153M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=3 -2: 0:00:04.924 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.924 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.924 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.924 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.947 1M / 153M INFO General (kmer_splitters.hpp : 131) Used 4 reads -2: 0:00:04.955 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.956 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 5 kmers in total. -2: 0:00:04.956 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index -2: 0:00:04.956 1M / 153M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. -2: 0:00:04.956 1M / 153M INFO General (file_limit.hpp : 42) Open file limit set to 1024 -2: 0:00:04.957 1M / 153M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb -2: 0:00:04.957 1M / 153M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 -2: 0:00:04.968 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 5 kmers. -2: 0:00:04.968 1M / 153M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. -2: 0:00:04.970 1M / 153M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. -2: 0:00:04.970 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:04.971 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 6 kmers, 4000 bytes occupied (5333.33 bits per kmer). -2: 0:00:04.971 1M / 153M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. -2: 0:00:04.979 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers -2: 0:00:04.979 1M / 153M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. -2: 0:00:04.980 1M / 153M INFO General (graph_construction.hpp : 57) Condensing graph -2: 0:00:04.980 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths -2: 0:00:04.980 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 5 sequences extracted -2: 0:00:04.980 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops -2: 0:00:04.980 1M / 153M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected -2: 0:00:04.980 1M / 153M INFO General (debruijn_graph_constructor: 487) Total 10 edges to create -2: 0:00:04.980 1M / 153M INFO General (debruijn_graph_constructor: 489) Collecting link records -2: 0:00:04.980 1M / 153M INFO General (debruijn_graph_constructor: 491) Ordering link records -2: 0:00:04.980 1M / 153M INFO General (debruijn_graph_constructor: 493) Sorting done -2: 0:00:04.980 1M / 153M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create -2: 0:00:04.980 1M / 153M INFO General (debruijn_graph_constructor: 506) Connecting the graph -2: 0:00:04.980 1M / 153M INFO General (graph_construction.hpp : 79) Building index with from graph -2: 0:00:04.980 1M / 153M INFO General (edge_index.hpp : 156) Using small index (max_id = 13) -2: 0:00:04.980 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:04.980 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 800 bytes occupied (1280 bits per kmer). -2: 0:00:04.980 1M / 153M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. -2: 0:00:04.980 1M / 153M INFO General (graph_construction.hpp : 93) Filling coverage index -2: 0:00:04.980 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices -2: 0:00:04.981 1M / 153M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 3200 bytes occupied (5120 bits per kmer). -2: 0:00:04.981 1M / 153M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. -2: 0:00:04.981 1M / 153M INFO General (graph_construction.hpp : 99) Filling coverage and flanking coverage from PHM -2: 0:00:04.981 1M / 153M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process -2: 0:00:04.981 1M / 153M INFO General (graph_pack.cpp : 79) Normalizing done -2: 0:00:05.012 10M / 153M INFO General (sequence_mapper_notifier.h: 95) Total 2 reads processed -2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (116 ms) -2: [----------] 9 tests from GraphConstruction (1165 ms total) +2: 0:00:04.642 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.642 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.642 1M / 151M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 +2: 0:00:04.642 1M / 151M INFO General (graph_construction.hpp : 45) Constructing DeBruijn graph for k=3 +2: 0:00:04.643 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.643 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.643 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.643 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.658 1M / 151M INFO General (kmer_splitters.hpp : 131) Used 4 reads +2: 0:00:04.658 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.659 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 5 kmers in total. +2: 0:00:04.659 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index +2: 0:00:04.659 1M / 151M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 10 files using 1 threads. This might take a while. +2: 0:00:04.659 1M / 151M INFO General (file_limit.hpp : 42) Open file limit set to 1024 +2: 0:00:04.659 1M / 151M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 5.72662e+09 Gb +2: 0:00:04.659 1M / 151M INFO General (kmer_splitter.hpp : 101) Using cell size of 6710886 +2: 0:00:04.674 601M / 601M INFO General (kmer_splitters.hpp : 199) Used 5 kmers. +2: 0:00:04.674 1M / 151M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. +2: 0:00:04.676 1M / 151M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 6 kmers in total. +2: 0:00:04.676 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.676 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 6 kmers, 4000 bytes occupied (5333.33 bits per kmer). +2: 0:00:04.676 1M / 151M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. +2: 0:00:04.677 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers +2: 0:00:04.677 1M / 151M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. +2: 0:00:04.677 1M / 151M INFO General (graph_construction.hpp : 57) Condensing graph +2: 0:00:04.677 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths +2: 0:00:04.677 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 5 sequences extracted +2: 0:00:04.677 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops +2: 0:00:04.677 1M / 151M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected +2: 0:00:04.677 1M / 151M INFO General (debruijn_graph_constructor: 487) Total 10 edges to create +2: 0:00:04.677 1M / 151M INFO General (debruijn_graph_constructor: 489) Collecting link records +2: 0:00:04.677 1M / 151M INFO General (debruijn_graph_constructor: 491) Ordering link records +2: 0:00:04.677 1M / 151M INFO General (debruijn_graph_constructor: 493) Sorting done +2: 0:00:04.677 1M / 151M INFO General (debruijn_graph_constructor: 503) Total 6 vertices to create +2: 0:00:04.677 1M / 151M INFO General (debruijn_graph_constructor: 506) Connecting the graph +2: 0:00:04.677 1M / 151M INFO General (graph_construction.hpp : 79) Building index with from graph +2: 0:00:04.677 1M / 151M INFO General (edge_index.hpp : 156) Using small index (max_id = 13) +2: 0:00:04.677 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.677 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 800 bytes occupied (1280 bits per kmer). +2: 0:00:04.677 1M / 151M INFO General (edge_index_builders.hpp : 252) Collecting edge information from graph, this takes a while. +2: 0:00:04.677 1M / 151M INFO General (graph_construction.hpp : 93) Filling coverage index +2: 0:00:04.677 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices +2: 0:00:04.679 1M / 151M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 5 kmers, 3200 bytes occupied (5120 bits per kmer). +2: 0:00:04.686 1M / 151M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. +2: 0:00:04.690 1M / 151M INFO General (graph_construction.hpp : 99) Filling coverage and flanking coverage from PHM +2: 0:00:04.690 1M / 151M INFO General (graph_pack.cpp : 77) Normalizing k-mer map. Total 0 kmers to process +2: 0:00:04.690 1M / 151M INFO General (graph_pack.cpp : 79) Normalizing done +2: 0:00:04.706 10M / 151M INFO General (sequence_mapper_notifier.h: 95) Total 2 reads