Diff of the two buildlogs: -- --- b1/build.log 2023-05-08 19:19:38.397408450 +0000 +++ b2/build.log 2023-05-08 19:23:03.452411174 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 8 07:14:39 -12 2023 -I: pbuilder-time-stamp: 1683573279 +I: Current time: Mon Jun 10 15:42:42 +14 2024 +I: pbuilder-time-stamp: 1717983762 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./ivar_1.3.1+dfsg.orig.tar.xz] I: copying [./ivar_1.3.1+dfsg-7.debian.tar.xz] I: Extracting source -gpgv: Signature made Wed Oct 5 21:19:35 2022 -12 +gpgv: Signature made Thu Oct 6 23:19:35 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -33,52 +33,84 @@ dpkg-source: info: applying gcc-12.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/7688/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/17545/tmp/hooks/D01_modify_environment starting +debug: Running on codethink9-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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 10 15:42 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/17545/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/17545/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:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + 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='7688' - 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=17545 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.7dkub3If/pbuilderrc_8gqZ --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.7dkub3If/b1 --logfile b1/build.log ivar_1.3.1+dfsg-7.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/r-b-build.7dkub3If/pbuilderrc_DV9b --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.7dkub3If/b2 --logfile b2/build.log --extrapackages usrmerge ivar_1.3.1+dfsg-7.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 codethink16-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 7 22:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/7688/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 8 06:49 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/17545/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -163,7 +195,7 @@ Get: 45 http://deb.debian.org/debian bookworm/main arm64 liblzma-dev arm64 5.4.1-0.2 [255 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libhts-dev arm64 1.16+ds-3 [1525 kB] -Fetched 23.3 MB in 1s (21.5 MB/s) +Fetched 23.3 MB in 1s (43.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19616 files and directories currently installed.) @@ -365,8 +397,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/ivar-1.3.1+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_1.3.1+dfsg-7_source.changes +I: user script /srv/workspace/pbuilder/17545/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/17545/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/ivar-1.3.1+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_1.3.1+dfsg-7_source.changes dpkg-buildpackage: info: source package ivar dpkg-buildpackage: info: source version 1.3.1+dfsg-7 dpkg-buildpackage: info: source distribution unstable @@ -376,9 +417,9 @@ debian/rules clean dh clean debian/rules override_dh_auto_clean -make[1]: Entering directory '/build/ivar-1.3.1+dfsg' +make[1]: Map '/build/ivar-1.3.1+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-1.3.1+dfsg' +make[1]: Map '/build/ivar-1.3.1+dfsg' wordt verlaten dh_clean debian/rules binary dh binary @@ -455,24 +496,26 @@ config.status: executing depfiles commands dh_auto_build make -j8 -make[1]: Entering directory '/build/ivar-1.3.1+dfsg' +make[1]: Map '/build/ivar-1.3.1+dfsg' wordt binnengegaan make all-recursive -make[2]: Entering directory '/build/ivar-1.3.1+dfsg' +make[2]: Map '/build/ivar-1.3.1+dfsg' wordt binnengegaan Making all in src -make[3]: Entering directory '/build/ivar-1.3.1+dfsg/src' +make[3]: Map '/build/ivar-1.3.1+dfsg/src' wordt binnengegaan g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o alignment.o alignment.cpp Using built-in specs. +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp COLLECT_GCC=g++ +Using built-in specs. Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --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-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 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccFknrEa.s -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o alignment.o alignment.cpp -Using built-in specs. + /usr/lib/gcc/aarch64-linux-gnu/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -versiong++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp + -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccixKXU2.s COLLECT_GCC=g++ Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --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-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 @@ -480,36 +523,18 @@ Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp - /usr/lib/gcc/aarch64-linux-gnu/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/cc8l8hHt.s -GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) - compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP + /usr/lib/gcc/aarch64-linux-gnu/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccFbJWJT.sUsing built-in specs. -warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -ignoring duplicate directory "/usr/include/aarch64-linux-gnu/c++/12" -ignoring nonexistent directory "/usr/local/include/aarch64-linux-gnu" -ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/12/include-fixed" -ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/12/../../../../aarch64-linux-gnu/include" -#include "..." search starts here: -#include <...> search starts here: - . - .. - /usr/include/c++/12 - /usr/include/aarch64-linux-gnu/c++/12 - /usr/include/c++/12/backward - /usr/lib/gcc/aarch64-linux-gnu/12/include - /usr/local/include - /usr/include/aarch64-linux-gnu - /usr/include -End of search list. -GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) - compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP - -warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp -Using built-in specs. +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp +COLLECT_GCC=g++ +Target: aarch64-linux-gnu +Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --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-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 +Thread model: posix +Supported LTO compression algorithms: zlib zstd +gcc version 12.2.0 (Debian 12.2.0-14) +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + /usr/lib/gcc/aarch64-linux-gnu/12/cc1plus -quiet -v -IUsing built-in specs. + . -I .. -imultiarch aarch64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 alignment.cpp -quiet -dumpbase alignment.cpp -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccpFGy6F.s COLLECT_GCC=g++ Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --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-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 @@ -517,52 +542,94 @@ Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/cciyW84g.s + /usr/lib/gcc/aarch64-linux-gnu/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/cczDsACI.s +Using built-in specs. +COLLECT_GCC=g++ +Target: aarch64-linux-gnu +Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --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-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 +Thread model: posix +Supported LTO compression algorithms: zlib zstd +gcc version 12.2.0 (Debian 12.2.0-14) +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccmT66eb.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) + compiled by GNU C version 12.2.0, GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) + compiled by GNU C version 12.2.0, GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP +GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP + +GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP + +warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. +warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 +GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 +GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 +ignoring duplicate directory "/usr/include/aarch64-linux-gnu/c++/12" ignoring duplicate directory "/usr/include/aarch64-linux-gnu/c++/12" +ignoring duplicate directory "/usr/include/aarch64-linux-gnu/c++/12" +ignoring nonexistent directory "/usr/local/include/aarch64-linux-gnu" +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/12/include-fixed" +ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/12/include-fixed" +ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/12/include-fixed" +ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/12/../../../../aarch64-linux-gnu/include" +ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/12/../../../../aarch64-linux-gnu/include" ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/12/../../../../aarch64-linux-gnu/include" -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp #include "..." search starts here: +#include "..." search starts here: +#include <...> search starts here: #include <...> search starts here: . + . +#include "..." search starts here: + .. .. /usr/include/c++/12 + /usr/include/c++/12 +#include <...