Diff of the two buildlogs: -- --- b1/build.log 2021-08-17 00:50:02.499126575 +0000 +++ b2/build.log 2021-08-17 00:52:04.522561529 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Sep 18 19:11:08 -12 2022 -I: pbuilder-time-stamp: 1663571468 +I: Current time: Tue Aug 17 14:50:05 +14 2021 +I: pbuilder-time-stamp: 1629161405 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ 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.vC3Pg2nr/trustedkeys.kbx': General error -gpgv: Signature made Sun Dec 13 10:44:37 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.EWlM4mLO/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 @@ -27,135 +27,169 @@ 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/22028/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/28980/tmp/hooks/D01_modify_environment starting +debug: Running on codethink14-arm64. +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/28980/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/28980/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='22028' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=28980 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.a6Zp5hlLpH/pbuilderrc_Xw4d --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.a6Zp5hlLpH/b1 --logfile b1/build.log ivar_1.3+dfsg-1.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.a6Zp5hlLpH/pbuilderrc_s0qO --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.a6Zp5hlLpH/b2 --logfile b2/build.log --extrapackages usrmerge ivar_1.3+dfsg-1.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink13-arm64 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-153-generic #160-Ubuntu SMP Thu Jul 29 07:06:07 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Aug 4 2021 bash - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 34808 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 34808 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 14264 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 39832 Sep 22 2020 cat - -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown - -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp - -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash - -rwxr-xr-x 1 root root 101384 Sep 22 2020 date - -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd - -rwxr-xr-x 1 root root 89824 Sep 22 2020 df - -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir - -rwxr-xr-x 1 root root 76152 Jul 28 2021 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 35632 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 64856 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 93744 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln - -rwxr-xr-x 1 root root 52720 Feb 7 2020 login - -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls - -rwxr-xr-x 1 root root 161960 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 51368 Jul 28 2021 more - -rwsr-xr-x 1 root root 51360 Jul 28 2021 mount - -rwxr-xr-x 1 root root 14496 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm - -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Sep 17 03:48 sh -> dash - -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty - -rwsr-xr-x 1 root root 67776 Jul 28 2021 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar - -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch - -rwxr-xr-x 1 root root 31512 Sep 22 2020 true - -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Jul 28 2021 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 Jul 28 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/22028/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 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 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 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 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 Jul 29 09:09 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 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 64856 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 93744 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 161960 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Jul 29 09:09 more + -rwsr-xr-x 1 root root 51360 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 14496 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 17 14:50 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 16 23:27 sh.distrib -> dash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Jul 29 09:09 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 535768 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/28980/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -240,7 +274,7 @@ Get: 45 http://deb.debian.org/debian bullseye/main arm64 liblzma-dev arm64 5.2.5-2 [227 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 libhts-dev arm64 1.11-4 [3856 kB] -Fetched 24.4 MB in 1s (25.3 MB/s) +Fetched 24.4 MB in 1s (46.0 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 ... 19646 files and directories currently installed.) @@ -443,8 +477,45 @@ 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 arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (1807 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 ... 21759 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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ivar_1.3+dfsg-1_source.changes +hostname: Temporary failure in name resolution +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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../ivar_1.3+dfsg-1_source.changes dpkg-buildpackage: info: source package ivar dpkg-buildpackage: info: source version 1.