processed +2: [ OK ] GraphConstruction.SimpleTestEarlyPairedInfo (76 ms) +2: [----------] 9 tests from GraphConstruction (480 ms total) 2: 2: [----------] 3 tests from Io 2: [ RUN ] Io.Order -2: 0:00:05.039 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.051 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.234 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.238 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: [ OK ] Io.Order (199 ms) +2: 0:00:04.719 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.722 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.804 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.814 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: [ OK ] Io.Order (103 ms) 2: [ RUN ] Io.PairedInfo -2: [ OK ] Io.PairedInfo (21 ms) +2: [ OK ] Io.PairedInfo (20 ms) 2: [ RUN ] Io.KmerMapper 2: [ OK ] Io.KmerMapper (1 ms) -2: [----------] 3 tests from Io (232 ms total) +2: [----------] 3 tests from Io (124 ms total) 2: 2: [----------] 8 tests from PathExtend 2: [ RUN ] PathExtend.BidirectionalPathConstructor -2: 0:00:05.272 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.283 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.291 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:05.303 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:05.319 1M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathConstructor (72 ms) +2: 0:00:04.842 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.850 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.858 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:04.866 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:04.882 1M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathConstructor (47 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemove -2: 0:00:05.343 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.355 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.363 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:05.383 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:05.391 1M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathAddRemove (48 ms) +2: 0:00:04.890 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.898 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.906 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:04.914 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:04.922 1M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathAddRemove (40 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveGaps -2: 0:00:05.391 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.391 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.391 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:05.392 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:05.392 1M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathAddRemoveGaps (0 ms) +2: 0:00:04.930 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.938 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.946 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:04.954 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:04.962 1M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathAddRemoveGaps (44 ms) 2: [ RUN ] PathExtend.BidirectionalPathEquals -2: 0:00:05.392 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.392 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.392 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:05.392 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:05.392 1M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathEquals (0 ms) +2: 0:00:04.974 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.974 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.974 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:04.974 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:04.974 1M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathEquals (1 ms) 2: [ RUN ] PathExtend.BidirectionalPathSubpaths -2: 0:00:05.393 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.393 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.393 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:05.393 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:05.393 1M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathSubpaths (1 ms) +2: 0:00:04.974 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.974 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.975 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:04.975 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:04.975 1M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathSubpaths (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathAddRemoveConjugate -2: 0:00:05.393 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.393 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.393 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:05.393 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:05.394 1M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathAddRemoveConjugate (0 ms) +2: 0:00:04.975 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.975 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.975 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:04.975 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:04.975 1M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathAddRemoveConjugate (1 ms) 2: [ RUN ] PathExtend.BidirectionalPathSearch -2: 0:00:05.394 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.394 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.394 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:05.394 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:05.394 1M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathSearch (1 ms) +2: 0:00:04.975 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.975 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.975 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:04.975 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:04.976 1M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathSearch (0 ms) 2: [ RUN ] PathExtend.BidirectionalPathLoopDetector -2: 0:00:05.394 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.394 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.394 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:05.394 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:05.395 1M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] PathExtend.BidirectionalPathLoopDetector (5 ms) -2: [----------] 8 tests from PathExtend (128 ms total) +2: 0:00:04.976 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.976 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.976 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:04.976 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:04.976 1M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] PathExtend.BidirectionalPathLoopDetector (0 ms) +2: [----------] 8 tests from PathExtend (133 ms total) 2: 2: [----------] 23 tests from OverlapRemoval 2: [ RUN ] OverlapRemoval.BasicNoDiff -2: 0:00:05.399 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.407 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.419 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:05.419 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:05.419 1M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] OverlapRemoval.BasicNoDiff (20 ms) +2: 0:00:04.976 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.976 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.976 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:04.976 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:04.977 1M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] OverlapRemoval.BasicNoDiff (1 ms) 2: [ RUN ] OverlapRemoval.BasicDiff -2: 0:00:05.420 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.420 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.420 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:05.420 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:05.420 1M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: [ OK ] OverlapRemoval.BasicDiff (1 ms) +2: 0:00:04.977 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.977 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.977 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:04.977 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:04.977 1M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: [ OK ] OverlapRemoval.BasicDiff (0 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatConjugateEdges -2: 0:00:05.420 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.420 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.420 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp -2: 0:00:05.420 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started -2: 0:00:05.420 1M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation -2: 0:00:05.421 1M / 153M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (0 ms) +2: 0:00:04.977 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.977 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.977 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation.grp +2: 0:00:04.977 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation started +2: 0:00:04.978 1M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/path_extend/distance_estimation +2: 0:00:04.978 1M / 151M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatConjugateEdges (13 ms) 2: [ RUN ] OverlapRemoval.BasicRepeat -2: 0:00:05.421 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.421 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.421 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:05.421 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:05.438 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:05.451 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeat (39 ms) +2: 0:00:04.990 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:04.990 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:04.990 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:04.990 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.162 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:05.170 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeat (181 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatUneven -2: 0:00:05.459 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.467 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.472 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:05.472 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:05.489 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:05.503 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatUneven (49 ms) +2: 0:00:05.170 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.170 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.170 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.170 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.187 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:05.187 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatUneven (17 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatAllDisconnected -2: 0:00:05.509 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.535 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.547 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:05.559 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:05.588 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:05.599 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:05.607 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (107 ms) +2: 0:00:05.188 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.188 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.188 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.188 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.204 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:05.204 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:05.204 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatAllDisconnected (16 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatNoEffect -2: 0:00:05.615 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.627 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.639 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:05.651 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:05.672 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:05.683 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (80 ms) +2: 0:00:05.204 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.204 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.204 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.204 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.221 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:05.221 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: [ OK ] OverlapRemoval.BasicRepeatNoEffect (17 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEnd -2: 0:00:05.695 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.707 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.732 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:05.752 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:05.806 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:05.812 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:05.831 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatEnd (152 ms) +2: 0:00:05.221 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.221 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.221 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.221 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.237 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:05.238 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:05.238 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatEnd (21 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatEndRetain -2: 0:00:05.847 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.859 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.871 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:05.883 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:05.908 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:05.911 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:05.923 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (88 ms) +2: 0:00:05.242 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.250 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.266 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.278 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.298 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:05.298 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:05.298 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatEndRetain (57 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStart -2: 0:00:05.935 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.947 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.959 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:05.959 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:05.972 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:05.979 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:05.987 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatStart (60 ms) +2: 0:00:05.299 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.299 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.299 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.299 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.307 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:05.310 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:05.310 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatStart (11 ms) 2: [ RUN ] OverlapRemoval.BasicRepeatStartRetain -2: 0:00:05.995 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:05.995 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:05.995 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:05.995 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:06.009 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:06.015 