Diff of the two buildlogs: -- --- b1/build.log 2021-07-04 17:33:37.963023874 +0000 +++ b2/build.log 2021-07-04 17:34:25.209248310 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jul 4 05:27:38 -12 2021 -I: pbuilder-time-stamp: 1625419658 +I: Current time: Sun Aug 7 13:56:38 +14 2022 +I: pbuilder-time-stamp: 1659830198 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 [./ivar_1.3+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.Jk5XnzEM/trustedkeys.kbx': General error -gpgv: Signature made Sun Dec 13 10:44:37 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.RizMirPf/trustedkeys.kbx': General error +gpgv: Signature made Mon Dec 14 12:44:37 2020 +14 gpgv: using RSA key E50AFD55ADD27AAB97163A8B21D20589974B3E96 gpgv: issuer "tmancill@debian.org" gpgv: Can't check signature: No public key @@ -28,137 +28,171 @@ dpkg-source: info: unpacking ivar_1.3+dfsg-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/8295/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/64524/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-i386. +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' +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/64524/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/64524/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='f7f8ad1f8d464036ae79eafc9e614917' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='8295' - PS1='# ' - PS2='> ' + INVOCATION_ID=20db22cf41614ba5b5488b70487a45d9 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=64524 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/tmp.c2ggZUUGZE/pbuilderrc_HIQD --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.c2ggZUUGZE/b1 --logfile b1/build.log ivar_1.3+dfsg-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - 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/tmp.c2ggZUUGZE/pbuilderrc_xIAe --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.c2ggZUUGZE/b2 --logfile b2/build.log --extrapackages usrmerge ivar_1.3+dfsg-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + 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 ionos12-i386 4.19.0-17-686-pae #1 SMP Debian 4.19.194-2 (2021-06-21) i686 GNU/Linux + Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin - total 5780 - -rwxr-xr-x 1 root root 1367848 Jun 21 14:25 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 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 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 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 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Feb 7 02:38 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 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 02:38 more - -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 14:25 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 3 21:29 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 02:38 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/8295/tmp/hooks/D02_print_environment finished + total 5776 + -rwxr-xr-x 1 root root 1367848 Jun 22 2021 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 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 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 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 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Feb 8 2021 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 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 2021 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 2021 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 2021 more + -rwsr-xr-x 1 root root 50720 Feb 8 2021 mount + -rwxr-xr-x 1 root root 13856 Feb 8 2021 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 2021 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 7 13:56 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 7 05:46 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 2021 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 2021 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Feb 8 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/64524/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -243,7 +277,7 @@ Get: 45 http://deb.debian.org/debian bullseye/main i386 liblzma-dev i386 5.2.5-2 [240 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libhts-dev i386 1.11-4 [3817 kB] -Fetched 25.2 MB in 12s (2080 kB/s) +Fetched 25.2 MB in 0s (80.6 MB/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 ... 19675 files and directories currently installed.) @@ -446,8 +480,44 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (5212 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 21785 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/ivar-1.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/ivar-1.