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -454,9 +525,9 @@ debian/rules clean dh clean debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/ivar-1.3+dfsg' +make[1]: Map '/build/ivar-1.3+dfsg' wordt binnengegaan 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]: Map '/build/ivar-1.3+dfsg' wordt verlaten dh_clean debian/rules binary dh binary @@ -471,7 +542,7 @@ ./configure --build=aarch64-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/aarch64-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 @@ -497,8 +568,8 @@ 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 @@ -533,19 +604,16 @@ config.status: executing depfiles commands dh_auto_build make -j8 -make[1]: Entering directory '/build/ivar-1.3+dfsg' +make[1]: Map '/build/ivar-1.3+dfsg' wordt binnengegaan make all-recursive -make[2]: Entering directory '/build/ivar-1.3+dfsg' +make[2]: Map '/build/ivar-1.3+dfsg' wordt binnengegaan Making all in src -make[3]: Entering directory '/build/ivar-1.3+dfsg/src' +make[3]: Map '/build/ivar-1.3+dfsg/src' wordt binnengegaan 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 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: aarch64-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,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex @@ -553,17 +621,17 @@ 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' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ivar.cpp -quiet -dumpbase ivar.cpp -mlittle-endian -mabi=lp64 -auxbase-strip ivar.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cccCnfd1.s Using built-in specs. + /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ivar.cpp -quiet -dumpbase ivar.cpp -mlittle-endian -mabi=lp64 -auxbase-strip ivar.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccWJlKuZ.s COLLECT_GCC=g++ Target: aarch64-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,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex 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' 'alignment.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 alignment.cpp -quiet -dumpbase alignment.cpp -mlittle-endian -mabi=lp64 -auxbase-strip alignment.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccZfJ1cf.s +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' '-mlittle-endian' '-mabi=lp64' + /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_consensus_pileup.cpp -quiet -dumpbase call_consensus_pileup.cpp -mlittle-endian -mabi=lp64 -auxbase-strip call_consensus_pileup.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccKDOPD4.s Using built-in specs. COLLECT_GCC=g++ Target: aarch64-linux-gnu @@ -571,26 +639,28 @@ 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' 'alignment.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' +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 + /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 alignment.cpp -quiet -dumpbase alignment.cpp -mlittle-endian -mabi=lp64 -auxbase-strip alignment.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccMi5Za8.s 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' 'suffix_tree.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 suffix_tree.cpp -quiet -dumpbase suffix_tree.cpp -mlittle-endian -mabi=lp64 -auxbase-strip suffix_tree.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc4fumBg.s COLLECT_GCC=g++ Target: aarch64-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,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex 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' 'trim_primer_quality.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 trim_primer_quality.cpp -quiet -dumpbase trim_primer_quality.cpp -mlittle-endian -mabi=lp64 -auxbase-strip trim_primer_quality.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc7lx9ql.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' 'suffix_tree.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 suffix_tree.cpp -quiet -dumpbase suffix_tree.cpp -mlittle-endian -mabi=lp64 -auxbase-strip suffix_tree.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccry342c.s Using built-in specs. COLLECT_GCC=g++ Target: aarch64-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,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix -Supported LTO compression algorithms: zlib zstd +Supported LTO compression algorithms: zlibg++ -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 + 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' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 remove_reads_from_amplicon.cpp -quiet -dumpbase remove_reads_from_amplicon.cpp -mlittle-endian -mabi=lp64 -auxbase-strip remove_reads_from_amplicon.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccnWoGPp.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' 'trim_primer_quality.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 trim_primer_quality.cpp -quiet -dumpbase trim_primer_quality.cpp -mlittle-endian -mabi=lp64 -auxbase-strip trim_primer_quality.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc17Zkpm.s Using built-in specs. COLLECT_GCC=g++ Target: aarch64-linux-gnu @@ -598,65 +668,45 @@ 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' 'call_consensus_pileup.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2Using built-in specs. - call_consensus_pileup.cpp -quiet -dumpbase call_consensus_pileup.cpp -mlittle-endian -mabi=lp64 -auxbase-strip call_consensus_pileup.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccjsSIJ7.s -COLLECT_GCC=g++ -Target: aarch64-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,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex -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' 'call_variants.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_variants.cpp -quiet -dumpbase call_variants.cpp -mlittle-endian -mabi=lp64 -auxbase-strip call_variants.