> search starts here: + /usr/include/aarch64-linux-gnu/c++/12 /usr/include/aarch64-linux-gnu/c++/12 + . + /usr/include/c++/12/backward /usr/include/c++/12/backward + .. /usr/lib/gcc/aarch64-linux-gnu/12/include + /usr/lib/gcc/aarch64-linux-gnu/12/include + /usr/include/c++/12 /usr/local/include + /usr/local/include + /usr/include/aarch64-linux-gnu/c++/12 + /usr/include/aarch64-linux-gnu + /usr/include/aarch64-linux-gnu + /usr/include + /usr/include/c++/12/backward + /usr/include + /usr/lib/gcc/aarch64-linux-gnu/12/include +End of search list. + /usr/local/include +End of search list. /usr/include/aarch64-linux-gnu /usr/include End of search list. GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) + compiled by GNU C version 12.2.0, GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) + compiled by GNU C version 12.2.0, GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP +GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP + +GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP + +warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. +warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 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 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --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-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 -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - /usr/lib/gcc/aarch64-linux-gnu/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccvbxSd6.s -Using built-in specs. -COLLECT_GCC=g++ -Target: aarch64-linux-gnu -Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --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-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 -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccdci0K7.s +GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 +GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP @@ -589,12 +656,9 @@ warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP -Using built-in specs. warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/aarch64-linux-gnu/c++/12" @@ -613,19 +677,12 @@ /usr/include/aarch64-linux-gnu /usr/include End of search list. -COLLECT_GCC=g++ -Target: aarch64-linux-gnu -Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --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-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 -Thread model: posix -Supported LTO compression algorithms: zlib zstd -gcc version 12.2.0 (Debian 12.2.0-14) GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 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' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccw36Ghy.s +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp Using built-in specs. COLLECT_GCC=g++ Target: aarch64-linux-gnu @@ -633,8 +690,13 @@ Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccN1niAj.s +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccEuj794.s +Compiler executable checksum: Compiler executable checksum: 7676d6d6f1f142427373b9b9515157578383c5c503037474b1b10909b3b35252 + +Compiler executable checksum: 76d6f14273b9515783c50374b109b352 +Compiler executable checksum: 76d6f14273b9515783c50374b109b352 +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 @@ -642,8 +704,9 @@ Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/cc0U96Ln.s +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccKBxoP6.s +Compiler executable checksum: 76d6f14273b9515783c50374b109b352 GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP @@ -665,6 +728,15 @@ /usr/include/aarch64-linux-gnu /usr/include End of search list. +Using built-in specs. +COLLECT_GCC=g++ +Target: aarch64-linux-gnu +Configured with: ../src/configure -v --with-pkgversion='Debian 12.2.0-14' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --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-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 +Thread model: posix +Supported LTO compression algorithms: zlib zstd +gcc version 12.2.0 (Debian 12.2.0-14) +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccJ8pcH4.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP @@ -696,12 +768,6 @@ warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -Compiler executable checksum: 76d6f14273b9515783c50374b109b352 -GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) - compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP - -warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP @@ -729,35 +795,10 @@ warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 76d6f14273b9515783c50374b109b352 -ignoring duplicate directory "/usr/include/aarch64-linux-gnu/c++/12" -ignoring nonexistent directory "/usr/local/include/aarch64-linux-gnu" -ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/12/include-fixed" -ignoring nonexistent directory "/usr/lib/gcc/aarch64-linux-gnu/12/../../../../aarch64-linux-gnu/include" -#include "..." search starts here: -#include <...