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package ivar dpkg-buildpackage: info: source version 1.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -457,9 +527,9 @@ debian/rules clean dh clean debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/ivar-1.3+dfsg' +make[1]: Verzeichnis „/build/ivar-1.3+dfsg“ wird betreten rm -f data/db/test_ref.fa.fai data/test.gap.fa data/test.gap.qual.txt data/test.indel.tsv data/test.masked_primer_indices.txt data/test.trimmed.masked.bam data/test.trimmed.masked.bam.bai data/test.trimmed.sorted.bam.bai data/test.unmapped.sorted.bam.bai -make[1]: Leaving directory '/build/ivar-1.3+dfsg' +make[1]: Verzeichnis „/build/ivar-1.3+dfsg“ wird verlassen dh_clean debian/rules binary dh binary @@ -474,7 +544,7 @@ ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a thread-safe mkdir -p... /bin/mkdir -p +checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -500,8 +570,8 @@ checking for main in -lhts... no checking for main in -lpthread... no checking for main in -lz... no -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes @@ -535,305 +605,319 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j10 -make[1]: Entering directory '/build/ivar-1.3+dfsg' + make -j18 +make[1]: Verzeichnis „/build/ivar-1.3+dfsg“ wird betreten make all-recursive -make[2]: Entering directory '/build/ivar-1.3+dfsg' +make[2]: Verzeichnis „/build/ivar-1.3+dfsg“ wird betreten Making all in src -make[3]: Entering directory '/build/ivar-1.3+dfsg/src' +make[3]: Verzeichnis „/build/ivar-1.3+dfsg/src“ wird betreten g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o ivar.o ivar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o call_consensus_pileup.o call_consensus_pileup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o alignment.o alignment.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp -Using built-in specs. -Using built-in specs. -Using built-in specs. -Using built-in specs. -Using built-in specs. -Using built-in specs. -Using built-in specs. Using built-in specs. +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp COLLECT_GCC=g++ Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) +Using built-in specs. +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=i686' + /usr/lib/gcc/i686-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ivar.cpp -quiet -dumpbase ivar.cpp -mtune=generic -march=i686 -auxbase-strip ivar.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc1lDYp9.s COLLECT_GCC=g++ Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=i686' +Using built-in specs. + /usr/lib/gcc/i686-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_consensus_pileup.cpp -quiet -dumpbase call_consensus_pileup.cpp -mtune=generic -march=i686 -auxbase-strip call_consensus_pileup.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccmXX6Nf.s COLLECT_GCC=g++ Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix -COLLECT_GCC=g++ -Supported LTO compression algorithms: zlib zstdTarget: i686-linux-gnu - -gcc version 10.2.1 20210110 (Debian 10.2.1-6) -Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu -Thread model: posix Supported LTO compression algorithms: zlib zstd -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' gcc version 10.2.1 20210110 (Debian 10.2.1-6) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=i686' +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=i686' +Using built-in specs. + /usr/lib/gcc/i686-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 alignment.cpp -quiet -dumpbase alignment.cpp -mtune=generic -march=i686 -auxbase-strip alignment.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccdihw1h.s COLLECT_GCC=g++ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp Target: i686-linux-gnu -COLLECT_GCC=g++ Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix -Target: i686-linux-gnu -Supported LTO compression algorithms: zlibCOLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=i686' - zstdConfigured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu - -Thread model: posix -gcc version 10.2.1 20210110 (Debian 10.2.1-6) Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=i686' -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=i686' +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' Using built-in specs. + /usr/lib/gcc/i686-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 suffix_tree.cpp -quiet -dumpbase suffix_tree.cpp -mtune=generic -march=i686 -auxbase-strip suffix_tree.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccnaPeKo.s COLLECT_GCC=g++ Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=i686' + /usr/lib/gcc/i686-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 trim_primer_quality.cpp -quiet -dumpbase trim_primer_quality.cpp -mtune=generic -march=i686 -auxbase-strip trim_primer_quality.