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccPA6ZMw.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' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 remove_reads_from_amplicon.cpp -quiet -dumpbase remove_reads_from_amplicon.cpp -mlittle-endian -mabi=lp64 -auxbase-strip remove_reads_from_amplicon.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccpwifxB.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-linux-gnu) - compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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 ignoring duplicate directory "/usr/include/aarch64-linux-gnu/c++/10" -ignoring duplicate directory "/usr/include/aarch64-linux-gnu/c++/10" -ignoring nonexistent directory "/usr/local/include/aarch64-linux-gnu" ignoring nonexistent directory "/usr/local/include/aarch64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/10/include-fixed" -ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/10/../../../../aarch64-linux-gnu/include" -ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/10/../../../../aarch64-linux-gnu/include" -#include "..." search starts here: #include "..." search starts here: #include <...> search starts here: -#include <...> search starts here: . - . - .. .. /usr/include/c++/10 - /usr/include/c++/10 /usr/include/aarch64-linux-gnu/c++/10 - /usr/include/aarch64-linux-gnu/c++/10 - /usr/include/c++/10/backward /usr/include/c++/10/backward /usr/lib/gcc/aarch64-linux-gnu/10/include - /usr/lib/gcc/aarch64-linux-gnu/10/include /usr/local/include - /usr/local/include - /usr/include/aarch64-linux-gnu /usr/include/aarch64-linux-gnu /usr/include - /usr/include -End of search list. End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-linux-gnu) - compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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 +GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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 +GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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/aarch64-linux-gnu/c++/10" +ignoring nonexistent directory "/usr/local/include/aarch64-linux-gnu" +ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/10/include-fixed" +ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/10/../../../../aarch64-linux-gnu/include" +#include "..." search starts here: GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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 @@ -705,14 +755,25 @@ 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 -GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-linux-gnu) - compiled by GNU C version 10.2.1 20210110, Compiler executable checksum: 7ff9b3e77ba341f92c3fc11acba5d5f9 -Compiler executable checksum: 7ff9b3e77ba341f92c3fc11acba5d5f9 -GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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: 7ff9b3e77ba341f92c3fc11acba5d5f9 +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 +Using built-in specs. +COLLECT_GCC=g++ +Target: aarch64-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,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex +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' 'call_variants.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_variants.cpp -quiet -dumpbase call_variants.cpp -mlittle-endian -mabi=lp64 -auxbase-strip call_variants.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccE0xqYM.s +Using built-in specs. +COLLECT_GCC=g++ +Target: aarch64-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,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex +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' 'primer_bed.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 primer_bed.cpp -quiet -dumpbase primer_bed.cpp -mlittle-endian -mabi=lp64 -auxbase-strip primer_bed.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccSi1k2X.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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 @@ -737,15 +798,10 @@ 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 -Using built-in specs. -COLLECT_GCC=g++ -Target: aarch64-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,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=aarch64-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-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex -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' 'primer_bed.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 primer_bed.cpp -quiet -dumpbase primer_bed.cpp -mlittle-endian -mabi=lp64 -auxbase-strip primer_bed.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccWAZP7F.s +GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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/aarch64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/aarch64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/10/include-fixed" @@ -766,9 +822,22 @@ 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 -GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP +#include <...