> search starts here: - . - .. - /usr/include/c++/12 - /usr/include/aarch64-linux-gnu/c++/12 - /usr/include/c++/12/backward - /usr/lib/gcc/aarch64-linux-gnu/12/include - /usr/local/include - /usr/include/aarch64-linux-gnu - /usr/include -End of search list. -GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) - compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP - -warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. -GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 -Compiler executable checksum: 76d6f14273b9515783c50374b109b352 -Compiler executable checksum: 76d6f14273b9515783c50374b109b352 -Compiler executable checksum: 76d6f14273b9515783c50374b109b352 -Compiler executable checksum: 76d6f14273b9515783c50374b109b352 Compiler executable checksum: 76d6f14273b9515783c50374b109b352 Compiler executable checksum: 76d6f14273b9515783c50374b109b352 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o alignment.o /tmp/ccvbxSd6.s + as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o alignment.o /tmp/ccpFGy6F.s GNU assembler version 2.40 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/ @@ -772,7 +813,7 @@ Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccmI4cHF.s + /usr/lib/gcc/aarch64-linux-gnu/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccpvC6pI.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP @@ -801,7 +842,7 @@ GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 76d6f14273b9515783c50374b109b352 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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 .. --gdwarf-5 -EL -mabi=lp64 -o remove_reads_from_amplicon.o /tmp/ccw36Ghy.s + as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o remove_reads_from_amplicon.o /tmp/ccEuj794.s GNU assembler version 2.40 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/ @@ -816,7 +857,7 @@ Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccA5TIuU.s + /usr/lib/gcc/aarch64-linux-gnu/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccBDp9ZZ.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP @@ -845,7 +886,7 @@ GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 76d6f14273b9515783c50374b109b352 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o call_variants.o /tmp/ccN1niAj.s + as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o call_variants.o /tmp/ccKBxoP6.s GNU assembler version 2.40 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/ @@ -860,7 +901,7 @@ Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccYm4SHr.s + /usr/lib/gcc/aarch64-linux-gnu/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccLw597v.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP @@ -888,13 +929,13 @@ warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 76d6f14273b9515783c50374b109b352 -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o ivar.o /tmp/ccFknrEa.s +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o suffix_tree.o /tmp/cczDsACI.s GNU assembler version 2.40 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../:/lib/:/usr/lib/ -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'ivar.' +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'suffix_tree.' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp Using built-in specs. COLLECT_GCC=g++ @@ -904,7 +945,7 @@ Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccAZhU6y.s + /usr/lib/gcc/aarch64-linux-gnu/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccTqwLfR.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP @@ -932,19 +973,16 @@ warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 76d6f14273b9515783c50374b109b352 -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o call_consensus_pileup.o /tmp/cc8l8hHt.s -GNU assembler version 2.40 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o suffix_tree.o /tmp/cciyW84g.s +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o primer_bed.o /tmp/ccJ8pcH4.s GNU assembler version 2.40 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o allele_functions.o /tmp/ccmI4cHF.s +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o ivar.o /tmp/ccixKXU2.s GNU assembler version 2.40 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../:/lib/:/usr/lib/ -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'call_consensus_pileup.' +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'ivar.' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o ref_seq.o ref_seq.cpp Using built-in specs. COLLECT_GCC=g++ @@ -954,7 +992,7 @@ Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/cccX528H.s + /usr/lib/gcc/aarch64-linux-gnu/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccqBYfJR.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP @@ -982,10 +1020,13 @@ warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 76d6f14273b9515783c50374b109b352 +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o call_consensus_pileup.o /tmp/ccFbJWJT.s +GNU assembler version 2.40 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../:/lib/:/usr/lib/ -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'suffix_tree.' +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'primer_bed.' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o interval_tree.o interval_tree.cpp Using built-in specs. COLLECT_GCC=g++ @@ -995,7 +1036,7 @@ Supported LTO compression algorithms: zlib zstd gcc version 12.2.0 (Debian 12.2.0-14) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-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/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/ccV7ZUwW.s + /usr/lib/gcc/aarch64-linux-gnu/12/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 -dumpbase-ext .cpp -mlittle-endian -mabi=lp64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -fasynchronous-unwind-tables -o /tmp/cc0sMyjX.s GNU C++11 (Debian 12.2.0-14) version 12.2.0 (aarch64-linux-gnu) compiled by GNU C version 12.2.0, GMP version 6.2.1, MPFR version 4.1.1-p1, MPC version 1.3.1, isl version isl-0.25-GMP @@ -1022,19 +1063,23 @@ warning: MPFR header version 4.1.1-p1 differs from library version 4.2.0. 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' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o allele_functions.o /tmp/ccpvC6pI.s +GNU assembler version 2.40 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 +Compiler executable checksum: 76d6f14273b9515783c50374b109b352 +MAKEFLAGS=w -j8 +COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/ +LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../:/lib/:/usr/lib/ +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'call_consensus_pileup.' MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'allele_functions.' -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o primer_bed.o /tmp/cc0U96Ln.s +COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' + as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o get_masked_amplicons.o /tmp/ccBDp9ZZ.s GNU assembler version 2.40 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 -Compiler executable checksum: 76d6f14273b9515783c50374b109b352 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' 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'-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o get_masked_amplicons.o /tmp/ccA5TIuU.s + as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o trim_primer_quality.o /tmp/ccmT66eb.s GNU assembler version 2.40 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/ @@ -1044,33 +1089,29 @@ COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'trim_primer_quality.' -MAKEFLAGS=w -j8 -COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/ -LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../:/lib/:/usr/lib/ -COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'primer_bed.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o interval_tree.o /tmp/ccV7ZUwW.s + as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o interval_tree.o /tmp/cc0sMyjX.s GNU assembler version 2.40 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'interval_tree.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' 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'-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'get_common_variants.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' 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'-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'ref_seq.' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' - as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o parse_gff.o /tmp/ccAZhU6y.s + as -v -I . -I .. --gdwarf-5 -EL -mabi=lp64 -o parse_gff.o /tmp/ccTqwLfR.s GNU assembler version 2.40 (aarch64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40 MAKEFLAGS=w -j8 COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/ @@ -1089,30 +1130,30 @@ COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'ivar.' - /usr/lib/gcc/aarch64-linux-gnu/12/collect2 -plugin /usr/lib/gcc/aarch64-linux-gnu/12/liblto_plugin.so -plugin-opt=/usr/lib/gcc/aarch64-linux-gnu/12/lto-wrapper -plugin-opt=-fresolution=/tmp/cc84Vqty.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/12/../../../aarch64-linux-gnu/Scrt1.