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc8Q4Mhx.s +Using built-in specs. +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp +Using built-in specs. COLLECT_GCC=g++ Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' 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. /usr/include +End of search list. +Compiler executable checksum: 660aGNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) + compiled by GNU C version 10.2.1 20210110, 673188b9GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP + +14b66d124eGGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 +305feeb5be +GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) + compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP + +GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 +ignoring duplicate directory "/usr/include/i386-linux-gnu/c++/10" +ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" +ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/10/include-fixed" +ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/10/../../../../i686-linux-gnu/include" +#include "..." search starts here: +#include <...> search starts here: + . .. /usr/include/c++/10 -End of search list. /usr/include/i386-linux-gnu/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/i686-linux-gnu/10/include @@ -842,64 +926,38 @@ /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) - compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) - compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) - compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) - compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) - compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP - -GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP +GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) - compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP -GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP - -GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP - -GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP - -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP - -GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP - -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 +ignoring duplicate directory "/usr/include/i386-linux-gnu/c++/10" +ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" +ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/10/include-fixed" +ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/10/../../../../i686-linux-gnu/include" +#include "..." search starts here: +#include <...> search starts here: + . + .. + /usr/include/c++/10 + /usr/include/i386-linux-gnu/c++/10 + /usr/include/c++/10/backward + /usr/lib/gcc/i686-linux-gnu/10/include + /usr/local/include + /usr/include/i386-linux-gnu + /usr/include +End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) - compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP -GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP - GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -Compiler executable checksum: Compiler executable checksum: Compiler executable checksum: 660aCompiler executable checksum: 6667660a0a66Compiler executable checksum: 3167670a8831b931676688880ab9b91467b6146d31b6146d311288b612884eb9Compiler executable checksum: 6d4e30b91412b6666d5f30145f4eeeCompiler executable checksum: b512eebe4e0a -b630b56d6612304e5f675fbe0a -30675fee3131eeeeb5b5b5bebebe8888 - - -b9b91414b6b66d6d12124e4e30305f5feeeeb5b5bebe - Compiler executable checksum: 660a673188b914b66d124e305feeb5be +Using built-in specs. Compiler executable checksum: 660a673188b914b66d124e305feeb5be Compiler executable checksum: 660a673188b914b66d124e305feeb5be -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=i686' - as -v -I . -I .. --32 -o alignment.o /tmp/ccRgecDt.s -GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 -MAKEFLAGS=w -j10 -COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ -LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=i686' -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp -Using built-in specs. COLLECT_GCC=g++ Target: i686-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu @@ -907,11 +965,16 @@ Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' - /usr/lib/gcc/i686-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_common_variants.cpp -quiet -dumpbase get_common_variants.cpp -mtune=generic -march=i686 -auxbase-strip get_common_variants.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc9YV1GU.s + /usr/lib/gcc/i686-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_common_variants.cpp -quiet -dumpbase get_common_variants.cpp -mtune=generic -march=i686 -auxbase-strip get_common_variants.