> search starts here: + . + .. + /usr/include/c++/10 + /usr/include/aarch64-linux-gnu/c++/10 + /usr/include/c++/10/backward + /usr/lib/gcc/aarch64-linux-gnu/10/include + /usr/local/include + /usr/include/aarch64-linux-gnu + /usr/include +End of search list. +GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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: 7ff9b3e77ba341f92c3fc11acba5d5f9 ignoring duplicate directory "/usr/include/aarch64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/aarch64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/10/include-fixed" @@ -789,10 +858,7 @@ 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 -GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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: 7ff9b3e77ba341f92c3fc11acba5d5f9 ignoring duplicate directory "/usr/include/aarch64-linux-gnu/c++/10" ignoring nonexistent directory "/usr/local/include/aarch64-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/10/include-fixed" @@ -814,20 +880,25 @@ GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 7ff9b3e77ba341f92c3fc11acba5d5f9 +GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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: 7ff9b3e77ba341f92c3fc11acba5d5f9 +Compiler executable checksum: 7ff9b3e77ba341f92c3fc11acba5Compiler executable checksum: d5f97f +f9b3e77ba341f92c3fc11acba5d5f9 Compiler executable checksum: 7ff9b3e77ba341f92c3fc11acba5d5f9 Compiler executable checksum: 7ff9b3e77ba341f92c3fc11acba5d5f9 -Compiler executable checksum: 7ff9b3e77ba341f92c3fc11acba5d5f9 -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' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. -EL -mabi=lp64 -o alignment.o /tmp/ccZfJ1cf.s -GNU assembler version 2.35.2 (aarch64-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' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. -EL -mabi=lp64 -o remove_reads_from_amplicon.o /tmp/ccnWoGPp.s + as -v -I . -I .. -EL -mabi=lp64 -o remove_reads_from_amplicon.o /tmp/ccpwifxB.s +GNU assembler version 2.35.2 (aarch64-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' 'alignment.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + as -v -I . -I .. -EL -mabi=lp64 -o alignment.o /tmp/ccMi5Za8.s GNU assembler version 2.35.2 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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' '-mlittle-endian' '-mabi=lp64' +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' '-mlittle-endian' '-mabi=lp64' 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++ @@ -837,9 +908,14 @@ 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' 'allele_functions.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 allele_functions.cpp -quiet -dumpbase allele_functions.cpp -mlittle-endian -mabi=lp64 -auxbase-strip allele_functions.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccz21dkr.s + /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 allele_functions.cpp -quiet -dumpbase allele_functions.cpp -mlittle-endian -mabi=lp64 -auxbase-strip allele_functions.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccZ88BUT.s +MAKEFLAGS=w -j8 +COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ +LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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' '-mlittle-endian' '-mabi=lp64' GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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 + compiled by GNU C version 10.2.1 20210110, 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 +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/aarch64-linux-gnu/c++/10" @@ -862,11 +938,6 @@ 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 -MAKEFLAGS=w -j8 -COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ -LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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' '-mlittle-endian' '-mabi=lp64' -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. COLLECT_GCC=g++ Target: aarch64-linux-gnu @@ -875,7 +946,7 @@ 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_masked_amplicons.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_masked_amplicons.cpp -quiet -dumpbase get_masked_amplicons.cpp -mlittle-endian -mabi=lp64 -auxbase-strip get_masked_amplicons.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccgHcYdE.s + /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_masked_amplicons.cpp -quiet -dumpbase get_masked_amplicons.cpp -mlittle-endian -mabi=lp64 -auxbase-strip get_masked_amplicons.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc4PkLna.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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 @@ -902,14 +973,17 @@ GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 7ff9b3e77ba341f92c3fc11acba5d5f9 Compiler executable checksum: 7ff9b3e77ba341f92c3fc11acba5d5f9 -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' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. -EL -mabi=lp64 -o primer_bed.o /tmp/ccWAZP7F.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' 'trim_primer_quality.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + as -v -I . -I .. -EL -mabi=lp64 -o trim_primer_quality.o /tmp/cc17Zkpm.s GNU assembler version 2.35.2 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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' 'primer_bed.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' +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' '-mlittle-endian' '-mabi=lp64' 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 +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' '-mlittle-endian' '-mabi=lp64' + as -v -I . -I .. -EL -mabi=lp64 -o suffix_tree.o /tmp/ccry342c.s +GNU assembler version 2.35.2 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 Using built-in specs. COLLECT_GCC=g++ Target: aarch64-linux-gnu @@ -918,7 +992,7 @@ 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' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_common_variants.cpp -quiet -dumpbase get_common_variants.cpp -mlittle-endian -mabi=lp64 -auxbase-strip get_common_variants.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccddo1UZ.s + /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_common_variants.cpp -quiet -dumpbase get_common_variants.cpp -mlittle-endian -mabi=lp64 -auxbase-strip get_common_variants.