Diff of the two buildlogs: -- --- b1/build.log 2023-04-26 03:13:31.155687949 +0000 +++ b2/build.log 2023-04-26 03:16:50.454849115 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 27 21:27:30 -12 2024 -I: pbuilder-time-stamp: 1716888450 +I: Current time: Wed Apr 26 17:13:33 +14 2023 +I: pbuilder-time-stamp: 1682478813 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 [./pbseqlib_5.3.5+dfsg.orig.tar.xz] I: copying [./pbseqlib_5.3.5+dfsg-4.debian.tar.xz] I: Extracting source -gpgv: Signature made Mon Mar 7 22:52:24 2022 -12 +gpgv: Signature made Wed Mar 9 00:52:24 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,135 +31,167 @@ dpkg-source: info: applying static+shared_lib.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2787689/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3483375/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 Apr 26 17:13 /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/3483375/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3483375/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='558bc24e68ea4a8a9d0aa85f54a86790' - 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='2787689' - PS1='# ' - PS2='> ' + INVOCATION_ID=dfbf053628e0435d97e96846d15b6f5c + 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=3483375 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.deoGoFCg/pbuilderrc_OzgY --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.deoGoFCg/b1 --logfile b1/build.log pbseqlib_5.3.5+dfsg-4.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.deoGoFCg/pbuilderrc_hMe1 --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.deoGoFCg/b2 --logfile b2/build.log --extrapackages usrmerge pbseqlib_5.3.5+dfsg-4.dsc' + SUDO_GID=111 + SUDO_UID=106 + 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.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) 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/2787689/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 Apr 26 17:13 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/3483375/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -321,7 +353,7 @@ Get: 100 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] -Fetched 64.7 MB in 2s (37.2 MB/s) +Fetched 64.7 MB in 2s (40.1 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.) @@ -746,8 +778,19 @@ 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/pbseqlib-5.3.5+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 > ../pbseqlib_5.3.5+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/3483375/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/3483375/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/pbseqlib-5.3.5+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 > ../pbseqlib_5.3.5+dfsg-4_source.changes dpkg-buildpackage: info: source package pbseqlib dpkg-buildpackage: info: source version 5.3.5+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -809,12 +852,13 @@ Found ninja-1.11.1 at /usr/bin/ninja dh_auto_build - cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j16 -v -[1/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o -c ../hdf/HDFAttributable.cpp -[2/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFData.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFData.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o -c ../hdf/HDFData.cpp -[3/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o -c ../hdf/HDFPulseH5Writer.cpp -[4/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o -c ../hdf/HDFCmpSupportedFields.cpp -[5/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o -c ../hdf/HDFFile.cpp + cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j15 -v +[1/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFData.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFData.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o -c ../hdf/HDFData.cpp +[2/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o -MF libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o.d -o libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o -c ../hdf/BufferedHDF2DArray.cpp +[3/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o -c ../hdf/HDFCmpSupportedFields.cpp +[4/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o -c ../hdf/HDFPulseH5Writer.cpp +[5/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o -c ../hdf/HDFAttributable.cpp +[6/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o -c ../hdf/HDFFile.cpp ../hdf/HDFFile.cpp: In member function ‘void HDFFile::Open(std::string, unsigned int, const H5::FileAccPropList&)’: ../hdf/HDFFile.cpp:34:75: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy] 34 | hdfFile = H5File(fileName.c_str(), H5F_ACC_TRUNC, filePropList); @@ -837,7 +881,7 @@ ../hdf/HDFFile.cpp:34:75: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here 34 | hdfFile = H5File(fileName.c_str(), H5F_ACC_TRUNC, filePropList); | ^ -[6/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o -c ../hdf/HDFGroup.cpp +[7/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o -c ../hdf/HDFGroup.cpp ../hdf/HDFGroup.cpp: In member function ‘int HDFGroup::Initialize(H5::Group&, std::string)’: ../hdf/HDFGroup.cpp:18:47: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 18 | group = fg.openGroup(groupName.c_str()); @@ -848,7 +892,6 @@ /usr/include/hdf5/serial/H5Group.h:63:5: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 63 | Group(const Group &original); | ^~~~~ -[7/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o -MF libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o.d -o libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o -c ../hdf/BufferedHDF2DArray.cpp [8/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o -MF libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o.d -o libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o -c ../hdf/DatasetCollection.cpp [9/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o -c ../hdf/HDFAtom.cpp ../hdf/HDFAtom.cpp: In member function ‘void HDFAtom::Create(H5::H5Object&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: @@ -1512,12 +1555,39 @@ | ^~~~~~~~~ [12/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o -MF libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o.d -o libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o -c ../hdf/BufferedHDFArray.cpp [13/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o -c ../hdf/HDFAlnGroupGroup.cpp -[14/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -c ../alignment/algorithms/alignment/sdp/SDPFragment.cpp -[15/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o -c ../hdf/HDFNewBasReader.cpp -[16/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o -c ../hdf/HDFPulseWriter.cpp -[17/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -c ../alignment/algorithms/alignment/BaseScoreFunction.cpp -[18/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o -c ../hdf/HDFBaxWriter.cpp -[19/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o -c ../hdf/HDFPulseDataFile.cpp +[14/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o -c ../hdf/HDFNewBasReader.cpp +[15/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o -c ../alignment/algorithms/alignment/sdp/SDPFragment.cpp +[16/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o -c ../hdf/HDFBaxWriter.cpp +[17/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o -c ../hdf/HDFRegionTableReader.cpp +In file included from ../hdf/HDFRegionTableReader.hpp:11, + from ../hdf/HDFRegionTableReader.cpp:1: +../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: +../hdf/HDFAtom.hpp:45:26: required from ‘int