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:06.023 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (36 ms) +2: 0:00:05.310 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.310 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.310 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.310 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.319 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:05.326 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:05.326 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicRepeatStartRetain (16 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplication -2: 0:00:06.031 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:06.031 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:06.031 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:06.031 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:06.045 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.BasicDeduplication (20 ms) +2: 0:00:05.326 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.326 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.326 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.326 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.335 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.BasicDeduplication (16 ms) 2: [ RUN ] OverlapRemoval.BasicDeduplicationEqual -2: 0:00:06.051 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:06.051 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:06.051 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:06.051 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:06.064 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (24 ms) +2: 0:00:05.342 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.342 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.342 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.342 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.351 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.BasicDeduplicationEqual (16 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiff -2: 0:00:06.075 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:06.087 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:06.095 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:06.095 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:06.108 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateDiff (40 ms) +2: 0:00:05.358 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.358 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.358 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.358 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.366 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateDiff (16 ms) 2: [ RUN ] OverlapRemoval.DeduplicateDiffGap -2: 0:00:06.115 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:06.123 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:06.131 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:06.131 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:06.144 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateDiffGap (40 ms) +2: 0:00:05.374 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.378 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.378 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.378 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.386 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateDiffGap (13 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen1 -2: 0:00:06.155 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:06.159 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:06.167 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:06.167 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:06.180 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (36 ms) +2: 0:00:05.386 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.386 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.386 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.386 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.395 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen1 (9 ms) 2: [ RUN ] OverlapRemoval.DeduplicateMinEdgeLen2 -2: 0:00:06.191 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:06.195 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:06.195 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:06.195 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:06.208 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (28 ms) +2: 0:00:05.395 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.395 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.395 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.395 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.404 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] OverlapRemoval.DeduplicateMinEdgeLen2 (8 ms) 2: [ RUN ] OverlapRemoval.EndEndMinEdgeLen -2: 0:00:06.219 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:06.223 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:06.231 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:06.231 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:06.248 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:06.251 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:06.263 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (56 ms) +2: 0:00:05.404 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.404 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.404 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.404 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.412 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:05.413 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:05.413 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.EndEndMinEdgeLen (9 ms) 2: [ RUN ] OverlapRemoval.Tricky0 -2: 0:00:06.275 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:06.283 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:06.291 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:06.299 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:06.328 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:06.339 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:06.347 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky0 (91 ms) +2: 0:00:05.413 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.413 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.413 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.413 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.421 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:05.421 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:05.421 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky0 (9 ms) 2: [ RUN ] OverlapRemoval.Tricky1 -2: 0:00:06.368 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:06.380 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:06.399 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:06.407 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:06.450 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:06.455 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:06.463 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky1 (108 ms) +2: 0:00:05.422 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.426 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.426 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.426 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.434 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:05.434 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:05.434 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky1 (13 ms) 2: [ RUN ] OverlapRemoval.Tricky2 -2: 0:00:06.475 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:06.475 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:06.475 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:06.475 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:06.492 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:06.499 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:06.499 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.Tricky2 (24 ms) +2: 0:00:05.434 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.434 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.434 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.435 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.443 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:05.443 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:05.443 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.Tricky2 (8 ms) 2: [ RUN ] OverlapRemoval.BasicMinEdgeLen -2: 0:00:06.499 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:06.499 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:06.499 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:06.499 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:06.512 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:06.523 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:06.535 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.BasicMinEdgeLen (36 ms) +2: 0:00:05.443 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.443 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.443 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.443 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.451 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:05.452 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:05.452 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.BasicMinEdgeLen (9 ms) 2: [ RUN ] OverlapRemoval.OverlapWithMiddle -2: 0:00:06.535 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:06.535 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:06.535 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:06.535 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:06.548 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:06.559 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps -2: 0:00:06.571 4M / 153M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps -2: [ OK ] OverlapRemoval.OverlapWithMiddle (44 ms) -2: [----------] 23 tests from OverlapRemoval (1180 ms total) +2: 0:00:05.452 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.452 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.452 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.452 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.460 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:05.460 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 116) Marking start/end overlaps +2: 0:00:05.460 4M / 151M INFO OverlapRemover (overlap_remover.hpp : 119) Marking remaining overlaps +2: [ OK ] OverlapRemoval.OverlapWithMiddle (9 ms) +2: [----------] 23 tests from OverlapRemoval (485 ms total) 2: 2: [----------] 5 tests from GraphAligner 2: [ RUN ] GraphAligner.EdlibSHWFULLTest -2: 0:00:06.579 1M / 153M INFO General (graph_alignment_test.cpp : 32) Edlib: Result status = 0 -2: [ OK ] GraphAligner.EdlibSHWFULLTest (7 ms) +2: 0:00:05.461 1M / 151M INFO General (graph_alignment_test.cpp : 32) Edlib: Result status = 0 +2: [ OK ] GraphAligner.EdlibSHWFULLTest (0 ms) 2: [ RUN ] GraphAligner.EdlibSHWFULLTestZero -2: 0:00:06.587 1M / 153M INFO General (graph_alignment_test.cpp : 62) Edlib: Result status = 0 -2: 0:00:06.599 1M / 153M INFO General (graph_alignment_test.cpp : 64) Edlib: Result ed = -1 -2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (12 ms) +2: 0:00:05.461 1M / 151M INFO General (graph_alignment_test.cpp : 62) Edlib: Result status = 0 +2: 0:00:05.461 1M / 151M INFO General (graph_alignment_test.cpp : 64) Edlib: Result ed = -1 +2: [ OK ] GraphAligner.EdlibSHWFULLTestZero (0 ms) 2: [ RUN ] GraphAligner.TrivialTest -2: 0:00:06.599 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:06.599 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:06.599 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:06.599 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:06.616 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: 0:00:06.648 5M / 153M INFO General (bwa_index.cpp : 173) Using BWA IS algorithm -2: [ OK ] GraphAligner.TrivialTest (1944 ms) +2: 0:00:05.461 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:05.461 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:05.461 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:05.461 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:05.469 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: 0:00:05.481 5M / 151M INFO General (bwa_index.cpp : 173) Using BWA IS algorithm +2: [ OK ] GraphAligner.TrivialTest (1185 ms) 2: [ RUN ] GraphAligner.DijkstraOneEdgeTest -2: 0:00:08.542 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:08.547 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:08.559 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:08.575 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:08.612 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] GraphAligner.DijkstraOneEdgeTest (77 ms) +2: 0:00:06.646 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:06.647 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:06.654 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:06.654 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:06.663 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] GraphAligner.DijkstraOneEdgeTest (20 ms) 2: [ RUN ] GraphAligner.DijkstraGrowEndsTest -2: 0:00:08.620 1M / 153M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 -2: 0:00:08.639 1M / 153M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 -2: 0:00:08.651 1M / 153M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp -2: 0:00:08.659 1M / 153M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started -2: 0:00:08.688 4M / 153M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation -2: [ OK ] GraphAligner.DijkstraGrowEndsTest (76 ms) -2: [----------] 5 tests from GraphAligner (2116 ms total) +2: 0:00:06.666 1M / 151M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 +2: 0:00:06.674 1M / 151M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 +2: 0:00:06.682 1M / 151M INFO General (graphio.cpp : 40) Trying to read conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation.grp +2: 0:00:06.690 1M / 151M INFO General (graphio.cpp : 51) Reading conjugate de bruijn graph from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation started +2: 0:00:06.706 4M / 151M INFO General (graphio.cpp : 140) Reading coverage from ./src/test/debruijn/graph_fragments/ecoli_400k/distance_estimation +2: [ OK ] GraphAligner.DijkstraGrowEndsTest (43 ms) +2: [----------] 5 tests from GraphAligner (1249 ms total) 2: 2: [----------] Global test environment tear-down -2: [==========] 98 tests from 10 test suites ran. (8696 ms total) +2: [==========] 98 tests from 10 test suites ran. (6700 ms total) 2: [ PASSED ] 98 tests. -2/2 Test #2: debruijn_test .................... Passed 8.72 sec +2/2 Test #2: debruijn_test .................... Passed 6.77 sec 100% tests passed, 0 tests failed out of 2 -Total Test time (real) = 8.73 sec +Total Test time (real) = 7.50 sec make[1]: Leaving directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_prep -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_auto_install --destdir=debian/spades/ -O--sourcedirectory=assembler/src -O--buildsystem=cmake - cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/spades-3.15.5\+dfsg/debian/spades AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/spades-3.15.5\+dfsg/debian/spades AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/spades-3.15.5+dfsg/assembler/src -B/build/spades-3.15.5+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -9063,12 +9106,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/4106413/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4106413/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/3234275 and its subdirectories -I: Current time: Wed May 10 10:59:09 -12 2023 -I: pbuilder-time-stamp: 1683759549 +I: removing directory /srv/workspace/pbuilder/4106413 and its subdirectories +I: Current time: Wed Jun 12 19:52:13 +14 2024 +I: pbuilder-time-stamp: 1718171533