Diff of the two buildlogs: -- --- b1/build.log 2023-01-05 19:23:54.353680645 +0000 +++ b2/build.log 2023-01-05 19:26:42.635941590 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 5 07:21:01 -12 2023 -I: pbuilder-time-stamp: 1672946461 +I: Current time: Thu Feb 8 15:47:14 +14 2024 +I: pbuilder-time-stamp: 1707356834 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./blasr_5.3.3+dfsg-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.4DsjrquL/trustedkeys.kbx': General error -gpgv: Signature made Mon Nov 16 00:54:45 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.hlYabXMp/trustedkeys.kbx': General error +gpgv: Signature made Tue Nov 17 02:54:45 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,135 +31,170 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3911120/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4021449/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +lrwxrwxrwx 1 root root 4 Feb 8 15:47 /bin/sh -> 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/4021449/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4021449/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,-fixfilepath parallel=15' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(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,-fixfilepath parallel=16' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='b57e2aaef4b544d190fd2dd2f2c1d5fd' - 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='3911120' - PS1='# ' - PS2='> ' + INVOCATION_ID=85379c26eb5946e9ae063480da51a108 + 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=4021449 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.puBRths4/pbuilderrc_lpaX --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.puBRths4/b1 --logfile b1/build.log blasr_5.3.3+dfsg-5.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://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.puBRths4/pbuilderrc_2G8j --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.puBRths4/b2 --logfile b2/build.log blasr_5.3.3+dfsg-5.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://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 5.10.0-20-amd64 #1 SMP Debian 5.10.158-2 (2022-12-13) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.0.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.0.12-1~bpo11+1 (2022-12-19) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 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 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jan 20 2022 more - -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount - -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Dec 20 21:25 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jan 20 2022 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 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 5898 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 8049 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/3911120/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jan 21 2022 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jan 21 2022 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 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 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jan 21 2022 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jan 21 2022 more + -rwsr-xr-x 1 root root 55528 Jan 21 2022 mount + -rwxr-xr-x 1 root root 18664 Jan 21 2022 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Feb 8 15:47 sh -> bash + lrwxrwxrwx 1 root root 4 Jan 24 05:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jan 21 2022 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jan 21 2022 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jan 21 2022 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 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 5898 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 8049 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/4021449/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -324,7 +359,7 @@ Get: 101 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 meson all 0.56.2-1 [437 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] -Fetched 64.3 MB in 26s (2453 kB/s) +Fetched 64.3 MB in 8s (7960 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19704 files and directories currently installed.) @@ -756,7 +791,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/blasr-5.3.3+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 > ../blasr_5.3.3+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/4021449/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/4021449/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/blasr-5.3.3+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 > ../blasr_5.3.3+dfsg-5_source.changes dpkg-buildpackage: info: source package blasr dpkg-buildpackage: info: source version 5.3.3+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -812,14 +851,16 @@ make[1]: Entering directory '/build/blasr-5.3.3+dfsg' ln -s build obj-x86_64-linux-gnu dh_auto_build - cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j15 -v + cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j16 -v [1/25] /usr/bin/meson --internal vcstagger ../BlasrGitHash.h.in BlasrGitHash.h '' /build/blasr-5.3.3+dfsg @BLASR_GIT_SHA1@ '(.