Diff of the two buildlogs: -- --- b1/build.log 2023-05-03 16:26:11.856717586 +0000 +++ b2/build.log 2023-05-03 16:36:18.958074150 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jun 4 10:47:03 -12 2024 -I: pbuilder-time-stamp: 1717541223 +I: Current time: Thu May 4 06:26:16 +14 2023 +I: pbuilder-time-stamp: 1683131176 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 [./sortmerna_4.3.6.orig.tar.gz] I: copying [./sortmerna_4.3.6-2.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Jan 7 04:09:20 2023 -12 +gpgv: Signature made Sun Jan 8 06:09:20 2023 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key @@ -31,135 +31,167 @@ dpkg-source: info: applying no_static_linking.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1783637/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3295274/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 May 4 06:27 /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/3295274/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3295274/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=16' - 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=15' + 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='0ee64a0654a14d46a84b7139c91aaabd' - 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='1783637' - PS1='# ' - PS2='> ' + INVOCATION_ID=26c4707219104e38b2a8abc03c32d583 + 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=3295274 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.zS5lmSi0/pbuilderrc_bTET --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.zS5lmSi0/b1 --logfile b1/build.log sortmerna_4.3.6-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.zS5lmSi0/pbuilderrc_ytx1 --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.zS5lmSi0/b2 --logfile b2/build.log --extrapackages usrmerge sortmerna_4.3.6-2.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://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 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 + Linux i-capture-the-hostname 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 2023 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 2023 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 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 2023 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 2022 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 2023 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 2023 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 2023 more - -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount - -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 2023 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 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 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 2023 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 2023 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 2023 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 2023 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 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 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/1783637/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 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 03:20 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 00:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 04:43 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 03:33 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 00:02 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 00:02 more + -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount + -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:23 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 06:31 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 4 06:27 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 00:02 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 14520 Nov 3 06:31 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 22:35 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 00:02 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 00:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 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/3295274/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -269,7 +301,7 @@ Get: 58 http://deb.debian.org/debian bookworm/main amd64 libzstd-dev amd64 1.5.4+dfsg2-5 [354 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 librocksdb-dev amd64 7.8.3-2 [4560 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.1 [97.7 kB] -Fetched 41.8 MB in 1s (70.9 MB/s) +Fetched 41.8 MB in 3s (12.