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/crtbeginS.o -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../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/12/../../.. -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/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crtn.o + /usr/lib/gcc/aarch64-linux-gnu/12/collect2 -plugin /usr/lib/gcc/aarch64-linux-gnu/12/liblto_plugin.so -plugin-opt=/usr/lib/gcc/aarch64-linux-gnu/12/lto-wrapper -plugin-opt=-fresolution=/tmp/ccEOcp1Y.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/12/../../../aarch64-linux-gnu/Scrt1.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/crtbeginS.o -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../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/12/../../.. -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/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'ivar.' -make[3]: Leaving directory '/build/ivar-1.3.1+dfsg/src' +make[3]: Map '/build/ivar-1.3.1+dfsg/src' wordt verlaten Making all in tests -make[3]: Entering directory '/build/ivar-1.3.1+dfsg/tests' -make[3]: Nothing to be done for 'all'. -make[3]: Leaving directory '/build/ivar-1.3.1+dfsg/tests' -make[3]: Entering directory '/build/ivar-1.3.1+dfsg' -make[3]: Leaving directory '/build/ivar-1.3.1+dfsg' -make[2]: Leaving directory '/build/ivar-1.3.1+dfsg' -make[1]: Leaving directory '/build/ivar-1.3.1+dfsg' +make[3]: Map '/build/ivar-1.3.1+dfsg/tests' wordt binnengegaan +make[3]: Er hoeft niets gedaan te worden voor 'all'. +make[3]: Map '/build/ivar-1.3.1+dfsg/tests' wordt verlaten +make[3]: Map '/build/ivar-1.3.1+dfsg' wordt binnengegaan +make[3]: Map '/build/ivar-1.3.1+dfsg' wordt verlaten +make[2]: Map '/build/ivar-1.3.1+dfsg' wordt verlaten +make[1]: Map '/build/ivar-1.3.1+dfsg' wordt verlaten debian/rules override_dh_auto_test -make[1]: Entering directory '/build/ivar-1.3.1+dfsg' +make[1]: Map '/build/ivar-1.3.1+dfsg' wordt binnengegaan dh_auto_test --no-parallel make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 -make[2]: Entering directory '/build/ivar-1.3.1+dfsg' +make[2]: Map '/build/ivar-1.3.1+dfsg' wordt binnengegaan Making check in src -make[3]: Entering directory '/build/ivar-1.3.1+dfsg/src' -make[3]: Nothing to be done for 'check'. -make[3]: Leaving directory '/build/ivar-1.3.1+dfsg/src' +make[3]: Map '/build/ivar-1.3.1+dfsg/src' wordt binnengegaan +make[3]: Er hoeft niets gedaan te worden voor 'check'. +make[3]: Map '/build/ivar-1.3.1+dfsg/src' wordt verlaten Making check in tests -make[3]: Entering directory '/build/ivar-1.3.1+dfsg/tests' +make[3]: Map '/build/ivar-1.3.1+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-1.3.1+dfsg/tests' +make[4]: Map '/build/ivar-1.3.1+dfsg/tests' wordt binnengegaan g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/primer_bed.o ../src/primer_bed.cpp @@ -1160,10 +1201,10 @@ g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -c -o test_amplicon_search.o test_amplicon_search.cpp g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-1.3.1+dfsg/tests' +make[4]: Map '/build/ivar-1.3.1+dfsg/tests' wordt verlaten make check-TESTS -make[4]: Entering directory '/build/ivar-1.3.1+dfsg/tests' -make[5]: Entering directory '/build/ivar-1.3.1+dfsg/tests' +make[4]: Map '/build/ivar-1.3.1+dfsg/tests' wordt binnengegaan +make[5]: Map '/build/ivar-1.3.1+dfsg/tests' wordt binnengegaan PASS: check_primer_trim PASS: check_trim PASS: check_quality_trim @@ -1193,20 +1234,20 @@ # XPASS: 0 # ERROR: 0 ============================================================================ -make[5]: Leaving directory '/build/ivar-1.3.1+dfsg/tests' -make[4]: Leaving directory '/build/ivar-1.3.1+dfsg/tests' -make[3]: Leaving directory '/build/ivar-1.3.1+dfsg/tests' -make[3]: Entering directory '/build/ivar-1.3.1+dfsg' -make[3]: Leaving directory '/build/ivar-1.3.1+dfsg' -make[2]: Leaving directory '/build/ivar-1.3.1+dfsg' -make[1]: Leaving directory '/build/ivar-1.3.1+dfsg' +make[5]: Map '/build/ivar-1.3.1+dfsg/tests' wordt verlaten +make[4]: Map '/build/ivar-1.3.1+dfsg/tests' wordt verlaten +make[3]: Map '/build/ivar-1.3.1+dfsg/tests' wordt verlaten +make[3]: Map '/build/ivar-1.3.1+dfsg' wordt binnengegaan +make[3]: Map '/build/ivar-1.3.1+dfsg' wordt verlaten +make[2]: Map '/build/ivar-1.3.1+dfsg' wordt verlaten +make[1]: Map '/build/ivar-1.3.1+dfsg' wordt verlaten create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j8 install DESTDIR=/build/ivar-1.3.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no -make[1]: Entering directory '/build/ivar-1.3.1+dfsg' +make[1]: Map '/build/ivar-1.3.1+dfsg' wordt binnengegaan Making install in src -make[2]: Entering directory '/build/ivar-1.3.1+dfsg/src' +make[2]: Map '/build/ivar-1.3.1+dfsg/src' wordt binnengegaan g++ -g -O2 -ffile-prefix-map=/build/ivar-1.