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc3qAhqU.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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 @@ -943,17 +1017,11 @@ 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' 'trim_primer_quality.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. -EL -mabi=lp64 -o trim_primer_quality.o /tmp/cc7lx9ql.s -GNU assembler version 2.35.2 (aarch64-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' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. -EL -mabi=lp64 -o suffix_tree.o /tmp/cc4fumBg.s Compiler executable checksum: 7ff9b3e77ba341f92c3fc11acba5d5f9 -GNU assembler version 2.35.2 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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' 'trim_primer_quality.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' +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' '-mlittle-endian' '-mabi=lp64' 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 Using built-in specs. COLLECT_GCC=g++ @@ -963,12 +1031,7 @@ 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' 'parse_gff.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 parse_gff.cpp -quiet -dumpbase parse_gff.cpp -mlittle-endian -mabi=lp64 -auxbase-strip parse_gff.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccIuU3JO.s -MAKEFLAGS=w -j8 -COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ -LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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' '-mlittle-endian' '-mabi=lp64' -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 + /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 parse_gff.cpp -quiet -dumpbase parse_gff.cpp -mlittle-endian -mabi=lp64 -auxbase-strip parse_gff.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cciDquFj.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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 @@ -993,6 +1056,15 @@ 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: 7ff9b3e77ba341f92c3fc11acba5d5f9 +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' '-mlittle-endian' '-mabi=lp64' + as -v -I . -I .. -EL -mabi=lp64 -o call_consensus_pileup.o /tmp/ccKDOPD4.s +GNU assembler version 2.35.2 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 +MAKEFLAGS=w -j8 +COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ +LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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' '-mlittle-endian' '-mabi=lp64' +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: aarch64-linux-gnu @@ -1001,7 +1073,7 @@ 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' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ref_seq.cpp -quiet -dumpbase ref_seq.cpp -mlittle-endian -mabi=lp64 -auxbase-strip ref_seq.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccx6p9IY.s + /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ref_seq.cpp -quiet -dumpbase ref_seq.cpp -mlittle-endian -mabi=lp64 -auxbase-strip ref_seq.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccczMkiO.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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 @@ -1026,15 +1098,14 @@ 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: 7ff9b3e77ba341f92c3fc11acba5d5f9 -Compiler executable checksum: 7ff9b3e77ba341f92c3fc11acba5d5f9 -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' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. -EL -mabi=lp64 -o call_variants.o /tmp/ccPA6ZMw.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' 'ivar.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + as -v -I . -I .. -EL -mabi=lp64 -o ivar.o /tmp/ccWJlKuZ.s GNU assembler version 2.35.2 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 +Compiler executable checksum: 7ff9b3e77ba341f92c3fc11acba5d5f9 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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' '-mlittle-endian' '-mabi=lp64' +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' '-mlittle-endian' '-mabi=lp64' 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 Using built-in specs. COLLECT_GCC=g++ @@ -1044,7 +1115,7 @@ 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' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 interval_tree.cpp -quiet -dumpbase interval_tree.cpp -mlittle-endian -mabi=lp64 -auxbase-strip interval_tree.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc0bULWN.s + /usr/lib/gcc/aarch64-linux-gnu/10/cc1plus -quiet -v -I . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 interval_tree.cpp -quiet -dumpbase interval_tree.cpp -mlittle-endian -mabi=lp64 -auxbase-strip interval_tree.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/cc0PpEBY.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (aarch64-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 @@ -1070,57 +1141,57 @@ GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 7ff9b3e77ba341f92c3fc11acba5d5f9 -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' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. -EL -mabi=lp64 -o ivar.o /tmp/cccCnfd1.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' 'get_masked_amplicons.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + as -v -I . -I .. -EL -mabi=lp64 -o get_masked_amplicons.o /tmp/cc4PkLna.s GNU assembler version 2.35.2 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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' '-mlittle-endian' '-mabi=lp64' -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' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. -EL -mabi=lp64 -o call_consensus_pileup.o /tmp/ccjsSIJ7.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' 'get_masked_amplicons.