*)' /build/blasr-5.3.3+dfsg/git describe --always '--dirty=*' -[2/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SALS.cpp.o -MF libblasr_impl.a.p/extrautils_SALS.cpp.o.d -o libblasr_impl.a.p/extrautils_SALS.cpp.o -c ../extrautils/SALS.cpp -[3/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SAModify.cpp.o -MF libblasr_impl.a.p/extrautils_SAModify.cpp.o.d -o libblasr_impl.a.p/extrautils_SAModify.cpp.o -c ../extrautils/SAModify.cpp -[4/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -MF libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o.d -o libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -c ../extrautils/BuildSequenceDB.cpp -[5/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o -MF libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o.d -o libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o -c ../extrautils/SimpleShredder.cpp -[6/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -MF libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o.d -o libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -c ../extrautils/ExciseRepeats.cpp -[7/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -MF libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o.d -o libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -c ../extrautils/SuffixArrayToBWT.cpp +[2/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -MF libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o.d -o libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -c ../extrautils/BwtToSuffixArray.cpp +[3/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SALS.cpp.o -MF libblasr_impl.a.p/extrautils_SALS.cpp.o.d -o libblasr_impl.a.p/extrautils_SALS.cpp.o -c ../extrautils/SALS.cpp +[4/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_Evolve.cpp.o -MF libblasr_impl.a.p/extrautils_Evolve.cpp.o.d -o libblasr_impl.a.p/extrautils_Evolve.cpp.o -c ../extrautils/Evolve.cpp +[5/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -MF libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o.d -o libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -c ../extrautils/ExciseRepeats.cpp +[6/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SAModify.cpp.o -MF libblasr_impl.a.p/extrautils_SAModify.cpp.o.d -o libblasr_impl.a.p/extrautils_SAModify.cpp.o -c ../extrautils/SAModify.cpp +[7/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -MF libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o.d -o libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -c ../extrautils/PrintTupleCountTable.cpp +[8/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -MF libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o.d -o libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -c ../extrautils/BuildSequenceDB.cpp +[9/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -MF libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o.d -o libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -c ../extrautils/SuffixArrayToBWT.cpp In file included from ../extrautils/SuffixArrayToBWT.cpp:4: /usr/include/pbseq/alignment/bwt/BWT.hpp: In member function ‘void Bwt::InitializeDNACharacterCount() [with T_BWT_Sequence = PackedDNASequence; T_DNASequence = FASTASequence]’: /usr/include/pbseq/alignment/bwt/BWT.hpp:192:21: warning: this statement may fall through [-Wimplicit-fallthrough=] @@ -852,7 +893,8 @@ /usr/include/pbseq/alignment/bwt/BWT.hpp:201:17: note: here 201 | case 4: //N | ^~~~ -[8/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SWMatcher.cpp.o -MF libblasr_impl.a.p/extrautils_SWMatcher.cpp.o.d -o libblasr_impl.a.p/extrautils_SWMatcher.cpp.o -c ../extrautils/SWMatcher.cpp +[10/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o -MF libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o.d -o libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o -c ../extrautils/SimpleShredder.cpp +[11/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SWMatcher.cpp.o -MF libblasr_impl.a.p/extrautils_SWMatcher.cpp.o.d -o libblasr_impl.a.p/extrautils_SWMatcher.cpp.o -c ../extrautils/SWMatcher.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../extrautils/SWMatcher.cpp:6: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: @@ -891,9 +933,6 @@ /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[9/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -MF libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o.d -o libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -c ../extrautils/BwtToSuffixArray.cpp -[10/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -MF libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o.d -o libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -c ../extrautils/PrintTupleCountTable.cpp -[11/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_Evolve.cpp.o -MF libblasr_impl.a.p/extrautils_Evolve.cpp.o.d -o libblasr_impl.a.p/extrautils_Evolve.cpp.o -c ../extrautils/Evolve.cpp [12/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamToM4.cpp.o -MF libblasr_impl.a.p/utils_SamToM4.cpp.o.d -o libblasr_impl.a.p/utils_SamToM4.cpp.o -c ../utils/SamToM4.