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc8zFYAq.s +Compiler executable checksum: 660a673188b914b66d124e305feeb5be +Compiler executable checksum: 660a673188b914b66d124e305feeb5be +Compiler executable checksum: 660a673188b914b66d124e305feeb5be +Compiler executable checksum: 660a673188b914b66d124e305feeb5be GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 +Compiler executable checksum: 660a673188b914b66d124e305feeb5be ignoring duplicate directory "/usr/include/i386-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/i386-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i686-linux-gnu/10/include-fixed" @@ -932,21 +995,9 @@ compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o ref_seq.o ref_seq.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o interval_tree.o interval_tree.cpp Compiler executable checksum: 660a673188b914b66d124e305feeb5be -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=i686' - as -v -I . -I .. --32 -o remove_reads_from_amplicon.o /tmp/cc2j5C3J.s -GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' - as -v -I . -I .. --32 -o suffix_tree.o /tmp/ccrmsHlC.s -GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 -MAKEFLAGS=w -j10 -COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ -LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=i686' -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=i686' - as -v -I . -I .. --32 -o get_masked_amplicons.o /tmp/ccrLw983.s -GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 Using built-in specs. COLLECT_GCC=g++ Target: i686-linux-gnu @@ -954,8 +1005,27 @@ Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) +Using built-in specs. COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=i686' - /usr/lib/gcc/i686-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 parse_gff.cpp -quiet -dumpbase parse_gff.cpp -mtune=generic -march=i686 -auxbase-strip parse_gff.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc2myn2y.s + /usr/lib/gcc/i686-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 parse_gff.cpp -quiet -dumpbase parse_gff.cpp -mtune=generic -march=i686 -auxbase-strip parse_gff.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccUxXwpM.s +COLLECT_GCC=g++ +Target: i686-linux-gnu +Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu +Thread model: posix +Supported LTO compression algorithms: zlib zstd +gcc version 10.2.1 20210110 (Debian 10.2.1-6) +Using built-in specs. +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=i686' + /usr/lib/gcc/i686-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ref_seq.cpp -quiet -dumpbase ref_seq.cpp -mtune=generic -march=i686 -auxbase-strip ref_seq.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccW2NIYR.s +COLLECT_GCC=g++ +Target: i686-linux-gnu +Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu +Thread model: posix +Supported LTO compression algorithms: zlib zstd +gcc version 10.2.1 20210110 (Debian 10.2.1-6) +Compiler executable checksum: 660a673188b914b66d124e305feeb5be +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' + /usr/lib/gcc/i686-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 interval_tree.cpp -quiet -dumpbase interval_tree.cpp -mtune=generic -march=i686 -auxbase-strip interval_tree.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccKKqrDX.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP @@ -980,21 +1050,6 @@ compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -Compiler executable checksum: 660a673188b914b66d124e305feeb5be -MAKEFLAGS=w -j10 -COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ -LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o ref_seq.o ref_seq.cpp -Using built-in specs. -COLLECT_GCC=g++ -Target: i686-linux-gnu -Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 10.2.1 20210110 (Debian 10.2.1-6) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=i686' - /usr/lib/gcc/i686-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ref_seq.cpp -quiet -dumpbase ref_seq.cpp -mtune=generic -march=i686 -auxbase-strip ref_seq.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccIkoYiL.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP @@ -1019,27 +1074,6 @@ compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -Compiler executable checksum: 660a673188b914b66d124e305feeb5be -MAKEFLAGS=w -j10 -COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ -LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=i686' -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o interval_tree.o interval_tree.cpp -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=i686' - as -v -I . -I .. --32 -o trim_primer_quality.o /tmp/ccmUYpbH.s -GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 -Using built-in specs. -COLLECT_GCC=g++ -Target: i686-linux-gnu -Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=i686-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-targets=all --enable-multiarch --disable-werror --with-arch-32=i686 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=i686-linux-gnu --host=i686-linux-gnu --target=i686-linux-gnu -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 10.2.1 20210110 (Debian 10.2.1-6) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=i686' - /usr/lib/gcc/i686-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch i386-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 interval_tree.cpp -quiet -dumpbase interval_tree.cpp -mtune=generic -march=i686 -auxbase-strip interval_tree.