HDFAtom::Initialize(HDFData&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ +../hdf/HDFRegionTableReader.cpp:31:31: required from here +../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 33 | attribute = object.openAttribute(attributeName.c_str()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/hdf5/serial/H5Cpp.h:34, + from ../hdf/HDFRegionTableReader.hpp:7: +/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 32 | Attribute(const Attribute &original); + | ^~~~~~~~~ +[18/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o -c ../alignment/algorithms/alignment/BaseScoreFunction.cpp +[19/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o -c ../hdf/HDFRegionsWriter.cpp +../hdf/HDFRegionsWriter.cpp: In member function ‘bool HDFRegionsWriter::Write(const std::vector&)’: +../hdf/HDFRegionsWriter.cpp:44:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] + 44 | for (auto annotation : annotations) + | ^~~~~~~~~~~ +In file included from ../pbdata/reads/RegionTable.hpp:17, + from ../pbdata/SMRTSequence.hpp:14, + from ../hdf/HDFWriterBase.hpp:17, + from ../hdf/HDFRegionsWriter.hpp:13, + from ../hdf/HDFRegionsWriter.cpp:3: +../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ + 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) + | ^~~~~~~~~~~~~~~~ +[20/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o -c ../hdf/HDFPulseWriter.cpp +[21/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o -c ../hdf/HDFPulseDataFile.cpp In file included from ../hdf/HDFScanDataReader.hpp:8, from ../hdf/HDFPulseDataFile.hpp:10, from ../hdf/HDFPulseDataFile.cpp:1: @@ -1550,7 +1620,8 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[20/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o -c ../hdf/HDFAlnInfoGroup.cpp +[22/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o -c ../hdf/HDFCmpExperimentGroup.cpp +[23/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o -c ../hdf/HDFAlnInfoGroup.cpp In file included from ../hdf/HDFAlnInfoGroup.hpp:10, from ../hdf/HDFAlnInfoGroup.cpp:1: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: @@ -1583,37 +1654,8 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[21/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o -c ../hdf/HDFRegionsWriter.cpp -../hdf/HDFRegionsWriter.cpp: In member function ‘bool HDFRegionsWriter::Write(const std::vector&)’: -../hdf/HDFRegionsWriter.cpp:44:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] - 44 | for (auto annotation : annotations) - | ^~~~~~~~~~~ -In file included from ../pbdata/reads/RegionTable.hpp:17, - from ../pbdata/SMRTSequence.hpp:14, - from ../hdf/HDFWriterBase.hpp:17, - from ../hdf/HDFRegionsWriter.hpp:13, - from ../hdf/HDFRegionsWriter.cpp:3: -../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ - 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) - | ^~~~~~~~~~~~~~~~ -[22/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o -c ../hdf/HDFRegionTableReader.cpp -In file included from ../hdf/HDFRegionTableReader.hpp:11, - from ../hdf/HDFRegionTableReader.cpp:1: -../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:45:26: required from ‘int HDFAtom::Initialize(HDFData&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ -../hdf/HDFRegionTableReader.cpp:31:31: required from here -../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 33 | attribute = object.openAttribute(attributeName.c_str()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/HDFRegionTableReader.hpp:7: -/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 32 | Attribute(const Attribute &original); - | ^~~~~~~~~ -[23/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -c ../alignment/algorithms/alignment/ScoreMatrices.cpp -[24/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o -c ../hdf/HDFCmpExperimentGroup.cpp -[25/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -c ../alignment/algorithms/alignment/StringToScoreMatrix.cpp -[26/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o -c ../hdf/HDFBaseCallsWriter.cpp +[24/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o -c ../alignment/algorithms/alignment/ScoreMatrices.cpp +[25/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o -c ../hdf/HDFBaseCallsWriter.cpp In file included from ../hdf/HDFBaseCallsWriter.hpp:11, from ../hdf/HDFBaseCallsWriter.cpp:5: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: @@ -1627,9 +1669,8 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[27/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o -c ../alignment/algorithms/anchoring/Coordinate.cpp -[28/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -c ../alignment/algorithms/anchoring/ClusterProbability.cpp -[29/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o -c ../hdf/HDFWriterBase.cpp +[26/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o -c ../alignment/algorithms/alignment/StringToScoreMatrix.cpp +[27/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o -c ../hdf/HDFWriterBase.cpp In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFWriterBase.cpp:3: ../hdf/HDFAtom.hpp: In instantiation of ‘void HDFAtom::Create(H5::H5Object&, const std::string&, const std::vector >&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: @@ -1652,58 +1693,10 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[30/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o -c ../hdf/HDFZMWMetricsWriter.cpp -In file included from ../hdf/HDFWriterBase.hpp:13, - from ../hdf/HDFZMWMetricsWriter.hpp:8, - from ../hdf/HDFZMWMetricsWriter.cpp:3: -../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here -../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 33 | attribute = object.openAttribute(attributeName.c_str()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/BufferedHDF2DArray.hpp:8, - from ../hdf/HDFZMWMetricsWriter.hpp:6: -/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 32 | Attribute(const Attribute &original); - | ^~~~~~~~~ -[31/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -c ../alignment/algorithms/sorting/DifferenceCovers.cpp -[32/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o -c ../hdf/HDFPulseCallsWriter.cpp -In file included from ../hdf/HDFPulseCallsWriter.hpp:11, - from ../hdf/HDFPulseCallsWriter.cpp:5: -../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here -../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 33 | attribute = object.openAttribute(attributeName.c_str()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/hdf5/serial/H5Cpp.h:34, - from ../hdf/HDFAtom.hpp:9: -/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 32 | Attribute(const Attribute &original); - | ^~~~~~~~~ -../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here -../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 33 | attribute = object.openAttribute(attributeName.c_str()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 32 | Attribute(const Attribute &original); - | ^~~~~~~~~ -../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: -../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ -../hdf/HDFAtom.hpp:38:9: required from here -../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] - 33 | attribute = object.openAttribute(attributeName.c_str()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ - 32 | Attribute(const Attribute &original); - | ^~~~~~~~~ -[33/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o -c ../hdf/HDFZMWReader.cpp -[34/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o -c ../alignment/algorithms/sorting/qsufsort.cpp -[35/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -c ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp +[28/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o -c ../alignment/algorithms/anchoring/Coordinate.cpp +[29/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o -c ../alignment/algorithms/anchoring/ClusterProbability.cpp +[30/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o -c ../alignment/algorithms/sorting/DifferenceCovers.cpp +[31/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o -c ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:9, from ../alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp:1: @@ -1734,7 +1727,8 @@ /usr/include/c++/12/bits/new_allocator.h:175:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[36/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -c ../alignment/algorithms/alignment/AlignmentUtils.cpp +[32/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o -c ../hdf/HDFZMWReader.cpp +[33/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o -c ../alignment/algorithms/alignment/AlignmentUtils.