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0: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.) @@ -523,8 +555,19 @@ 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/sortmerna-4.3.6/ && 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 > ../sortmerna_4.3.6-2_source.changes +I: user script /srv/workspace/pbuilder/3295274/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/3295274/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/sortmerna-4.3.6/ && 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 > ../sortmerna_4.3.6-2_source.changes dpkg-buildpackage: info: source package sortmerna dpkg-buildpackage: info: source version 4.3.6-2 dpkg-buildpackage: info: source distribution unstable @@ -556,8 +599,8 @@ CMAKE_CXX_COMPILER_ID = GNU CMAKE_CONFIGURATION_TYPES = CMAKE_HOST_SYSTEM_NAME = Linux -CMAKE_HOST_SYSTEM_VERSION = 6.1.0-0.deb11.6-amd64 -CMAKE_HOST_SYSTEM = Linux-6.1.0-0.deb11.6-amd64 +CMAKE_HOST_SYSTEM_VERSION = 5.10.0-22-amd64 +CMAKE_HOST_SYSTEM = Linux-5.10.0-22-amd64 PROJECT_BINARY_DIR = /build/sortmerna-4.3.6/obj-x86_64-linux-gnu CMAKE_BINARY_DIR = /build/sortmerna-4.3.6/obj-x86_64-linux-gnu CMAKE_CURRENT_BINARY_DIR = /build/sortmerna-4.3.6/obj-x86_64-linux-gnu @@ -606,7 +649,7 @@ -- Build files have been written to: /build/sortmerna-4.3.6/obj-x86_64-linux-gnu dh_auto_build - cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/sortmerna-4.3.6/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/sortmerna-4.3.6 -B/build/sortmerna-4.3.6/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/CMakeFiles /build/sortmerna-4.3.6/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -616,15 +659,15 @@ make[3]: Entering directory '/build/sortmerna-4.3.6/obj-x86_64-linux-gnu' cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sortmerna-4.3.6 /build/sortmerna-4.3.6 /build/sortmerna-4.3.6/obj-x86_64-linux-gnu /build/sortmerna-4.3.6/obj-x86_64-linux-gnu /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/CMakeFiles/build_version.dir/DependInfo.cmake --color= make -f 3rdparty/cmph/CMakeFiles/cmph.dir/build.make 3rdparty/cmph/CMakeFiles/cmph.dir/depend -make -f 3rdparty/alp/CMakeFiles/alp.dir/build.make 3rdparty/alp/CMakeFiles/alp.dir/depend make[3]: Entering directory '/build/sortmerna-4.3.6/obj-x86_64-linux-gnu' cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sortmerna-4.3.6 /build/sortmerna-4.3.6/3rdparty/cmph /build/sortmerna-4.3.6/obj-x86_64-linux-gnu /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph/CMakeFiles/cmph.dir/DependInfo.cmake --color= +make -f 3rdparty/alp/CMakeFiles/alp.dir/build.make 3rdparty/alp/CMakeFiles/alp.dir/depend make[3]: Entering directory '/build/sortmerna-4.3.6/obj-x86_64-linux-gnu' cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sortmerna-4.3.6 /build/sortmerna-4.3.6/3rdparty/alp /build/sortmerna-4.3.6/obj-x86_64-linux-gnu /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp/CMakeFiles/alp.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/sortmerna-4.3.6/obj-x86_64-linux-gnu' make -f CMakeFiles/build_version.dir/build.make CMakeFiles/build_version.dir/build -make[3]: Leaving directory '/build/sortmerna-4.3.6/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sortmerna-4.3.6/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/sortmerna-4.3.6/obj-x86_64-linux-gnu' make -f 3rdparty/cmph/CMakeFiles/cmph.dir/build.make 3rdparty/cmph/CMakeFiles/cmph.dir/build make[3]: Leaving directory '/build/sortmerna-4.3.6/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/sortmerna-4.3.6/obj-x86_64-linux-gnu' @@ -633,64 +676,64 @@ [ 1%] Building CXX object CMakeFiles/build_version.dir/build_version.cpp.o /usr/bin/c++ -I/build/sortmerna-4.3.6/include -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++17 -MD -MT CMakeFiles/build_version.dir/build_version.cpp.o -MF CMakeFiles/build_version.dir/build_version.cpp.o.d -o CMakeFiles/build_version.dir/build_version.cpp.o -c /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/build_version.cpp [ 2%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o -[ 4%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o -[ 5%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o -MF CMakeFiles/cmph.dir/bdz.c.o.d -o CMakeFiles/cmph.dir/bdz.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/bdz.c -/build/sortmerna-4.3.6/obj-x86_64-linux-gnu/build_version.cpp:4:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 4 | const char* sortmerna_build_compile_date = __DATE__; - | ^~~~~~~~ +[ 4%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o +[ 5%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o +[ 7%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogprob.cpp.o.d -o CMakeFiles/alp.dir/njn_dynprogprob.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/njn_dynprogprob.cpp -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o -MF CMakeFiles/cmph.dir/bdz_ph.c.o.d -o CMakeFiles/cmph.dir/bdz_ph.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/bdz_ph.c -[ 7%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o -[ 8%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o -[ 9%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o -[ 11%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o -MF CMakeFiles/cmph.dir/bdz.c.o.d -o CMakeFiles/cmph.dir/bdz.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/bdz.c cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o.d -o CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/njn_dynprogproblim.cpp -make[3]: Leaving directory '/build/sortmerna-4.3.6/obj-x86_64-linux-gnu' -[ 12%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o -[ 14%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o -MF CMakeFiles/cmph.dir/bmz.c.o.d -o CMakeFiles/cmph.dir/bmz.