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' +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' '-mlittle-endian' '-mabi=lp64' + as -v -I . -I .. -EL -mabi=lp64 -o primer_bed.o /tmp/ccSi1k2X.s GNU assembler version 2.35.2 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 -MAKEFLAGS=w -j8 -COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ -LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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' '-mlittle-endian' '-mabi=lp64' -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' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. -EL -mabi=lp64 -o allele_functions.o /tmp/ccz21dkr.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' '-mlittle-endian' '-mabi=lp64' + as -v -I . -I .. -EL -mabi=lp64 -o call_variants.o /tmp/ccE0xqYM.s GNU assembler version 2.35.2 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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' 'allele_functions.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' -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' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. -EL -mabi=lp64 -o get_masked_amplicons.o /tmp/ccgHcYdE.s -GNU assembler version 2.35.2 (aarch64-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' 'primer_bed.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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' '-mlittle-endian' '-mabi=lp64' +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' '-mlittle-endian' '-mabi=lp64' 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' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. -EL -mabi=lp64 -o get_common_variants.o /tmp/ccddo1UZ.s + as -v -I . -I .. -EL -mabi=lp64 -o get_common_variants.o /tmp/cc3qAhqU.s GNU assembler version 2.35.2 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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_common_variants.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' +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' '-mlittle-endian' '-mabi=lp64' + as -v -I . -I .. -EL -mabi=lp64 -o allele_functions.o /tmp/ccZ88BUT.s +GNU assembler version 2.35.2 (aarch64-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' 'interval_tree.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. -EL -mabi=lp64 -o interval_tree.o /tmp/cc0bULWN.s + as -v -I . -I .. -EL -mabi=lp64 -o interval_tree.o /tmp/cc0PpEBY.s GNU assembler version 2.35.2 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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' 'allele_functions.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' +MAKEFLAGS=w -j8 +COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ +LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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' 'interval_tree.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' 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' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. -EL -mabi=lp64 -o ref_seq.o /tmp/ccx6p9IY.s + as -v -I . -I .. -EL -mabi=lp64 -o ref_seq.o /tmp/ccczMkiO.s GNU assembler version 2.35.2 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-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' 'ref_seq.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' 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' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. -EL -mabi=lp64 -o parse_gff.o /tmp/ccIuU3JO.s + as -v -I . -I .. -EL -mabi=lp64 -o parse_gff.o /tmp/cciDquFj.s GNU assembler version 2.35.2 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ @@ -1139,30 +1210,30 @@ COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/collect2 -plugin /usr/lib/gcc/aarch64-linux-gnu/10/liblto_plugin.so -plugin-opt=/usr/lib/gcc/aarch64-linux-gnu/10/lto-wrapper -plugin-opt=-fresolution=/tmp/ccLNdAYX.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 --hash-style=gnu --as-needed -dynamic-linker /lib/ld-linux-aarch64.so.1 -X -EL -maarch64linux --fix-cortex-a53-843419 -pie -o ivar /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/Scrt1.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/crtbeginS.o -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-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/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crtn.o + /usr/lib/gcc/aarch64-linux-gnu/10/collect2 -plugin /usr/lib/gcc/aarch64-linux-gnu/10/liblto_plugin.so -plugin-opt=/usr/lib/gcc/aarch64-linux-gnu/10/lto-wrapper -plugin-opt=-fresolution=/tmp/cce5xJn4.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 --hash-style=gnu --as-needed -dynamic-linker /lib/ld-linux-aarch64.so.1 -X -EL -maarch64linux --fix-cortex-a53-843419 -pie -o ivar /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/Scrt1.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/crtbeginS.o -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-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/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' -make[3]: Leaving directory '/build/ivar-1.3+dfsg/src' +make[3]: Map '/build/ivar-1.3+dfsg/src' wordt verlaten 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]: Map '/build/ivar-1.3+dfsg/tests' wordt binnengegaan +make[3]: Er hoeft niets gedaan te worden voor 'all'. +make[3]: Map '/build/ivar-1.3+dfsg/tests' wordt verlaten +make[3]: Map '/build/ivar-1.3+dfsg' wordt binnengegaan +make[3]: Map '/build/ivar-1.3+dfsg' wordt verlaten +make[2]: Map '/build/ivar-1.3+dfsg' wordt verlaten +make[1]: Map '/build/ivar-1.3+dfsg' wordt verlaten debian/rules override_dh_auto_test -make[1]: Entering directory '/build/ivar-1.3+dfsg' +make[1]: Map '/build/ivar-1.3+dfsg' wordt binnengegaan dh_auto_test --no-parallel make -j1 