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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++ @@ -1220,28 +1261,28 @@ COMPILER_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/aarch64-linux-gnu/12/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib/:/lib/aarch64-linux-gnu/:/lib/../lib/:/usr/lib/aarch64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/aarch64-linux-gnu/12/../../../:/lib/:/usr/lib/ COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'ivar.' - /usr/lib/gcc/aarch64-linux-gnu/12/collect2 -plugin /usr/lib/gcc/aarch64-linux-gnu/12/liblto_plugin.so -plugin-opt=/usr/lib/gcc/aarch64-linux-gnu/12/lto-wrapper -plugin-opt=-fresolution=/tmp/ccIywtJR.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/12/../../../aarch64-linux-gnu/Scrt1.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/crtbeginS.o -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../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/12/../../.. -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/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crtn.o + /usr/lib/gcc/aarch64-linux-gnu/12/collect2 -plugin /usr/lib/gcc/aarch64-linux-gnu/12/liblto_plugin.so -plugin-opt=/usr/lib/gcc/aarch64-linux-gnu/12/lto-wrapper -plugin-opt=-fresolution=/tmp/ccbGSjA2.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/12/../../../aarch64-linux-gnu/Scrt1.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/crtbeginS.o -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../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/12/../../.. -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/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crtn.o COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/ivar-1.3.1+dfsg=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mlittle-endian' '-mabi=lp64' '-dumpdir' 'ivar.' -make[3]: Entering directory '/build/ivar-1.3.1+dfsg/src' +make[3]: Map '/build/ivar-1.3.1+dfsg/src' wordt binnengegaan +make[3]: Er hoeft niets gedaan te worden voor 'install-data-am'. /usr/bin/mkdir -p '/build/ivar-1.3.1+dfsg/debian/tmp/usr/bin' -make[3]: Nothing to be done for 'install-data-am'. /usr/bin/install -c ivar '/build/ivar-1.3.1+dfsg/debian/tmp/usr/bin' -make[3]: Leaving directory '/build/ivar-1.3.1+dfsg/src' -make[2]: Leaving directory '/build/ivar-1.3.1+dfsg/src' +make[3]: Map '/build/ivar-1.3.1+dfsg/src' wordt verlaten +make[2]: Map '/build/ivar-1.3.1+dfsg/src' wordt verlaten Making install in tests -make[2]: Entering directory '/build/ivar-1.3.1+dfsg/tests' -make[3]: Entering directory '/build/ivar-1.3.1+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-1.3.1+dfsg/tests' -make[2]: Leaving directory '/build/ivar-1.3.1+dfsg/tests' -make[2]: Entering directory '/build/ivar-1.3.1+dfsg' -make[3]: Entering directory '/build/ivar-1.3.1+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-1.3.1+dfsg' -make[2]: Leaving directory '/build/ivar-1.3.1+dfsg' -make[1]: Leaving directory '/build/ivar-1.3.1+dfsg' +make[2]: Map '/build/ivar-1.3.1+dfsg/tests' wordt binnengegaan +make[3]: Map '/build/ivar-1.3.1+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-1.3.1+dfsg/tests' wordt verlaten +make[2]: Map '/build/ivar-1.3.1+dfsg/tests' wordt verlaten +make[2]: Map '/build/ivar-1.3.1+dfsg' wordt binnengegaan +make[3]: Map '/build/ivar-1.3.1+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-1.3.1+dfsg' wordt verlaten +make[2]: Map '/build/ivar-1.3.1+dfsg' wordt verlaten +make[1]: Map '/build/ivar-1.3.1+dfsg' wordt verlaten dh_install dh_installdocs dh_installchangelogs @@ -1261,9 +1302,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'ivar-doc' in '../ivar-doc_1.3.1+dfsg-7_all.deb'. -dpkg-deb: building package 'ivar-dbgsym' in '../ivar-dbgsym_1.3.1+dfsg-7_arm64.deb'. -dpkg-deb: building package 'ivar' in '../ivar_1.3.1+dfsg-7_arm64.deb'. +dpkg-deb: pakket 'ivar' wordt gebouwd in '../ivar_1.3.1+dfsg-7_arm64.deb'. +dpkg-deb: pakket 'ivar-dbgsym' wordt gebouwd in '../ivar-dbgsym_1.3.1+dfsg-7_arm64.deb'. +dpkg-deb: pakket 'ivar-doc' wordt gebouwd in '../ivar-doc_1.3.1+dfsg-7_all.deb'. dpkg-genbuildinfo --build=binary -O../ivar_1.3.1+dfsg-7_arm64.buildinfo dpkg-genchanges --build=binary -O../ivar_1.3.1+dfsg-7_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1271,12 +1312,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/17545/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/17545/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/7688 and its subdirectories -I: Current time: Mon May 8 07:19:37 -12 2023 -I: pbuilder-time-stamp: 1683573577 +I: removing directory /srv/workspace/pbuilder/17545 and its subdirectories +I: Current time: Mon Jun 10 15:46:02 +14 2024 +I: pbuilder-time-stamp: 1717983962