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/bmz.c +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o -MF CMakeFiles/cmph.dir/bdz_ph.c.o.d -o CMakeFiles/cmph.dir/bdz_ph.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/bdz_ph.c +[ 8%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o +[ 9%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o +[ 11%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o.d -o CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/njn_dynprogprobproto.cpp -[ 15%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o -MF CMakeFiles/cmph.dir/bmz8.c.o.d -o CMakeFiles/cmph.dir/bmz8.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/bmz8.c +[ 12%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o -MF CMakeFiles/cmph.dir/bmz.c.o.d -o CMakeFiles/cmph.dir/bmz.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/bmz.c +[ 14%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o -MF CMakeFiles/alp.dir/njn_ioutil.cpp.o.d -o CMakeFiles/alp.dir/njn_ioutil.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/njn_ioutil.cpp -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o -MF CMakeFiles/cmph.dir/brz.c.o.d -o CMakeFiles/cmph.dir/brz.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/brz.c +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o -MF CMakeFiles/cmph.dir/bmz8.c.o.d -o CMakeFiles/cmph.dir/bmz8.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/bmz8.c +/build/sortmerna-4.3.6/obj-x86_64-linux-gnu/build_version.cpp:4:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 4 | const char* sortmerna_build_compile_date = __DATE__; + | ^~~~~~~~ +[ 15%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o -MF CMakeFiles/alp.dir/njn_localmaxstat.cpp.o.d -o CMakeFiles/alp.dir/njn_localmaxstat.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/njn_localmaxstat.cpp [ 16%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_entry.c.o +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o -MF CMakeFiles/cmph.dir/brz.c.o.d -o CMakeFiles/cmph.dir/brz.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/brz.c [ 18%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o cd 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/build/sortmerna-4.3.6/3rdparty/alp/njn_localmaxstatmatrix.cpp -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o -MF CMakeFiles/cmph.dir/buffer_manager.c.o.d -o CMakeFiles/cmph.dir/buffer_manager.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/buffer_manager.c -[ 19%] Built target build_version -[ 22%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o +[ 19%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o [ 21%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o -MF CMakeFiles/cmph.dir/buffer_manager.c.o.d -o CMakeFiles/cmph.dir/buffer_manager.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/buffer_manager.c cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o -MF CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o.d -o CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/njn_localmaxstatutil.cpp +make[3]: Leaving directory '/build/sortmerna-4.3.6/obj-x86_64-linux-gnu' +[ 21%] Built target build_version +[ 22%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o -MF CMakeFiles/alp.dir/njn_random.cpp.o.d -o CMakeFiles/alp.dir/njn_random.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/njn_random.cpp +[ 23%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o -MF CMakeFiles/cmph.dir/chd.c.o.d -o CMakeFiles/cmph.dir/chd.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/chd.c -[ 23%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.c.o +[ 26%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o +[ 26%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.c.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.c.o -MF CMakeFiles/cmph.dir/chd_ph.c.o.d -o CMakeFiles/cmph.dir/chd_ph.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/chd_ph.c -[ 25%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o -MF CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o.d -o CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/sls_alignment_evaluer.cpp +[ 28%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o -MF CMakeFiles/alp.dir/sls_alp.cpp.o.d -o CMakeFiles/alp.dir/sls_alp.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/sls_alp.cpp +[ 29%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o -MF CMakeFiles/cmph.dir/chm.c.o.d -o CMakeFiles/cmph.dir/chm.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/chm.c -[ 26%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o +[ 30%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o -MF CMakeFiles/cmph.dir/cmph.c.o.d -o CMakeFiles/cmph.dir/cmph.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/cmph.c -[ 28%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o -MF CMakeFiles/alp.dir/njn_random.cpp.o.d -o CMakeFiles/alp.dir/njn_random.