check VERBOSE=1 -make[2]: Entering directory '/build/ivar-1.3+dfsg' +make[2]: Map '/build/ivar-1.3+dfsg' wordt binnengegaan 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]: Map '/build/ivar-1.3+dfsg/src' wordt binnengegaan +make[3]: Er hoeft niets gedaan te worden voor 'check'. +make[3]: Map '/build/ivar-1.3+dfsg/src' wordt verlaten Making check in tests -make[3]: Entering directory '/build/ivar-1.3+dfsg/tests' +make[3]: Map '/build/ivar-1.3+dfsg/tests' wordt binnengegaan 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]: Map '/build/ivar-1.3+dfsg/tests' wordt binnengegaan 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 @@ -1210,10 +1281,10 @@ 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]: Map '/build/ivar-1.3+dfsg/tests' wordt verlaten 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]: Map '/build/ivar-1.3+dfsg/tests' wordt binnengegaan +make[5]: Map '/build/ivar-1.3+dfsg/tests' wordt binnengegaan PASS: check_primer_trim PASS: check_trim PASS: check_quality_trim @@ -1243,20 +1314,20 @@ # 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]: Map '/build/ivar-1.3+dfsg/tests' wordt verlaten +make[4]: Map '/build/ivar-1.3+dfsg/tests' wordt verlaten +make[3]: Map '/build/ivar-1.3+dfsg/tests' wordt verlaten +make[3]: Map '/build/ivar-1.3+dfsg' wordt binnengegaan +make[3]: Map '/build/ivar-1.3+dfsg' wordt verlaten +make[2]: Map '/build/ivar-1.3+dfsg' wordt verlaten +make[1]: Map '/build/ivar-1.3+dfsg' wordt verlaten create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j8 install DESTDIR=/build/ivar-1.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no -make[1]: Entering directory '/build/ivar-1.3+dfsg' +make[1]: Map '/build/ivar-1.3+dfsg' wordt binnengegaan Making install in src -make[2]: Entering directory '/build/ivar-1.3+dfsg/src' +make[2]: Map '/build/ivar-1.3+dfsg/src' wordt binnengegaan 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++ @@ -1270,28 +1341,28 @@ COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/10/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-linux-gnu/10/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/10/collect2 -plugin /usr/lib/gcc/aarch64-linux-gnu/10/liblto_plugin.so -plugin-opt=/usr/lib/gcc/aarch64-linux-gnu/10/lto-wrapper -plugin-opt=-fresolution=/tmp/ccCUQ6LT.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 --hash-style=gnu --as-needed -dynamic-linker /lib/ld-linux-aarch64.so.1 -X -EL -maarch64linux --fix-cortex-a53-843419 -pie -o ivar /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/Scrt1.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/crtbeginS.o -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-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/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crtn.o + /usr/lib/gcc/aarch64-linux-gnu/10/collect2 -plugin /usr/lib/gcc/aarch64-linux-gnu/10/liblto_plugin.so -plugin-opt=/usr/lib/gcc/aarch64-linux-gnu/10/lto-wrapper -plugin-opt=-fresolution=/tmp/cc9izt79.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 --hash-style=gnu --as-needed -dynamic-linker /lib/ld-linux-aarch64.so.1 -X -EL -maarch64linux --fix-cortex-a53-843419 -pie -o ivar /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/Scrt1.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/crtbeginS.o -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-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/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' -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]: Map '/build/ivar-1.3+dfsg/src' wordt binnengegaan +make[3]: Er hoeft niets gedaan te worden voor 'install-data-am'. + /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]: Map '/build/ivar-1.3+dfsg/src' wordt verlaten +make[2]: Map '/build/ivar-1.3+dfsg/src' wordt verlaten 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]: Map '/build/ivar-1.3+dfsg/tests' wordt binnengegaan +make[3]: Map '/build/ivar-1.3+dfsg/tests' wordt binnengegaan +make[3]: Er hoeft niets gedaan te worden voor 'install-exec-am'. +make[3]: Er hoeft niets gedaan te worden voor 'install-data-am'. +make[3]: Map '/build/ivar-1.3+dfsg/tests' wordt verlaten +make[2]: Map '/build/ivar-1.3+dfsg/tests' wordt verlaten +make[2]: Map '/build/ivar-1.3+dfsg' wordt binnengegaan +make[3]: Map '/build/ivar-1.3+dfsg' wordt binnengegaan +make[3]: Er hoeft niets gedaan te worden voor 'install-exec-am'. +make[3]: Er hoeft niets gedaan te worden voor 'install-data-am'. +make[3]: Map '/build/ivar-1.3+dfsg' wordt verlaten +make[2]: Map '/build/ivar-1.3+dfsg' wordt verlaten +make[1]: Map '/build/ivar-1.3+dfsg' wordt verlaten dh_install dh_installdocs dh_installchangelogs @@ -1311,9 +1382,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'ivar' in '../ivar_1.3+dfsg-1_arm64.deb'. -dpkg-deb: building package 'ivar-dbgsym' in '../ivar-dbgsym_1.3+dfsg-1_arm64.deb'. -dpkg-deb: building package 'ivar-doc' in '../ivar-doc_1.3+dfsg-1_all.deb'. +dpkg-deb: pakket 'ivar' wordt gebouwd in '../ivar_1.3+dfsg-1_arm64.deb'. +dpkg-deb: pakket 'ivar-dbgsym' wordt gebouwd in '../ivar-dbgsym_1.3+dfsg-1_arm64.deb'. +dpkg-deb: pakket 'ivar-doc' wordt gebouwd in '../ivar-doc_1.3+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../ivar_1.3+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1321,12 +1392,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/28980/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/28980/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/22028 and its subdirectories -I: Current time: Sun Sep 18 19:13:01 -12 2022 -I: pbuilder-time-stamp: 1663571581 +I: removing directory /srv/workspace/pbuilder/28980 and its subdirectories +I: Current time: Tue Aug 17 14:52:03 +14 2021 +I: pbuilder-time-stamp: 1629161523