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamToM4.cpp:21: @@ -973,13 +1012,32 @@ /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[15/25] c++ -ItoAfg.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ toAfg.p/utils_ToAfg.cpp.o -MF toAfg.p/utils_ToAfg.cpp.o.d -o toAfg.p/utils_ToAfg.cpp.o -c ../utils/ToAfg.cpp +[15/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_PulseToFasta.cpp.o -MF libblasr_impl.a.p/utils_PulseToFasta.cpp.o.d -o libblasr_impl.a.p/utils_PulseToFasta.cpp.o -c ../utils/PulseToFasta.cpp +In file included from ../utils/PulseToFasta.cpp:8: +/usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: +/usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] + 549 | } catch (DataSetIException e) { + | ^ +In file included from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, + from ../utils/PulseToFasta.cpp:5: +/usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’: +../utils/PulseToFasta.cpp:157:41: required from here +/usr/include/pbseq/hdf/HDFBasReader.hpp:760:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] + 760 | } catch (H5::DataSetIException e) { + | ^ +/usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = FASTASequence]’: +/usr/include/pbseq/hdf/HDFBasReader.hpp:726:40: required from ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’ +../utils/PulseToFasta.cpp:157:41: required from here +/usr/include/pbseq/hdf/HDFBasReader.hpp:647:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] + 647 | } catch (H5::DataSetIException e) { + | ^ +[16/25] c++ -ItoAfg.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ toAfg.p/utils_ToAfg.cpp.o -MF toAfg.p/utils_ToAfg.cpp.o.d -o toAfg.p/utils_ToAfg.cpp.o -c ../utils/ToAfg.cpp In file included from ../utils/ToAfg.cpp:9: /usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: /usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] 549 | } catch (DataSetIException e) { | ^ -[16/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamToCmpH5.cpp.o -MF libblasr_impl.a.p/utils_SamToCmpH5.cpp.o.d -o libblasr_impl.a.p/utils_SamToCmpH5.cpp.o -c ../utils/SamToCmpH5.cpp +[17/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamToCmpH5.cpp.o -MF libblasr_impl.a.p/utils_SamToCmpH5.cpp.o.d -o libblasr_impl.a.p/utils_SamToCmpH5.cpp.o -c ../utils/SamToCmpH5.cpp In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFAlnGroupGroup.hpp:6, @@ -1050,65 +1108,7 @@ /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:28:5: note: because ‘RefGroupNameId’ has user-provided ‘RefGroupNameId::RefGroupNameId(const RefGroupNameId&)’ 28 | RefGroupNameId(const RefGroupNameId &rhs) | ^~~~~~~~~~~~~~ -[17/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_PulseToFasta.cpp.o -MF libblasr_impl.a.p/utils_PulseToFasta.cpp.o.d -o libblasr_impl.a.p/utils_PulseToFasta.cpp.o -c ../utils/PulseToFasta.cpp -In file included from ../utils/PulseToFasta.cpp:8: -/usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: -/usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] - 549 | } catch (DataSetIException e) { - | ^ -In file included from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, - from ../utils/PulseToFasta.cpp:5: -/usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’: -../utils/PulseToFasta.cpp:157:41: required from here -/usr/include/pbseq/hdf/HDFBasReader.hpp:760:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] - 760 | } catch (H5::DataSetIException e) { - | ^ -/usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader::GetNext(FASTQSequence&) [with T_Sequence = FASTASequence]’: -/usr/include/pbseq/hdf/HDFBasReader.hpp:726:40: required from ‘int T_HDFBasReader::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’ -../utils/PulseToFasta.cpp:157:41: required from here -/usr/include/pbseq/hdf/HDFBasReader.hpp:647:40: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=] - 647 | } catch (H5::DataSetIException e) { - | ^ -[18/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamFilter.cpp.o -MF libblasr_impl.a.p/utils_SamFilter.cpp.o.d -o libblasr_impl.a.p/utils_SamFilter.cpp.o -c ../utils/SamFilter.cpp -In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, - from ../utils/SamFilter.cpp:32: -/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: -/usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ -/usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ -/usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here -/usr/include/pbseq/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 - | ^~~~~~~~~~~~~~~~ -/usr/include/pbseq/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); - | ^~~~~~~~ -/usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, - from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, - from ../utils/SamFilter.cpp:32: -/usr/include/pbseq/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); - | ^~~~~~~~ -In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, - from ../utils/SamFilter.cpp:32: -/usr/include/pbseq/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++/10/bits/c++allocator.h:33, - from /usr/include/c++/10/bits/allocator.h:46, - from /usr/include/c++/10/string:41, - from /usr/include/c++/10/bits/locale_classes.h:40, - from /usr/include/c++/10/bits/ios_base.h:41, - from /usr/include/c++/10/ios:42, - from /usr/include/c++/10/ostream:38, - from /usr/include/c++/10/iostream:39, - from ../utils/SamFilter.cpp:29: -/usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here - 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[19/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o -MF libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o.d -o libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o -c ../extrautils/StoreQualityByContextFromCmpH5.cpp +[18/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o -MF libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o.d -o libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o -c ../extrautils/StoreQualityByContextFromCmpH5.cpp In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217, from /usr/include/pbseq/hdf/HDFArray.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:13, @@ -1165,6 +1165,45 @@ /usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[19/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamFilter.cpp.o -MF libblasr_impl.a.p/utils_SamFilter.cpp.o.d -o libblasr_impl.a.p/utils_SamFilter.cpp.o -c ../utils/SamFilter.cpp +In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, + from ../utils/SamFilter.cpp:32: +/usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: +/usr/include/c++/10/bits/alloc_traits.h:512:17: required from ‘static void std::allocator_traits >::construct(std::allocator_traits >::allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; std::allocator_traits >::allocator_type = std::allocator]’ +/usr/include/c++/10/bits/stl_vector.h:1192:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::value_type = blasr::CompSeqAlignment]’ +/usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:39: required from here +/usr/include/pbseq/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 + | ^~~~~~~~~~~~~~~~ +/usr/include/pbseq/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); + | ^~~~~~~~ +/usr/include/pbseq/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 /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8, + from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, + from ../utils/SamFilter.cpp:32: +/usr/include/pbseq/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); + | ^~~~~~~~ +In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, + from ../utils/SamFilter.cpp:32: +/usr/include/pbseq/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++/10/bits/c++allocator.h:33, + from /usr/include/c++/10/bits/allocator.h:46, + from /usr/include/c++/10/string:41, + from /usr/include/c++/10/bits/locale_classes.h:40, + from /usr/include/c++/10/bits/ios_base.h:41, + from /usr/include/c++/10/ios:42, + from /usr/include/c++/10/ostream:38, + from /usr/include/c++/10/iostream:39, + from ../utils/SamFilter.cpp:29: +/usr/include/c++/10/ext/new_allocator.h:150:4: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here + 150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [20/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_LoadPulses.cpp.o -MF libblasr_impl.a.p/utils_LoadPulses.cpp.o.d -o libblasr_impl.a.p/utils_LoadPulses.cpp.o -c ../utils/LoadPulses.cpp In file included from ../utils/LoadPulses.cpp:19: /usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’: @@ -1510,8 +1549,8 @@ dh_gencontrol -O--buildsystem=meson dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson -dpkg-deb: building package 'blasr' in '../blasr_5.3.3+dfsg-5_amd64.deb'. dpkg-deb: building package 'blasr-dbgsym' in '../blasr-dbgsym_5.3.3+dfsg-5_amd64.deb'. +dpkg-deb: building package 'blasr' in '../blasr_5.3.3+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../blasr_5.3.3+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1519,12 +1558,14 @@ 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/4021449/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4021449/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/3911120 and its subdirectories -I: Current time: Thu Jan 5 07:23:53 -12 2023 -I: pbuilder-time-stamp: 1672946633 +I: removing directory /srv/workspace/pbuilder/4021449 and its subdirectories +I: Current time: Thu Feb 8 15:49:42 +14 2024 +I: pbuilder-time-stamp: 1707356982