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/njn_random.cpp -[ 29%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/cmph_structs.c.o +[ 32%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/cmph_structs.c.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/cmph_structs.c.o -MF CMakeFiles/cmph.dir/cmph_structs.c.o.d -o CMakeFiles/cmph.dir/cmph_structs.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/cmph_structs.c -[ 30%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o -MF CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o.d -o CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/sls_alignment_evaluer.cpp -[ 32%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.c.o -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.c.o -MF CMakeFiles/cmph.dir/compressed_rank.c.o.d -o CMakeFiles/cmph.dir/compressed_rank.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/compressed_rank.c [ 33%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_seq.c.o +[ 35%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.c.o +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.c.o -MF CMakeFiles/cmph.dir/compressed_rank.c.o.d -o CMakeFiles/cmph.dir/compressed_rank.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/compressed_rank.c cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/fch_buckets.c.o -MF CMakeFiles/cmph.dir/fch_buckets.c.o.d -o CMakeFiles/cmph.dir/fch_buckets.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/fch_buckets.c -[ 38%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/graph.c.o +[ 39%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/graph.c.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/graph.c.o -MF CMakeFiles/cmph.dir/graph.c.o.d -o CMakeFiles/cmph.dir/graph.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/graph.c -[ 39%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o -MF CMakeFiles/alp.dir/sls_alp.cpp.o.d -o CMakeFiles/alp.dir/sls_alp.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/sls_alp.cpp [ 40%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/hash.c.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/hash.c.o -MF CMakeFiles/cmph.dir/hash.c.o.d -o CMakeFiles/cmph.dir/hash.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/hash.c [ 42%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o @@ -700,13 +743,13 @@ [ 45%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o -MF CMakeFiles/cmph.dir/select.c.o.d -o CMakeFiles/cmph.dir/select.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/select.c [ 46%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o -[ 47%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o -MF CMakeFiles/cmph.dir/vqueue.c.o.d -o CMakeFiles/cmph.dir/vqueue.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/vqueue.c +[ 47%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o -MF CMakeFiles/cmph.dir/vstack.c.o.d -o CMakeFiles/cmph.dir/vstack.c.o -c /build/sortmerna-4.3.6/3rdparty/cmph/vstack.c [ 49%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o -MF CMakeFiles/alp.dir/sls_alp_data.cpp.o.d -o CMakeFiles/alp.dir/sls_alp_data.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/sls_alp_data.cpp [ 50%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o -MF CMakeFiles/alp.dir/sls_alp_regression.cpp.o.d -o CMakeFiles/alp.dir/sls_alp_regression.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/sls_alp_regression.cpp +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o -MF CMakeFiles/alp.dir/sls_alp_data.cpp.o.d -o CMakeFiles/alp.dir/sls_alp_data.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/sls_alp_data.cpp [ 52%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o -MF CMakeFiles/alp.dir/sls_alp_sim.cpp.o.d -o CMakeFiles/alp.dir/sls_alp_sim.cpp.o -c /build/sortmerna-4.3.6/3rdparty/alp/sls_alp_sim.cpp [ 53%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_basic.cpp.o @@ -726,44 +769,33 @@ [ 56%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/alignment.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/alignment.cpp.o -MF CMakeFiles/smr_objs.dir/alignment.cpp.o.d -o CMakeFiles/smr_objs.dir/alignment.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/alignment.cpp [ 57%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/bitvector.cpp.o -[ 59%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/cmd.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/bitvector.cpp.o -MF CMakeFiles/smr_objs.dir/bitvector.cpp.o.d -o CMakeFiles/smr_objs.dir/bitvector.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/bitvector.cpp +[ 59%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/cmd.cpp.o [ 60%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/izlib.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/cmd.cpp.o -MF CMakeFiles/smr_objs.dir/cmd.cpp.o.d -o CMakeFiles/smr_objs.dir/cmd.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/cmd.cpp -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/izlib.cpp.o -MF CMakeFiles/smr_objs.dir/izlib.cpp.o.d -o CMakeFiles/smr_objs.dir/izlib.