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccYrJCxU.s -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=i686' - as -v -I . -I .. --32 -o primer_bed.o /tmp/ccMFibYR.s -GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (i686-linux-gnu) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP @@ -1064,68 +1098,104 @@ compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=i686' - as -v -I . -I .. --32 -o allele_functions.o /tmp/ccovMBDY.s -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' - as -v -I . -I .. --32 -o call_variants.o /tmp/cc6erx2O.s Compiler executable checksum: 660a673188b914b66d124e305feeb5be +Compiler executable checksum: 660a673188b914b66d124e305feeb5be +Compiler executable checksum: 660a673188b914b66d124e305feeb5be +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' + as -v -I . -I .. --32 -o get_common_variants.o /tmp/cc8zFYAq.s +GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=i686' + as -v -I . -I .. --32 -o trim_primer_quality.o /tmp/cc8Q4Mhx.s GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' 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'-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=i686' + as -v -I . -I .. --32 -o call_consensus_pileup.o /tmp/ccmXX6Nf.s +GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 +GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 +MAKEFLAGS=w -j18 +COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ +LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=i686' +MAKEFLAGS=w -j18 +COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ +LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=i686' +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=i686' + as -v -I . -I .. --32 -o ivar.o /tmp/cc1lDYp9.s +GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 +MAKEFLAGS=w -j18 +COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ +LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=i686' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=i686' - as -v -I . -I .. --32 -o parse_gff.o /tmp/cc2myn2y.s + as -v -I . -I .. --32 -o parse_gff.o /tmp/ccUxXwpM.s GNU assembler version 2.35.2 (i686-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 -MAKEFLAGS=w -j10 +MAKEFLAGS=w -j18 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=i686' @@ -1138,34 +1208,34 @@ Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) -MAKEFLAGS=w -j10 +MAKEFLAGS=w -j18 COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=i686' - /usr/lib/gcc/i686-linux-gnu/10/collect2 -plugin /usr/lib/gcc/i686-linux-gnu/10/liblto_plugin.so -plugin-opt=/usr/lib/gcc/i686-linux-gnu/10/lto-wrapper -plugin-opt=-fresolution=/tmp/ccxwOQin.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_i386 --hash-style=gnu --as-needed -dynamic-linker /lib/ld-linux.so.2 -pie -o ivar /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/Scrt1.o /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/10/crtbeginS.o -L/usr/lib/gcc/i686-linux-gnu/10 -L/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/10/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/10/../../.. -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/i686-linux-gnu/10/crtendS.o /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/crtn.o + /usr/lib/gcc/i686-linux-gnu/10/collect2 -plugin /usr/lib/gcc/i686-linux-gnu/10/liblto_plugin.so -plugin-opt=/usr/lib/gcc/i686-linux-gnu/10/lto-wrapper -plugin-opt=-fresolution=/tmp/ccRnEknp.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_i386 --hash-style=gnu --as-needed -dynamic-linker /lib/ld-linux.so.2 -pie -o ivar /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/Scrt1.o /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/10/crtbeginS.o -L/usr/lib/gcc/i686-linux-gnu/10 -L/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/10/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/10/../../.. -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/i686-linux-gnu/10/crtendS.o /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=i686' -make[3]: Leaving directory '/build/ivar-1.3+dfsg/src' +make[3]: Verzeichnis „/build/ivar-1.3+dfsg/src“ wird verlassen Making all in tests -make[3]: Entering directory '/build/ivar-1.3+dfsg/tests' -make[3]: Nothing to be done for 'all'. -make[3]: Leaving directory '/build/ivar-1.3+dfsg/tests' -make[3]: Entering directory '/build/ivar-1.3+dfsg' -make[3]: Leaving directory '/build/ivar-1.3+dfsg' -make[2]: Leaving directory '/build/ivar-1.3+dfsg' -make[1]: Leaving directory '/build/ivar-1.3+dfsg' +make[3]: Verzeichnis „/build/ivar-1.3+dfsg/tests“ wird betreten +make[3]: Für das Ziel „all“ ist nichts zu tun. +make[3]: Verzeichnis „/build/ivar-1.3+dfsg/tests“ wird verlassen +make[3]: Verzeichnis „/build/ivar-1.3+dfsg“ wird betreten +make[3]: Verzeichnis „/build/ivar-1.3+dfsg“ wird verlassen +make[2]: Verzeichnis „/build/ivar-1.3+dfsg“ wird verlassen +make[1]: Verzeichnis „/build/ivar-1.3+dfsg“ wird verlassen debian/rules override_dh_auto_test -make[1]: Entering directory '/build/ivar-1.3+dfsg' +make[1]: Verzeichnis „/build/ivar-1.3+dfsg“ wird betreten dh_auto_test --no-parallel make -j1 check VERBOSE=1 -make[2]: Entering directory '/build/ivar-1.3+dfsg' +make[2]: Verzeichnis „/build/ivar-1.3+dfsg“ wird betreten Making check in src -make[3]: Entering directory '/build/ivar-1.3+dfsg/src' -make[3]: Nothing to be done for 'check'. -make[3]: Leaving directory '/build/ivar-1.3+dfsg/src' +make[3]: Verzeichnis „/build/ivar-1.3+dfsg/src“ wird betreten +make[3]: Für das Ziel „check“ ist nichts zu tun. +make[3]: Verzeichnis „/build/ivar-1.3+dfsg/src“ wird verlassen Making check in tests -make[3]: Entering directory '/build/ivar-1.3+dfsg/tests' +make[3]: Verzeichnis „/build/ivar-1.3+dfsg/tests“ wird betreten make check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search -make[4]: Entering directory '/build/ivar-1.3+dfsg/tests' +make[4]: Verzeichnis „/build/ivar-1.3+dfsg/tests“ wird betreten g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_trim.o test_primer_trim.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/trim_primer_quality.o ../src/trim_primer_quality.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/primer_bed.o ../src/primer_bed.cpp @@ -1213,10 +1283,10 @@ g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_interval_tree test_interval_tree.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_amplicon_search.o test_amplicon_search.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_amplicon_search test_amplicon_search.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread -make[4]: Leaving directory '/build/ivar-1.3+dfsg/tests' +make[4]: Verzeichnis „/build/ivar-1.3+dfsg/tests“ wird verlassen make check-TESTS -make[4]: Entering directory '/build/ivar-1.3+dfsg/tests' -make[5]: Entering directory '/build/ivar-1.3+dfsg/tests' +make[4]: Verzeichnis „/build/ivar-1.3+dfsg/tests“ wird betreten +make[5]: Verzeichnis „/build/ivar-1.3+dfsg/tests“ wird betreten PASS: check_primer_trim PASS: check_trim PASS: check_quality_trim @@ -1246,20 +1316,20 @@ # XPASS: 0 # ERROR: 0 ============================================================================ -make[5]: Leaving directory '/build/ivar-1.3+dfsg/tests' -make[4]: Leaving directory '/build/ivar-1.3+dfsg/tests' -make[3]: Leaving directory '/build/ivar-1.3+dfsg/tests' -make[3]: Entering directory '/build/ivar-1.3+dfsg' -make[3]: Leaving directory '/build/ivar-1.3+dfsg' -make[2]: Leaving directory '/build/ivar-1.3+dfsg' -make[1]: Leaving directory '/build/ivar-1.3+dfsg' +make[5]: Verzeichnis „/build/ivar-1.3+dfsg/tests“ wird verlassen +make[4]: Verzeichnis „/build/ivar-1.3+dfsg/tests“ wird verlassen +make[3]: Verzeichnis „/build/ivar-1.3+dfsg/tests“ wird verlassen +make[3]: Verzeichnis „/build/ivar-1.3+dfsg“ wird betreten +make[3]: Verzeichnis „/build/ivar-1.3+dfsg“ wird verlassen +make[2]: Verzeichnis „/build/ivar-1.3+dfsg“ wird verlassen +make[1]: Verzeichnis „/build/ivar-1.3+dfsg“ wird verlassen create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j10 install DESTDIR=/build/ivar-1.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no -make[1]: Entering directory '/build/ivar-1.3+dfsg' + make -j18 install DESTDIR=/build/ivar-1.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no +make[1]: Verzeichnis „/build/ivar-1.3+dfsg“ wird betreten Making install in src -make[2]: Entering directory '/build/ivar-1.3+dfsg/src' +make[2]: Verzeichnis „/build/ivar-1.3+dfsg/src“ wird betreten g++ -v -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o ivar ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread Using built-in specs. COLLECT_GCC=g++ @@ -1269,32 +1339,32 @@ Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) -MAKEFLAGS=w -j10 -- DESTDIR=/build/ivar-1.3+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no +MAKEFLAGS=w -j18 -- DESTDIR=/build/ivar-1.3+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/10/:/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/10/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=i686' - /usr/lib/gcc/i686-linux-gnu/10/collect2 -plugin /usr/lib/gcc/i686-linux-gnu/10/liblto_plugin.so -plugin-opt=/usr/lib/gcc/i686-linux-gnu/10/lto-wrapper -plugin-opt=-fresolution=/tmp/ccmL4teZ.