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/AlignmentUtils.cpp:1: ../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: @@ -1764,10 +1758,40 @@ /usr/include/c++/12/bits/new_allocator.h:175:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[37/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o -c ../alignment/datastructures/alignment/AlignmentStats.cpp -[38/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -c ../alignment/datastructures/alignment/AlignmentContext.cpp -[39/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o -c ../alignment/datastructures/alignment/AlignmentMap.cpp -[40/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -c ../alignment/algorithms/alignment/ExtendAlign.cpp +[34/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o -c ../hdf/HDFPulseCallsWriter.cpp +In file included from ../hdf/HDFPulseCallsWriter.hpp:11, + from ../hdf/HDFPulseCallsWriter.cpp:5: +../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 33 | attribute = object.openAttribute(attributeName.c_str()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/hdf5/serial/H5Cpp.h:34, + from ../hdf/HDFAtom.hpp:9: +/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 32 | Attribute(const Attribute &original); + | ^~~~~~~~~ +../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’: +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = unsigned int; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 33 | attribute = object.openAttribute(attributeName.c_str()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 32 | Attribute(const Attribute &original); + | ^~~~~~~~~ +../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 33 | attribute = object.openAttribute(attributeName.c_str()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 32 | Attribute(const Attribute &original); + | ^~~~~~~~~ +[35/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o -c ../alignment/algorithms/sorting/qsufsort.cpp +[36/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o -c ../alignment/algorithms/alignment/ExtendAlign.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, from ../alignment/algorithms/alignment/ExtendAlign.hpp:9, @@ -1799,7 +1823,26 @@ /usr/include/c++/12/bits/new_allocator.h:175:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[41/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o -c ../alignment/datastructures/alignment/CmpFile.cpp +[37/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o -c ../hdf/HDFZMWMetricsWriter.cpp +In file included from ../hdf/HDFWriterBase.hpp:13, + from ../hdf/HDFZMWMetricsWriter.hpp:8, + from ../hdf/HDFZMWMetricsWriter.cpp:3: +../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: +../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’ +../hdf/HDFAtom.hpp:38:9: required from here +../hdf/HDFAtom.hpp:33:19: warning: implicitly-declared ‘H5::Attribute& H5::Attribute::operator=(const H5::Attribute&)’ is deprecated [-Wdeprecated-copy] + 33 | attribute = object.openAttribute(attributeName.c_str()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/hdf5/serial/H5Cpp.h:34, + from ../hdf/BufferedHDF2DArray.hpp:8, + from ../hdf/HDFZMWMetricsWriter.hpp:6: +/usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ + 32 | Attribute(const Attribute &original); + | ^~~~~~~~~ +[38/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o -c ../alignment/datastructures/alignment/AlignmentStats.cpp +[39/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o -c ../alignment/datastructures/alignment/AlignmentContext.cpp +[40/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -c ../alignment/algorithms/alignment/IDSScoreFunction.cpp +[41/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o -c ../alignment/datastructures/alignment/AlignmentMap.cpp [42/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o -c ../alignment/algorithms/alignment/KBandAlign.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/algorithms/alignment/KBandAlign.hpp:10, @@ -1831,8 +1874,44 @@ /usr/include/c++/12/bits/new_allocator.h:175:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[43/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o -c ../alignment/algorithms/alignment/IDSScoreFunction.cpp -[44/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o -c ../hdf/HDFZMWWriter.cpp +[43/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -c ../alignment/algorithms/alignment/GuidedAlign.cpp +In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, + from ../alignment/algorithms/alignment/GuidedAlign.hpp:11, + from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: +../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: +/usr/include/c++/12/bits/alloc_traits.h:516:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ +/usr/include/c++/12/bits/stl_vector.h:1281:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ +../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here +../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] + 209 | class CompSeqAlignment : public Alignment + | ^~~~~~~~~~~~~~~~ +../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ + 103 | Alignment &operator=(const Alignment &rhs); + | ^~~~~~~~ +../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] + 58 | class Alignment : public AlignmentStats + | ^~~~~~~~~ +In file included from ../alignment/datastructures/alignment/Alignment.hpp:8: +../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ + 19 | AlignmentStats &operator=(const AlignmentStats &rhs); + | ^~~~~~~~ +../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here + 209 | class CompSeqAlignment : public Alignment + | ^~~~~~~~~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/c++/12/bits/c++allocator.h:33, + from /usr/include/c++/12/bits/allocator.h:46, + from /usr/include/c++/12/string:41, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from ../alignment/algorithms/alignment/GuidedAlign.hpp:6: +/usr/include/c++/12/bits/new_allocator.h:175:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here + 175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[44/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -c ../alignment/algorithms/alignment/QualityValueScoreFunction.cpp +[45/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o -c ../alignment/datastructures/alignment/CmpFile.cpp +[46/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o -c ../hdf/HDFZMWWriter.cpp In file included from ../hdf/HDFWriterBase.hpp:13, from ../hdf/HDFZMWWriter.hpp:12, from ../hdf/HDFZMWWriter.cpp:5: @@ -1848,7 +1927,7 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[45/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o -c ../hdf/HDFUtils.cpp +[47/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o -MF libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o.d -o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o -c ../hdf/HDFUtils.cpp In file included from /usr/include/c++/12/cassert:44, from ../pbdata/reads/RegionTypeMap.hpp:7, from ../pbdata/reads/RegionAnnotation.hpp:17, @@ -1906,50 +1985,18 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[46/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o -c ../alignment/algorithms/alignment/QualityValueScoreFunction.cpp -[47/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o -c ../alignment/algorithms/alignment/GuidedAlign.cpp -In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, - from ../alignment/algorithms/alignment/GuidedAlign.hpp:11, - from ../alignment/algorithms/alignment/GuidedAlign.cpp:1: -../alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: -/usr/include/c++/12/bits/alloc_traits.h:516:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ -/usr/include/c++/12/bits/stl_vector.h:1281:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ -../alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here -../alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] - 209 | class CompSeqAlignment : public Alignment - | ^~~~~~~~~~~~~~~~ -../alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ - 103 | Alignment &operator=(const Alignment &rhs); - | ^~~~~~~~ -../alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] - 58 | class Alignment : public AlignmentStats - | ^~~~~~~~~ -In file included from ../alignment/datastructures/alignment/Alignment.hpp:8: -../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ - 19 | AlignmentStats &operator=(const AlignmentStats &rhs); - | ^~~~~~~~ -../alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here - 209 | class CompSeqAlignment : public Alignment - | ^~~~~~~~~~~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/c++/12/bits/c++allocator.h:33, - from /usr/include/c++/12/bits/allocator.h:46, - from /usr/include/c++/12/string:41, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from ../alignment/algorithms/alignment/GuidedAlign.hpp:6: -/usr/include/c++/12/bits/new_allocator.h:175:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here - 175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[48/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor 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libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o -c ../alignment/datastructures/alignment/AlignmentCandidate.cpp +[53/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -MF libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o.d -o libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o -c ../alignment/algorithms/sorting/LightweightSuffixArray.cpp +[54/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o -c ../alignment/datastructures/anchoring/AnchorParameters.cpp +[55/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o -c ../alignment/datastructures/alignmentset/SAMQVConversion.cpp +[56/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o -c ../alignment/datastructures/anchoring/ClusterList.cpp +[57/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o -c ../alignment/datastructures/alignmentset/SAMSupplementalQVList.cpp +[58/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o -c ../alignment/datastructures/anchoring/MatchPos.cpp +[59/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o -c ../alignment/datastructures/alignment/Alignment.cpp ../alignment/datastructures/alignment/Alignment.cpp: In member function ‘void blasr::Alignment::CopyStats(blasr::Alignment&)’: ../alignment/datastructures/alignment/Alignment.cpp:35:47: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 35 | AlignmentStats::CopyStats((AlignmentStats)rhs); @@ -1959,13 +2006,8 @@ ../alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ -[56/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o -c ../alignment/datastructures/alignmentset/SAMSupplementalQVList.cpp -[57/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o -c ../alignment/datastructures/anchoring/ClusterList.cpp -[58/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o -c ../alignment/datastructures/anchoring/AnchorParameters.cpp -[59/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o -c ../alignment/datastructures/anchoring/MatchPos.cpp -[60/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o -c ../alignment/datastructures/alignment/FilterCriteria.cpp -[61/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -c ../alignment/datastructures/anchoring/WeightedInterval.cpp -[62/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o -c ../alignment/format/CompareSequencesPrinter.cpp +[60/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o -c ../alignment/datastructures/anchoring/WeightedInterval.cpp +[61/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o -c ../alignment/format/CompareSequencesPrinter.cpp In file included from ../alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../alignment/format/CompareSequencesPrinter.hpp:7, from ../alignment/format/CompareSequencesPrinter.cpp:1: @@ -2001,16 +2043,14 @@ /usr/include/c++/12/bits/new_allocator.h:175:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[63/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o -c 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-std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o -MF libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o.d -o libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o -c ../alignment/statistics/cdfs.cpp -[66/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o -c ../alignment/files/FragmentCCSIterator.cpp -[67/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o -MF libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o.d -o libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o -c ../alignment/tuples/BaseTuple.cpp -[68/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o -c ../alignment/format/IntervalPrinter.cpp -[69/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o -MF libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o.d -o libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o -c ../alignment/tuples/TupleMetrics.cpp -[70/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o -MF libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o.d -o libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o -c ../alignment/statistics/StatUtils.cpp -[71/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o -MF libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o.d -o libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o -c ../alignment/statistics/pdfs.cpp -[72/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o -MF libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o.d -o libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o -c ../alignment/simulator/LengthHistogram.cpp +[62/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o -c ../alignment/files/CCSIterator.cpp +[63/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o -MF libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o -c ../alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp +[64/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB 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libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o.d -o libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o -c ../alignment/statistics/pdfs.cpp +[69/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o -MF libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o.d -o libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o -c ../alignment/simulator/LengthHistogram.cpp In file included from /usr/include/c++/12/cassert:44, from ../alignment/statistics/StatUtils.hpp:5, from ../alignment/simulator/CDFMap.hpp:8, @@ -2021,39 +2061,44 @@ ../alignment/simulator/CDFMap.hpp:37:23: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 37 | assert(cdf.size() >= 0); | ~~~~~~~~~~~^~~~ +[70/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o -c ../alignment/format/IntervalPrinter.cpp +[71/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra 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libblasr.so.