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/izlib.cpp -[ 63%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.cpp.o [ 61%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/index.cpp.o -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.cpp.o -MF CMakeFiles/smr_objs.dir/kseq_load.cpp.o.d -o CMakeFiles/smr_objs.dir/kseq_load.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/kseq_load.cpp +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/indexdb.cpp.o -MF CMakeFiles/smr_objs.dir/indexdb.cpp.o.d -o CMakeFiles/smr_objs.dir/indexdb.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/indexdb.cpp -[ 66%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/options.cpp.o -[ 67%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kvdb.cpp.o +[ 64%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.cpp.o +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.cpp.o -MF CMakeFiles/smr_objs.dir/kseq_load.cpp.o.d -o CMakeFiles/smr_objs.dir/kseq_load.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/kseq_load.cpp +[ 66%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kvdb.cpp.o +[ 67%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/options.cpp.o +[ 69%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/summary.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/kvdb.cpp.o -MF CMakeFiles/smr_objs.dir/kvdb.cpp.o.d -o CMakeFiles/smr_objs.dir/kvdb.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/kvdb.cpp cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/options.cpp.o -MF CMakeFiles/smr_objs.dir/options.cpp.o.d -o CMakeFiles/smr_objs.dir/options.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/options.cpp -[ 69%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/output.cpp.o +[ 70%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/output.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/output.cpp.o -MF CMakeFiles/smr_objs.dir/output.cpp.o.d -o CMakeFiles/smr_objs.dir/output.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/output.cpp -[ 70%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/summary.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/summary.cpp.o -MF CMakeFiles/smr_objs.dir/summary.cpp.o.d -o CMakeFiles/smr_objs.dir/summary.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/summary.cpp -[ 71%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o -MF CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o.d -o CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/paralleltraversal.cpp -[ 73%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o -[ 74%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/processor.cpp.o -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o -MF CMakeFiles/smr_objs.dir/read.cpp.o.d -o CMakeFiles/smr_objs.dir/read.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/read.cpp +[ 71%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/processor.cpp.o +[ 73%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/processor.cpp.o -MF CMakeFiles/smr_objs.dir/processor.cpp.o.d -o CMakeFiles/smr_objs.dir/processor.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/processor.cpp +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o -MF CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o.d -o CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/paralleltraversal.cpp +[ 74%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o [ 76%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o -MF CMakeFiles/smr_objs.dir/read.cpp.o.d -o CMakeFiles/smr_objs.dir/read.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/read.cpp cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o -MF CMakeFiles/smr_objs.dir/readfeed.cpp.o.d -o CMakeFiles/smr_objs.dir/readfeed.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/readfeed.cpp -[ 77%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o -MF CMakeFiles/smr_objs.dir/readstats.cpp.o.d -o CMakeFiles/smr_objs.dir/readstats.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/readstats.cpp -/build/sortmerna-4.3.6/src/sortmerna/izlib.cpp: In member function 'int Izlib::inflatez(std::ifstream&)': -/build/sortmerna-4.3.6/src/sortmerna/izlib.cpp:243:29: warning: this statement may fall through [-Wimplicit-fallthrough=] - 243 | ret = Z_DATA_ERROR; /* and fall through */ - | ^ -/build/sortmerna-4.3.6/src/sortmerna/izlib.cpp:244:17: note: here - 244 | case Z_DATA_ERROR: - | ^~~~ -[ 78%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o -MF CMakeFiles/smr_objs.dir/references.cpp.o.d -o CMakeFiles/smr_objs.dir/references.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/references.cpp /build/sortmerna-4.3.6/src/sortmerna/readfeed.cpp: In member function 'void Readfeed::init(std::vector >&, const int&)': /build/sortmerna-4.3.6/src/sortmerna/readfeed.cpp:105:69: warning: unused parameter 'dbg' [-Wunused-parameter] 105 | void Readfeed::init(std::vector& readfiles, const int& dbg) @@ -780,18 +812,53 @@ /build/sortmerna-4.3.6/src/sortmerna/readfeed.cpp:553:39: warning: unused parameter 'ifs' [-Wunused-parameter] 553 | bool Readfeed::hasnext(std::ifstream& ifs) | ~~~~~~~~~~~~~~~^~~ -[ 80%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o -MF CMakeFiles/smr_objs.dir/refstats.cpp.o.d -o CMakeFiles/smr_objs.dir/refstats.