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_i386 --hash-style=gnu --as-needed -dynamic-linker /lib/ld-linux.so.2 -pie -o ivar /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/Scrt1.o /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/10/crtbeginS.o -L/usr/lib/gcc/i686-linux-gnu/10 -L/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/10/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/10/../../.. -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/i686-linux-gnu/10/crtendS.o /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/crtn.o + /usr/lib/gcc/i686-linux-gnu/10/collect2 -plugin /usr/lib/gcc/i686-linux-gnu/10/liblto_plugin.so -plugin-opt=/usr/lib/gcc/i686-linux-gnu/10/lto-wrapper -plugin-opt=-fresolution=/tmp/ccfe5J5B.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_i386 --hash-style=gnu --as-needed -dynamic-linker /lib/ld-linux.so.2 -pie -o ivar /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/Scrt1.o /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/10/crtbeginS.o -L/usr/lib/gcc/i686-linux-gnu/10 -L/usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/10/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/10/../../.. -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/i686-linux-gnu/10/crtendS.o /usr/lib/gcc/i686-linux-gnu/10/../../../i386-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mtune=generic' '-march=i686' -make[3]: Entering directory '/build/ivar-1.3+dfsg/src' -make[3]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/ivar-1.3+dfsg/debian/tmp/usr/bin' +make[3]: Verzeichnis „/build/ivar-1.3+dfsg/src“ wird betreten +make[3]: Für das Ziel „install-data-am“ ist nichts zu tun. + /usr/bin/mkdir -p '/build/ivar-1.3+dfsg/debian/tmp/usr/bin' /usr/bin/install -c ivar '/build/ivar-1.3+dfsg/debian/tmp/usr/bin' -make[3]: Leaving directory '/build/ivar-1.3+dfsg/src' -make[2]: Leaving directory '/build/ivar-1.3+dfsg/src' +make[3]: Verzeichnis „/build/ivar-1.3+dfsg/src“ wird verlassen +make[2]: Verzeichnis „/build/ivar-1.3+dfsg/src“ wird verlassen Making install in tests -make[2]: Entering directory '/build/ivar-1.3+dfsg/tests' -make[3]: Entering directory '/build/ivar-1.3+dfsg/tests' -make[3]: Nothing to be done for 'install-exec-am'. -make[3]: Nothing to be done for 'install-data-am'. -make[3]: Leaving directory '/build/ivar-1.3+dfsg/tests' -make[2]: Leaving directory '/build/ivar-1.3+dfsg/tests' -make[2]: Entering directory '/build/ivar-1.3+dfsg' -make[3]: Entering directory '/build/ivar-1.3+dfsg' -make[3]: Nothing to be done for 'install-exec-am'. -make[3]: Nothing to be done for 'install-data-am'. -make[3]: Leaving directory '/build/ivar-1.3+dfsg' -make[2]: Leaving directory '/build/ivar-1.3+dfsg' -make[1]: Leaving directory '/build/ivar-1.3+dfsg' +make[2]: Verzeichnis „/build/ivar-1.3+dfsg/tests“ wird betreten +make[3]: Verzeichnis „/build/ivar-1.3+dfsg/tests“ wird betreten +make[3]: Für das Ziel „install-exec-am“ ist nichts zu tun. +make[3]: Für das Ziel „install-data-am“ ist nichts zu tun. +make[3]: Verzeichnis „/build/ivar-1.3+dfsg/tests“ wird verlassen +make[2]: Verzeichnis „/build/ivar-1.3+dfsg/tests“ wird verlassen +make[2]: Verzeichnis „/build/ivar-1.3+dfsg“ wird betreten +make[3]: Verzeichnis „/build/ivar-1.3+dfsg“ wird betreten +make[3]: Für das Ziel „install-exec-am“ ist nichts zu tun. +make[3]: Für das Ziel „install-data-am“ ist nichts zu tun. +make[3]: Verzeichnis „/build/ivar-1.3+dfsg“ wird verlassen +make[2]: Verzeichnis „/build/ivar-1.3+dfsg“ wird verlassen +make[1]: Verzeichnis „/build/ivar-1.3+dfsg“ wird verlassen dh_install dh_installdocs dh_installchangelogs @@ -1314,21 +1384,23 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'ivar-dbgsym' in '../ivar-dbgsym_1.3+dfsg-1_i386.deb'. -dpkg-deb: building package 'ivar-doc' in '../ivar-doc_1.3+dfsg-1_all.deb'. -dpkg-deb: building package 'ivar' in '../ivar_1.3+dfsg-1_i386.deb'. +dpkg-deb: Paket »ivar« wird in »../ivar_1.3+dfsg-1_i386.deb« gebaut. +dpkg-deb: Paket »ivar-dbgsym« wird in »../ivar-dbgsym_1.3+dfsg-1_i386.deb« gebaut. +dpkg-deb: Paket »ivar-doc« wird in »../ivar-doc_1.3+dfsg-1_all.deb« gebaut. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../ivar_1.3+dfsg-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/64524/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/64524/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/8295 and its subdirectories -I: Current time: Sun Jul 4 05:33:37 -12 2021 -I: pbuilder-time-stamp: 1625420017 +I: removing directory /srv/workspace/pbuilder/64524 and its subdirectories +I: Current time: Sun Aug 7 13:57:23 +14 2022 +I: pbuilder-time-stamp: 1659830243