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o -c ../alignment/query/PbiFilterZmwGroupQuery.cpp +[96/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o -c ../pbdata/reads/ZMWGroupEntry.cpp +[97/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o -c ../pbdata/saf/AlnGroup.cpp [100/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o -c 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-I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o -MF libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o -c ../pbdata/saf/RefInfo.cpp [104/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o -c ../pbdata/reads/RegionTypeMap.cpp -[105/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o -c ../pbdata/reads/RegionAnnotations.cpp +[105/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o -c ../pbdata/sam/ReadGroup.cpp +[106/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o -c ../pbdata/sam/ReferenceSequence.cpp +[107/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o -c ../pbdata/reads/RegionAnnotations.cpp ../pbdata/reads/RegionAnnotations.cpp: In constructor ‘RegionAnnotations::RegionAnnotations(UInt, const std::vector&, const std::vector&)’: ../pbdata/reads/RegionAnnotations.cpp:14:28: warning: implicitly-declared ‘constexpr RegionAnnotation::RegionAnnotation(const RegionAnnotation&)’ is deprecated [-Wdeprecated-copy] 14 | for (auto annotation : annotations) { @@ -2098,27 +2143,23 @@ ../pbdata/reads/RegionAnnotation.hpp:115:26: note: because ‘RegionAnnotation’ has user-provided ‘RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation&)’ 115 | inline RegionAnnotation &RegionAnnotation::operator=(const RegionAnnotation &rhs) | ^~~~~~~~~~~~~~~~ -[106/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ 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-ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o -c ../pbdata/reads/ScanData.cpp [109/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o.d -o 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-Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o -c ../alignment/format/SAMHeaderPrinter.cpp +[124/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o -MF libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o.d -o libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o -c ../alignment/format/SAMHeaderPrinter.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/format/SAMHeaderPrinter.hpp:14, @@ -2154,10 +2195,11 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ +[125/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o -MF libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o -c ../pbdata/reads/PulseFile.cpp +[126/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o -MF libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o -c ../pbdata/ReverseCompressIndex.cpp [127/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o -MF libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o -c ../pbdata/CommandLineParser.cpp [128/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o -c ../pbdata/StringUtils.cpp -[129/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o -c ../pbdata/utils/SMRTReadUtils.cpp -[130/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o -c ../alignment/files/ReaderAgglomerate.cpp +[129/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o -MF libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o.d -o libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o -c ../alignment/files/ReaderAgglomerate.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../alignment/files/ReaderAgglomerate.cpp:1: @@ -2195,10 +2237,10 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[131/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o -c ../pbdata/DNASequence.cpp -[132/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o -c ../pbdata/PackedDNASequence.cpp -[133/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o -c ../pbdata/BlasrFASTQReader.cpp -[134/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o -c ../pbdata/BlasrFASTAReader.cpp +[130/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o -MF libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o -c ../pbdata/utils/SMRTReadUtils.cpp +[131/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o -c ../pbdata/BlasrFASTQReader.cpp +[132/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o -c ../pbdata/CCSSequence.cpp +[133/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o -MF libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o -c ../pbdata/BlasrFASTAReader.cpp In file included from ../pbdata/FASTAReader.hpp:7, from ../pbdata/BlasrFASTAReader.cpp:2: ../pbdata/FASTASequence.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = FASTASequence; _Args = {FASTASequence}; _Tp = FASTASequence]’: @@ -2224,13 +2266,16 @@ /usr/include/c++/12/bits/new_allocator.h:175:11: note: synthesized method ‘constexpr FASTASequence::FASTASequence(const FASTASequence&)’ first required here 175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[135/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o -c ../pbdata/CCSSequence.cpp -[136/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o -c ../pbdata/FASTASequence.cpp +[134/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o -c ../pbdata/FASTASequence.cpp +[135/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o -c ../pbdata/DNASequence.cpp +[136/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o -c ../pbdata/PackedDNASequence.cpp [137/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o -c ../pbdata/FASTQSequence.cpp [138/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_datastructures_alignment_AlignmentMap_gtest.cpp.o -c ../unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp [139/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_FileUtils_gtest.cpp.o -c ../unittest/alignment/utils/FileUtils_gtest.cpp -[140/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -c ../unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp -[141/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o -c ../pbdata/SMRTSequence.cpp +[140/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -c ../unittest/hdf/HDFScanDataWriter_gtest.cpp +[141/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -c ../unittest/alignment/utils/RangeUtils_gtest.cpp +[142/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_datastructures_alignment_CmpIndexedStringTable_gtest.cpp.o -c ../unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp +[143/187] c++ -Ilibblasr.so.5.3.5.p -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -fPIC -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o -MF libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o.d -o libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o -c ../pbdata/SMRTSequence.cpp ../pbdata/SMRTSequence.cpp: In member function ‘void SMRTSequence::MadeFromSubreadsAsPolymerase(const std::vector&)’: ../pbdata/SMRTSequence.cpp:354:25: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 354 | for (auto subread : subreads) { @@ -2244,10 +2289,9 @@ ../pbdata/SMRTSequence.cpp:208:15: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 208 | SMRTSequence &SMRTSequence::operator=(const SMRTSequence &rhs) | ^~~~~~~~~~~~ -[142/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RangeUtils_gtest.cpp.o -c ../unittest/alignment/utils/RangeUtils_gtest.cpp -[143/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -c ../unittest/alignment/files/CCSIterator_gtest.cpp +[144/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, - from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: + from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:27: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here @@ -2259,10 +2303,10 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[144/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataWriter_gtest.cpp.o -c ../unittest/hdf/HDFScanDataWriter_gtest.cpp -[145/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp +[145/187] rm -f libblasr.a && gcc-ar csrD libblasr.a libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.5.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.5.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.5.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.5.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.5.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o +[146/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_CCSIterator_gtest.cpp.o -c ../unittest/alignment/files/CCSIterator_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, - from ../unittest/alignment/files/FragmentCCSIterator_gtest.cpp:27: + from ../unittest/alignment/files/CCSIterator_gtest.cpp:23: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: ../hdf/HDFAtom.hpp:40:26: required from ‘int HDFAtom::Initialize(HDFGroup&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’ ../hdf/HDFAtom.hpp:38:9: required from here @@ -2274,7 +2318,7 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[146/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp +[147/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_FragmentCCSIterator_other_gtest.cpp.o -c ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:29: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: @@ -2288,13 +2332,12 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[147/187] rm -f libblasr.a && gcc-ar csrD libblasr.a libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.5.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.5.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.5.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.5.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.5.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o [148/187] c++ -o libblasr.so.5.3.5 libblasr.so.5.3.5.p/hdf_BufferedHDF2DArray.cpp.o libblasr.so.5.3.5.p/hdf_BufferedHDFArray.cpp.o libblasr.so.5.3.5.p/hdf_DatasetCollection.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnGroupGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAlnInfoGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFAtom.cpp.o libblasr.so.5.3.5.p/hdf_HDFAttributable.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFBaxWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpExperimentGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFCmpSupportedFields.cpp.o libblasr.so.5.3.5.p/hdf_HDFData.cpp.o libblasr.so.5.3.5.p/hdf_HDFFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFGroup.cpp.o libblasr.so.5.3.5.p/hdf_HDFNewBasReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseCallsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseDataFile.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseH5Writer.cpp.o libblasr.so.5.3.5.p/hdf_HDFPulseWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFRegionTableReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFScanDataWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFUtils.cpp.o libblasr.so.5.3.5.p/hdf_HDFWriterBase.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWMetricsWriter.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWReader.cpp.o libblasr.so.5.3.5.p/hdf_HDFZMWWriter.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SDPFragment.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_sdp_SparseDynamicProgramming.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_AlignmentUtils.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_BaseScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ExtendAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_GuidedAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_IDSScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_KBandAlign.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_QualityValueScoreFunction.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_ScoreMatrices.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_alignment_StringToScoreMatrix.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_BWTSearch.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_ClusterProbability.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_Coordinate.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_anchoring_FindMaxInterval.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_DifferenceCovers.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_LightweightSuffixArray.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_MultikeyQuicksort.cpp.o libblasr.so.5.3.5.p/alignment_algorithms_sorting_qsufsort.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentCandidate.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentContext.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_Alignment.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentMap.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_AlignmentStats.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_CmpFile.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_FilterCriteria.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignment_SAMToAlignmentCandidateAdapter.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMQVConversion.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_alignmentset_SAMSupplementalQVList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_AnchorParameters.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_ClusterList.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_MatchPos.cpp.o libblasr.so.5.3.5.p/alignment_datastructures_anchoring_WeightedInterval.cpp.o libblasr.so.5.3.5.p/alignment_files_BaseSequenceIO.cpp.o libblasr.so.5.3.5.p/alignment_files_CCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_FragmentCCSIterator.cpp.o libblasr.so.5.3.5.p/alignment_files_ReaderAgglomerate.cpp.o libblasr.so.5.3.5.p/alignment_format_CompareSequencesPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_IntervalPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMHeaderPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SAMPrinter.cpp.o libblasr.so.5.3.5.p/alignment_format_SummaryPrinter.cpp.o libblasr.so.5.3.5.p/alignment_query_PbiFilterZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_query_SequentialZmwGroupQuery.cpp.o libblasr.so.5.3.5.p/alignment_qvs_QualityValueProfile.