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/refstats.cpp +/build/sortmerna-4.3.6/src/sortmerna/izlib.cpp: In member function 'int Izlib::inflatez(std::ifstream&)': +/build/sortmerna-4.3.6/src/sortmerna/izlib.cpp:243:29: warning: this statement may fall through [-Wimplicit-fallthrough=] + 243 | ret = Z_DATA_ERROR; /* and fall through */ + | ^ +/build/sortmerna-4.3.6/src/sortmerna/izlib.cpp:244:17: note: here + 244 | case Z_DATA_ERROR: + | ^~~~ /build/sortmerna-4.3.6/src/sortmerna/readfeed.cpp: In member function 'bool Readfeed::define_format(const int&)': /build/sortmerna-4.3.6/src/sortmerna/readfeed.cpp:857:36: warning: comparison is always false due to limited range of data type [-Wtype-limits] 857 | if (str[i] > 127 || str[i] < 0) { +[ 78%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o +[ 77%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o -MF CMakeFiles/smr_objs.dir/readstats.cpp.o.d -o CMakeFiles/smr_objs.dir/readstats.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/readstats.cpp +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o -MF CMakeFiles/smr_objs.dir/references.cpp.o.d -o CMakeFiles/smr_objs.dir/references.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/references.cpp +/build/sortmerna-4.3.6/src/sortmerna/kvdb.cpp: In member function 'int KeyValueDatabase::clear(std::string)': +/build/sortmerna-4.3.6/src/sortmerna/kvdb.cpp:58:41: warning: unused parameter 'dbpath' [-Wunused-parameter] + 58 | int KeyValueDatabase::clear(std::string dbpath) + | ~~~~~~~~~~~~^~~~~~ +/build/sortmerna-4.3.6/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdIndex(Runopts&, std::string&)': +/build/sortmerna-4.3.6/src/sortmerna/cmd.cpp:250:68: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 250 | if (index.positions_tbl[it->id].arr[i].seq == std::stoi(refid)) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +/build/sortmerna-4.3.6/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdTest(Runopts&, std::string&)': +/build/sortmerna-4.3.6/src/sortmerna/cmd.cpp:317:36: warning: unused parameter 'opts' [-Wunused-parameter] + 317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd) + | ~~~~~~~~~~^~~~ +/build/sortmerna-4.3.6/src/sortmerna/cmd.cpp:317:56: warning: unused parameter 'cmd' [-Wunused-parameter] + 317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd) + | ~~~~~~~~~~~~~~^~~ +/build/sortmerna-4.3.6/src/sortmerna/indexdb.cpp:916:14: warning: 'void {anonymous}::help()' defined but not used [-Wunused-function] + 916 | void help() + | ^~~~ +In file included from /build/sortmerna-4.3.6/src/sortmerna/paralleltraversal.cpp:47: +/build/sortmerna-4.3.6/include/ThreadPool.hpp: In member function 'void ThreadPool::threadEntry(int)': +/build/sortmerna-4.3.6/include/ThreadPool.hpp:92:38: warning: unused parameter 'i' [-Wunused-parameter] + 92 | void threadEntry(int i) + | ~~~~^ +/build/sortmerna-4.3.6/src/sortmerna/paralleltraversal.cpp: In function 'void traverse(Runopts&, Index&, References&, Readstats&, Refstats&, Read&, bool)': +/build/sortmerna-4.3.6/src/sortmerna/paralleltraversal.cpp:289:99: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 289 | bool is_last_idx = (index.index_num == opts.indexfiles.size() - 1) && (index.part == refstats.num_index_parts[index.index_num] - 1); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 80%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o -MF CMakeFiles/smr_objs.dir/refstats.cpp.o.d -o CMakeFiles/smr_objs.dir/refstats.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/refstats.cpp /build/sortmerna-4.3.6/src/sortmerna/read.cpp: In member function 'void Read::unmarshallJson(KeyValueDatabase&)': /build/sortmerna-4.3.6/src/sortmerna/read.cpp:540:46: warning: unused parameter 'kvdb' [-Wunused-parameter] 540 | void Read::unmarshallJson(KeyValueDatabase & kvdb) | ~~~~~~~~~~~~~~~~~~~^~~~ -/build/sortmerna-4.3.6/src/sortmerna/indexdb.cpp:916:14: warning: 'void {anonymous}::help()' defined but not used [-Wunused-function] - 916 | void help() - | ^~~~ /build/sortmerna-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_log(const std::string&)': /build/sortmerna-4.3.6/src/sortmerna/options.cpp:284:42: warning: unused parameter 'val' [-Wunused-parameter] 284 | void Runopts::opt_log(const std::string& val) @@ -836,10 +903,6 @@ /build/sortmerna-4.3.6/src/sortmerna/options.cpp:471:44: warning: unused parameter 'val' [-Wunused-parameter] 471 | void Runopts::opt_fastx(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ -/build/sortmerna-4.3.6/src/sortmerna/kvdb.cpp: In member function 'int KeyValueDatabase::clear(std::string)': -/build/sortmerna-4.3.6/src/sortmerna/kvdb.cpp:58:41: warning: unused parameter 'dbpath' [-Wunused-parameter] - 58 | int KeyValueDatabase::clear(std::string dbpath) - | ~~~~~~~~~~~~^~~~~~ /build/sortmerna-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_sam(const std::string&)': /build/sortmerna-4.3.6/src/sortmerna/options.cpp:484:42: warning: unused parameter 'val' [-Wunused-parameter] 484 | void Runopts::opt_sam(const std::string &val) @@ -864,10 +927,12 @@ /build/sortmerna-4.3.6/src/sortmerna/options.cpp:740:46: warning: unused parameter 'val' [-Wunused-parameter] 740 | void Runopts::opt_version(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ +[ 81%] Building C object src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o /build/sortmerna-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_unknown(char**, int&, char*)': /build/sortmerna-4.3.6/src/sortmerna/options.cpp:750:34: warning: unused parameter 'argv' [-Wunused-parameter] 750 | void Runopts::opt_unknown(char **argv, int &narg, char * opt) | ~~~~~~~^~~~ +cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/cc -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o -MF CMakeFiles/smr_objs.dir/ssw.c.o.d -o CMakeFiles/smr_objs.dir/ssw.c.o -c /build/sortmerna-4.3.6/src/sortmerna/ssw.c /build/sortmerna-4.3.6/src/sortmerna/options.cpp:750:45: warning: unused parameter 'narg' [-Wunused-parameter] 750 | void Runopts::opt_unknown(char **argv, int &narg, char * opt) | ~~~~~^~~~ @@ -887,15 +952,17 @@ /build/sortmerna-4.3.6/src/sortmerna/options.cpp:819:40: warning: unused parameter 'val' [-Wunused-parameter] 819 | void Runopts::opt_v(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ +/build/sortmerna-4.3.6/src/sortmerna/index.cpp: In member function 'void Index::load(uint32_t, uint32_t, std::vector, std::__cxx11::basic_string > >&, Refstats&)': +/build/sortmerna-4.3.6/src/sortmerna/index.cpp:211:58: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] + 211 | ((NodeElement *&)dst) += 4; + | ^~~ +/build/sortmerna-4.3.6/src/sortmerna/index.cpp:257:82: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] + 257 | ((NodeElement *&)dst) += 4; + | ^~~ /build/sortmerna-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_dbg_put_db(const std::string&)': /build/sortmerna-4.3.6/src/sortmerna/options.cpp:937:49: warning: unused parameter 'val' [-Wunused-parameter] 937 | void Runopts::opt_dbg_put_db(const std::string& val) | ~~~~~~~~~~~~~~~~~~~^~~ -In file included from /build/sortmerna-4.3.6/src/sortmerna/paralleltraversal.cpp:47: -/build/sortmerna-4.3.6/include/ThreadPool.hpp: In member function 'void ThreadPool::threadEntry(int)': -/build/sortmerna-4.3.6/include/ThreadPool.hpp:92:38: warning: unused parameter 'i' [-Wunused-parameter] - 92 | void threadEntry(int i) - | ~~~~^ /build/sortmerna-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_cmd(const std::string&)': /build/sortmerna-4.3.6/src/sortmerna/options.cpp:980:42: warning: unused parameter 'val' [-Wunused-parameter] 980 | void Runopts::opt_cmd(const std::string &val) @@ -912,35 +979,10 @@ /build/sortmerna-4.3.6/src/sortmerna/options.cpp:1198:45: warning: unused parameter 'val' [-Wunused-parameter] 1198 | void Runopts::opt_filter(const std::string& val) | ~~~~~~~~~~~~~~~~~~~^~~ -[ 81%] Building C object src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o -cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/cc -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o -MF CMakeFiles/smr_objs.dir/ssw.c.o.d -o CMakeFiles/smr_objs.dir/ssw.c.o -c /build/sortmerna-4.3.6/src/sortmerna/ssw.c /build/sortmerna-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::process(int, char**, bool)': /build/sortmerna-4.3.6/src/sortmerna/options.cpp:1368:50: warning: unused parameter 'dryrun' [-Wunused-parameter] 1368 | void Runopts::process(int argc, char**argv, bool dryrun) | ~~~~~^~~~~~ -/build/sortmerna-4.3.6/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdIndex(Runopts&, std::string&)': -/build/sortmerna-4.3.6/src/sortmerna/cmd.cpp:250:68: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 250 | if (index.positions_tbl[it->id].arr[i].seq == std::stoi(refid)) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -/build/sortmerna-4.3.6/src/sortmerna/paralleltraversal.cpp: In function 'void traverse(Runopts&, Index&, References&, Readstats&, Refstats&, Read&, bool)': -/build/sortmerna-4.3.6/src/sortmerna/paralleltraversal.cpp:289:99: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 289 | bool is_last_idx = (index.index_num == opts.indexfiles.size() - 1) && (index.part == refstats.num_index_parts[index.index_num] - 1); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/sortmerna-4.3.6/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdTest(Runopts&, std::string&)': -/build/sortmerna-4.3.6/src/sortmerna/cmd.cpp:317:36: warning: unused parameter 'opts' [-Wunused-parameter] - 317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd) - | ~~~~~~~~~~^~~~ -/build/sortmerna-4.3.6/src/sortmerna/cmd.cpp:317:56: warning: unused parameter 'cmd' [-Wunused-parameter] - 317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd) - | ~~~~~~~~~~~~~~^~~ -/build/sortmerna-4.3.6/src/sortmerna/index.cpp: In member function 'void Index::load(uint32_t, uint32_t, std::vector, std::__cxx11::basic_string > >&, Refstats&)': -/build/sortmerna-4.3.6/src/sortmerna/index.cpp:211:58: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] - 211 | ((NodeElement *&)dst) += 4; - | ^~~ -/build/sortmerna-4.3.6/src/sortmerna/index.cpp:257:82: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] - 257 | ((NodeElement *&)dst) += 4; - | ^~~ -[ 83%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o In file included from /build/sortmerna-4.3.6/src/sortmerna/paralleltraversal.cpp:41: /build/sortmerna-4.3.6/include/kseq_load.hpp: At global scope: /build/sortmerna-4.3.6/include/kseq.h:171:20: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] @@ -952,6 +994,7 @@ /build/sortmerna-4.3.6/include/kseq_load.hpp:43:1: note: in expansion of macro 'KSEQ_INIT' 43 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ +[ 83%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o -MF CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o.d -o CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/traverse_bursttrie.cpp In file included from /build/sortmerna-4.3.6/include/kseq_load.hpp:40, from /build/sortmerna-4.3.6/src/sortmerna/readstats.cpp:52: @@ -976,22 +1019,22 @@ cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_fastx.cpp.o -MF CMakeFiles/smr_objs.dir/report_fastx.cpp.o.d -o CMakeFiles/smr_objs.dir/report_fastx.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/report_fastx.cpp [ 91%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_other.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_other.cpp.o -MF CMakeFiles/smr_objs.dir/report_fx_other.cpp.o.d -o CMakeFiles/smr_objs.dir/report_fx_other.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/report_fx_other.cpp -/build/sortmerna-4.3.6/src/sortmerna/report.cpp: In constructor 'Report::Report(Runopts&)': -/build/sortmerna-4.3.6/src/sortmerna/report.cpp:39:25: warning: unused parameter 'opts' [-Wunused-parameter] - 39 | Report::Report(Runopts& opts) : pid_str(std::to_string(getpid())), is_zip(false) {} - | ~~~~~~~~~^~~~ [ 92%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_blast.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_blast.cpp.o -MF CMakeFiles/smr_objs.dir/report_blast.cpp.o.d -o CMakeFiles/smr_objs.dir/report_blast.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/report_blast.cpp [ 94%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_denovo.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_denovo.cpp.o -MF CMakeFiles/smr_objs.dir/report_denovo.cpp.o.d -o CMakeFiles/smr_objs.dir/report_denovo.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/report_denovo.cpp -/build/sortmerna-4.3.6/src/sortmerna/report_fx_base.cpp: In member function 'void ReportFxBase::write_a_read(std::ostream&, Read&, Readstate&, Izlib&, bool, const int&)': -/build/sortmerna-4.3.6/src/sortmerna/report_fx_base.cpp:201:123: warning: unused parameter 'dbg' [-Wunused-parameter] - 201 | void ReportFxBase::write_a_read(std::ostream& strm, Read& read, Readstate& rstate, Izlib& izlib, bool is_last, const int& dbg) - | ~~~~~~~~~~~^~~ [ 95%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.cpp.o -MF CMakeFiles/smr_objs.dir/report_biom.cpp.o.d -o CMakeFiles/smr_objs.dir/report_biom.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/report_biom.cpp [ 97%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_sam.cpp.o cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/sortmerna-4.3.6/include -I/build/sortmerna-4.3.6/3rdparty/cmph -I/build/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_sam.cpp.o -MF CMakeFiles/smr_objs.dir/report_sam.cpp.o.d -o CMakeFiles/smr_objs.dir/report_sam.cpp.o -c /build/sortmerna-4.3.6/src/sortmerna/report_sam.cpp +/build/sortmerna-4.3.6/src/sortmerna/report.cpp: In constructor 'Report::Report(Runopts&)': +/build/sortmerna-4.3.6/src/sortmerna/report.cpp:39:25: warning: unused parameter 'opts' [-Wunused-parameter] + 39 | Report::Report(Runopts& opts) : pid_str(std::to_string(getpid())), is_zip(false) {} + | ~~~~~~~~~^~~~ +/build/sortmerna-4.3.6/src/sortmerna/report_fx_base.cpp: In member function 'void ReportFxBase::write_a_read(std::ostream&, Read&, Readstate&, Izlib&, bool, const int&)': +/build/sortmerna-4.3.6/src/sortmerna/report_fx_base.cpp:201:123: warning: unused parameter 'dbg' [-Wunused-parameter] + 201 | void ReportFxBase::write_a_read(std::ostream& strm, Read& read, Readstate& rstate, Izlib& izlib, bool is_last, const int& dbg) + | ~~~~~~~~~~~^~~ /build/sortmerna-4.3.6/src/sortmerna/report_biom.cpp: In member function 'virtual void ReportBiom::init(Readfeed&, Runopts&)': /build/sortmerna-4.3.6/src/sortmerna/report_biom.cpp:41:33: warning: unused parameter 'readfeed' [-Wunused-parameter] 41 | void ReportBiom::init(Readfeed& readfeed, Runopts& opts) @@ -1013,7 +1056,7 @@ cd /build/sortmerna-4.3.6/obj-x86_64-linux-gnu/src/sortmerna && /usr/bin/cmake -E cmake_link_script CMakeFiles/sortmerna.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -Wl,-z,relro -Wl,-z,now CMakeFiles/sortmerna.dir/main.cpp.o 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