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSample.cpp.o libblasr.so.5.3.5.p/alignment_simulator_ContextSet.cpp.o libblasr.so.5.3.5.p/alignment_simulator_LengthHistogram.cpp.o libblasr.so.5.3.5.p/alignment_simulator_QualitySample.cpp.o libblasr.so.5.3.5.p/alignment_statistics_cdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_LookupAnchorDistribution.cpp.o libblasr.so.5.3.5.p/alignment_statistics_pdfs.cpp.o libblasr.so.5.3.5.p/alignment_statistics_StatUtils.cpp.o libblasr.so.5.3.5.p/alignment_tuples_BaseTuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_DNATuple.cpp.o libblasr.so.5.3.5.p/alignment_tuples_TupleMetrics.cpp.o libblasr.so.5.3.5.p/alignment_utils_BlasrFileUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_FileOfFileNames.cpp.o libblasr.so.5.3.5.p/alignment_utils_LogUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_PhredUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RangeUtils.cpp.o libblasr.so.5.3.5.p/alignment_utils_RegionUtils.cpp.o libblasr.so.5.3.5.p/alignment_MappingMetrics.cpp.o libblasr.so.5.3.5.p/pbdata_alignment_CmpAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_amos_AfgBasWriter.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MetricField.cpp.o libblasr.so.5.3.5.p/pbdata_loadpulses_MovieAlnIndexLookupTable.cpp.o libblasr.so.5.3.5.p/pbdata_metagenome_TitleTable.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_BlasrQualityValue.cpp.o libblasr.so.5.3.5.p/pbdata_qvs_QualityTransform.cpp.o libblasr.so.5.3.5.p/pbdata_reads_AcqParams.cpp.o libblasr.so.5.3.5.p/pbdata_reads_BaseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_HoleXY.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseBaseCommon.cpp.o libblasr.so.5.3.5.p/pbdata_reads_PulseFile.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ReadType.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotation.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionAnnotations.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTable.cpp.o libblasr.so.5.3.5.p/pbdata_reads_RegionTypeMap.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ScanData.cpp.o libblasr.so.5.3.5.p/pbdata_reads_ZMWGroupEntry.cpp.o libblasr.so.5.3.5.p/pbdata_saf_AlnGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_MovieInfo.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefGroup.cpp.o libblasr.so.5.3.5.p/pbdata_saf_RefInfo.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReadGroup.cpp.o libblasr.so.5.3.5.p/pbdata_sam_ReferenceSequence.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMAlignment.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMHeader.cpp.o libblasr.so.5.3.5.p/pbdata_sam_SAMKeywordValuePair.cpp.o libblasr.so.5.3.5.p/pbdata_utils_BitUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTReadUtils.cpp.o libblasr.so.5.3.5.p/pbdata_utils_SMRTTitle.cpp.o libblasr.so.5.3.5.p/pbdata_utils_TimeUtils.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTAReader.cpp.o libblasr.so.5.3.5.p/pbdata_BlasrFASTQReader.cpp.o libblasr.so.5.3.5.p/pbdata_CCSSequence.cpp.o libblasr.so.5.3.5.p/pbdata_ChangeListID.cpp.o libblasr.so.5.3.5.p/pbdata_CommandLineParser.cpp.o libblasr.so.5.3.5.p/pbdata_DNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTASequence.cpp.o libblasr.so.5.3.5.p/pbdata_FASTQSequence.cpp.o libblasr.so.5.3.5.p/pbdata_GFFFile.cpp.o libblasr.so.5.3.5.p/pbdata_MD5Utils.cpp.o libblasr.so.5.3.5.p/pbdata_NucConversion.cpp.o libblasr.so.5.3.5.p/pbdata_PackedDNASequence.cpp.o libblasr.so.5.3.5.p/pbdata_ReverseCompressIndex.cpp.o libblasr.so.5.3.5.p/pbdata_SMRTSequence.cpp.o libblasr.so.5.3.5.p/pbdata_StringUtils.cpp.o -I/usr/include/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libblasr.so.5.3.5 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,-rpath-link,/usr/lib/x86_64-linux-gnu/hdf5/serial /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lrt /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_hl.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so -Wl,--end-group [149/187] /usr/bin/meson --internal symbolextractor /build/pbseqlib-5.3.5+dfsg/obj-x86_64-linux-gnu libblasr.so.5.3.5 libblasr.so.5.3.5 libblasr.so.5.3.5.p/libblasr.so.5.3.5.symbols [150/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMPrinter_gtest.cpp [151/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_SequentialZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp [152/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_metagenome_TitleTable_gtest.cpp.o -c ../unittest/pbdata/metagenome/TitleTable_gtest.cpp -[153/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp +[153/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -c ../unittest/pbdata/saf/RefInfo_gtest.cpp [154/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFScanDataReader_gtest.cpp.o -c ../unittest/hdf/HDFScanDataReader_gtest.cpp In file included from ../hdf/HDFScanDataReader.hpp:8, from ../unittest/hdf/HDFScanDataReader_gtest.cpp:4: @@ -2327,10 +2370,8 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[155/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_RefInfo_gtest.cpp.o -c ../unittest/pbdata/saf/RefInfo_gtest.cpp -[156/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMHeaderPrinter_gtest.cpp -[157/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -c ../unittest/pbdata/saf/MovieInfo_gtest.cpp -[158/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -c ../unittest/alignment/utils/RegionUtils_gtest.cpp +[155/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_query_PbiFilterZmwGroupQuery_gtest.cpp.o -c ../unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp +[156/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_utils_RegionUtils_gtest.cpp.o -c ../unittest/alignment/utils/RegionUtils_gtest.cpp In file included from ../hdf/HDFRegionTableReader.hpp:11, from ../unittest/alignment/utils/RegionUtils_gtest.cpp:23: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::vector >; std::string = std::__cxx11::basic_string]’: @@ -2344,9 +2385,12 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[159/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -c ../unittest/hdf/HDFZMWReader_gtest.cpp -[160/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -c ../unittest/pbdata/saf/AlnGroup_gtest.cpp -[161/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -c ../unittest/hdf/HDFUtils_gtest.cpp +[157/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_MovieInfo_gtest.cpp.o -c ../unittest/pbdata/saf/MovieInfo_gtest.cpp +[158/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_saf_AlnGroup_gtest.cpp.o -c ../unittest/pbdata/saf/AlnGroup_gtest.cpp +[159/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o -c ../unittest/hdf/HDF2DArray_gtest.cpp +[160/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_format_SAMHeaderPrinter_gtest.cpp.o -c ../unittest/alignment/format/SAMHeaderPrinter_gtest.cpp +[161/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -c ../unittest/pbdata/utils/SMRTTitle_gtest.cpp +[162/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFUtils_gtest.cpp.o -c ../unittest/hdf/HDFUtils_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFUtils.hpp:7, from ../unittest/hdf/HDFUtils_gtest.cpp:22: @@ -2363,8 +2407,8 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[162/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDF2DArray_gtest.cpp.o -c ../unittest/hdf/HDF2DArray_gtest.cpp -[163/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -c ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp +[163/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFZMWReader_gtest.cpp.o -c ../unittest/hdf/HDFZMWReader_gtest.cpp +[164/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -MF unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o.d -o unittest/libblasr_unittest.p/alignment_files_ReaderAgglomerate_gtest.cpp.o -c ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../alignment/files/ReaderAgglomerate.hpp:8, from ../unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25: @@ -2399,16 +2443,17 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[164/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_SMRTTitle_gtest.cpp.o -c ../unittest/pbdata/utils/SMRTTitle_gtest.cpp [165/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_ReadType_gtest.cpp.o -c ../unittest/pbdata/reads/ReadType_gtest.cpp [166/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_RegionTypeMap_gtest.cpp.o -c ../unittest/pbdata/reads/RegionTypeMap_gtest.cpp [167/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_qvs_QualityValueVector_gtest.cpp.o -c ../unittest/pbdata/qvs/QualityValueVector_gtest.cpp -[168/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -c ../unittest/pbdata/ScanData_gtest.cpp -[169/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o -c ../unittest/pbdata/VectorUtils_gtest.cpp +[168/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_VectorUtils_gtest.cpp.o -c ../unittest/pbdata/VectorUtils_gtest.cpp +[169/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_ScanData_gtest.cpp.o -c ../unittest/pbdata/ScanData_gtest.cpp [170/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_defs_gtest.cpp.o -c ../unittest/pbdata/defs_gtest.cpp -[171/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -c ../unittest/pbdata/NucConversion_gtest.cpp -[172/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o -c ../unittest/pbdata/ChangeListID_gtest.cpp -[173/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o -c ../unittest/hdf/HDFPlsReader_gtest.cpp +[171/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_ChangeListID_gtest.cpp.o -c ../unittest/pbdata/ChangeListID_gtest.cpp +[172/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -c ../unittest/pbdata/reads/RegionAnnotations_gtest.cpp +[173/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_NucConversion_gtest.cpp.o -c ../unittest/pbdata/NucConversion_gtest.cpp +[174/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -c ../unittest/pbdata/StringUtils_gtest.cpp +[175/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFPlsReader_gtest.cpp.o -c ../unittest/hdf/HDFPlsReader_gtest.cpp In file included from ../hdf/HDFPlsReader.hpp:11, from ../unittest/hdf/HDFPlsReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = float; std::string = std::__cxx11::basic_string]’: @@ -2442,10 +2487,7 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ -[174/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_StringUtils_gtest.cpp.o -c ../unittest/pbdata/StringUtils_gtest.cpp -[175/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_reads_RegionAnnotations_gtest.cpp.o -c ../unittest/pbdata/reads/RegionAnnotations_gtest.cpp -[176/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -c ../unittest/pbdata/utils_gtest.cpp -[177/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -c ../unittest/hdf/HDFBasReader_gtest.cpp +[176/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFBasReader_gtest.cpp.o -c ../unittest/hdf/HDFBasReader_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../unittest/hdf/HDFBasReader_gtest.cpp:22: ../hdf/HDFAtom.hpp: In instantiation of ‘int HDFAtom::Initialize(H5::H5Object&, const std::string&) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string]’: @@ -2482,6 +2524,7 @@ /usr/include/hdf5/serial/H5Attribute.h:32:5: note: because ‘H5::Attribute’ has user-provided ‘H5::Attribute::Attribute(const H5::Attribute&)’ 32 | Attribute(const Attribute &original); | ^~~~~~~~~ +[177/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_utils_gtest.cpp.o -c ../unittest/pbdata/utils_gtest.cpp [178/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/hdf_HDFCCSReader_gtest.cpp.o -c ../unittest/hdf/HDFCCSReader_gtest.cpp In file included from ../hdf/HDFBasReader.hpp:14, from ../hdf/HDFCCSReader.hpp:4, @@ -2523,10 +2566,10 @@ | ^~~~~~~~~ [179/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SeqUtils_gtest.cpp.o -c ../unittest/pbdata/SeqUtils_gtest.cpp [180/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQReader_gtest.cpp.o -c ../unittest/pbdata/FASTQReader_gtest.cpp -[181/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -c ../unittest/pbdata/FASTQSequence_gtest.cpp -[182/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -c ../unittest/pbdata/CCSSequence_gtest.cpp -[183/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -c ../unittest/pbdata/FASTAReader_gtest.cpp -[184/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -c ../unittest/pbdata/FASTASequence_gtest.cpp +[181/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTAReader_gtest.cpp.o -c ../unittest/pbdata/FASTAReader_gtest.cpp +[182/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTQSequence_gtest.cpp.o -c ../unittest/pbdata/FASTQSequence_gtest.cpp +[183/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_FASTASequence_gtest.cpp.o -c ../unittest/pbdata/FASTASequence_gtest.cpp +[184/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_CCSSequence_gtest.cpp.o -c ../unittest/pbdata/CCSSequence_gtest.cpp [185/187] c++ -Iunittest/libblasr_unittest.p -Iunittest -I../unittest -I. -I.. -I/usr/include/hdf5/serial -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -g -O2 -ffile-prefix-map=/build/pbseqlib-5.3.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -O3 -DGTEST_HAS_PTHREAD=1 -DBOOST_ALL_NO_LIB -Wno-delete-non-virtual-dtor -Wno-unused-variable -Wno-non-virtual-dtor -MD -MQ unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -MF unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o.d -o unittest/libblasr_unittest.p/pbdata_SMRTSequence_gtest.cpp.o -c ../unittest/pbdata/SMRTSequence_gtest.cpp ../unittest/pbdata/SMRTSequence_gtest.cpp: In function ‘SMRTSequence _make_a_smrt_read_(const std::string&, const UInt&, DNALength, DNALength, const std::string&, bool, bool, bool, int, int, char, int, char)’: ../unittest/pbdata/SMRTSequence_gtest.cpp:66:12: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] @@ -2974,12 +3017,12 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'libblasr-dev' in '../libblasr-dev_5.3.5+dfsg-4_amd64.deb'. -dpkg-deb: building package 'libblasr5.3.5' in '../libblasr5.3.5_5.3.5+dfsg-4_amd64.deb'. dpkg-deb: building package 'libblasr5.3.5-dbgsym' in '../libblasr5.3.5-dbgsym_5.3.5+dfsg-4_amd64.deb'. +dpkg-deb: building package 'libblasr5.3.5' in '../libblasr5.3.5_5.3.5+dfsg-4_amd64.deb'. dpkg-deb: building package 'libpbseq-dev' in '../libpbseq-dev_5.3.5+dfsg-4_amd64.deb'. -dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.5+dfsg-4_amd64.deb'. -dpkg-deb: building package 'libpbseq' in '../libpbseq_5.3.5+dfsg-4_amd64.deb'. dpkg-deb: building package 'libpbdata-dev' in '../libpbdata-dev_5.3.5+dfsg-4_amd64.deb'. +dpkg-deb: building package 'libpbseq' in '../libpbseq_5.3.5+dfsg-4_amd64.deb'. +dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.5+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../pbseqlib_5.3.5+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../pbseqlib_5.3.5+dfsg-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2987,12 +3030,14 @@ 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/3483375/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3483375/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/2787689 and its subdirectories -I: Current time: Mon May 27 21:36:32 -12 2024 -I: pbuilder-time-stamp: 1716888992 +I: removing directory /srv/workspace/pbuilder/3483375 and its subdirectories +I: Current time: Wed Apr 26 17:16:50 +14 2023 +I: pbuilder-time-stamp: 1682479010