Diff of the two buildlogs: -- --- b1/build.log 2024-11-18 13:54:03.135740998 +0000 +++ b2/build.log 2024-11-18 13:54:57.653272554 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Nov 18 01:53:15 -12 2024 -I: pbuilder-time-stamp: 1731937995 +I: Current time: Tue Nov 19 03:54:06 +14 2024 +I: pbuilder-time-stamp: 1731938046 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ dpkg-source: info: applying gcc14.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4181860/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2083236/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 Nov 18 13:54 /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/2083236/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2083236/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - 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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + 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=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='10d7873ef4794cffb9345b6ee0c972e7' - 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='4181860' - PS1='# ' - PS2='> ' + INVOCATION_ID=db29b268fa6742de9ce2da2020197798 + 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=2083236 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.dtZbYRvx/pbuilderrc_3cyO --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dtZbYRvx/b1 --logfile b1/build.log libpsortb_1.0+dfsg-7.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.dtZbYRvx/pbuilderrc_Advw --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dtZbYRvx/b2 --logfile b2/build.log libpsortb_1.0+dfsg-7.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink02-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4181860/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/2083236/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -161,7 +193,7 @@ Get: 36 http://deb.debian.org/debian unstable/main arm64 libsvm-dev arm64 3.24+ds-6+b1 [59.4 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] -Fetched 19.9 MB in 1s (39.3 MB/s) +Fetched 19.9 MB in 0s (125 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 ... 20084 files and directories currently installed.) @@ -328,7 +360,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libpsortb-1.0+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 > ../libpsortb_1.0+dfsg-7_source.changes +I: user script /srv/workspace/pbuilder/2083236/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2083236/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libpsortb-1.0+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 > ../libpsortb_1.0+dfsg-7_source.changes dpkg-buildpackage: info: source package libpsortb dpkg-buildpackage: info: source version 1.0+dfsg-7 dpkg-buildpackage: info: source distribution unstable @@ -518,13 +554,13 @@ make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' Making all in svmloc make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o binding.lo binding.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o svmloc.lo svmloc.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c svmloc.cpp -fPIC -DPIC -o .libs/svmloc.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o binding.lo binding.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o svmloc.lo svmloc.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c binding.cpp -fPIC -DPIC -o .libs/binding.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c svmloc.cpp -fPIC -DPIC -o .libs/svmloc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c binding.cpp -o binding.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c svmloc.cpp -o svmloc.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/aarch64-linux-gnu binding.lo svmloc.lo -lm +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/aarch64-linux-gnu binding.lo svmloc.lo -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/14/crtbeginS.o .libs/binding.o .libs/svmloc.o -lsvm -L/usr/lib/gcc/aarch64-linux-gnu/14 -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/14/../../../../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/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/14/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/14/../../../aarch64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libsvmloc.so.0 -o .libs/libsvmloc.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libsvmloc.so.0" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so.0") libtool: link: (cd ".libs" && rm -f "libsvmloc.so" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so") @@ -534,24 +570,24 @@ make[3]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' Making all in modhmm0.92b make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o core_algorithms_multialpha.lo core_algorithms_multialpha.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o debug_funcs.lo debug_funcs.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o hmmsearch.lo hmmsearch.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readhmm.lo readhmm.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readhmm_multialpha.lo readhmm_multialpha.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readseqs_multialpha.lo readseqs_multialpha.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o std_calculation_funcs.lo std_calculation_funcs.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o std_funcs.lo std_funcs.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o training_algorithms_multialpha.lo training_algorithms_multialpha.c -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm.c -fPIC -DPIC -o .libs/readhmm.o +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o core_algorithms_multialpha.lo core_algorithms_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o debug_funcs.lo debug_funcs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o hmmsearch.lo hmmsearch.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readhmm.lo readhmm.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readhmm_multialpha.lo readhmm_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o readseqs_multialpha.lo readseqs_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o std_calculation_funcs.lo std_calculation_funcs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o std_funcs.lo std_funcs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o training_algorithms_multialpha.lo training_algorithms_multialpha.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c hmmsearch.c -fPIC -DPIC -o .libs/hmmsearch.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c debug_funcs.c -fPIC -DPIC -o .libs/debug_funcs.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_funcs.c -fPIC -DPIC -o .libs/std_funcs.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm_multialpha.c -fPIC -DPIC -o .libs/readhmm_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c core_algorithms_multialpha.c -fPIC -DPIC -o .libs/core_algorithms_multialpha.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm_multialpha.c -fPIC -DPIC -o .libs/readhmm_multialpha.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readhmm.c -fPIC -DPIC -o .libs/readhmm.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c training_algorithms_multialpha.c -fPIC -DPIC -o .libs/training_algorithms_multialpha.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o debug_funcs.c:7:76: warning: 'struct hmm_multi_s' declared inside parameter list will not be visible outside of this definition or declaration 7 | int read_multi_prior_file_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, FILE *priorfile, int alphabet); | ^~~~~~~~~~~ @@ -574,19 +610,94 @@ | ~^ ~~~~~~~~~ | | | | char * struct letter_s * +readseqs_multialpha.c: In function 'get_sequence_std_multi': +readseqs_multialpha.c:121:55: warning: unknown escape sequence: '\s' + 121 | if(line[0] == '<' || line[0] == '#' || line[0] == '\s' || line[0] == '\n' || line[0] == '/') { + | ^~~~ hmmsearch.c:712:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] 712 | printf("Could not find letter %s when scoring null model\n", &seq[l]); | ~^ ~~~~~~~ | | | | char * struct letter_s * +readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': +readseqs_multialpha.c:372:18: warning: unknown escape sequence: '\s' + 372 | else if(i == '\s' && i == '\n') { + | ^~~~ +std_funcs.c: In function 'get_replacement_letter_index_single': +std_funcs.c:680:62: warning: comparison between pointer and integer + 680 | if(((replacement_letters->letters + a_index)->letter)[0] == c) { + | ^~ +training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': +training_algorithms_multialpha.c:701:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 701 | alphabet = (int)hmmp->alphabet; + | ^ +training_algorithms_multialpha.c:710:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 710 | alphabet = (int)hmmp->alphabet_2; + | ^ +training_algorithms_multialpha.c:719:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 719 | alphabet = (int)hmmp->alphabet_3; + | ^ +training_algorithms_multialpha.c:728:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 728 | alphabet = (int)hmmp->alphabet_4; + | ^ +std_calculation_funcs.c: In function 'update_labelings': +std_calculation_funcs.c:1295:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1295 | cur_address = (int)((cur_rowp+v)->labeling); + | ^ +std_calculation_funcs.c:1309:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1309 | if((int)((cur_rowp+w)->labeling) == cur_address && (cur_rowp + w)->is_updated == NO) { + | ^ +training_algorithms_multialpha.c: In function 'extended_msa_baum_welch_dirichlet_multi': +std_calculation_funcs.c: In function 'deallocate_row_labelings': +std_calculation_funcs.c:1425:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1425 | cur_address = (int)((prev_rowp+v)->labeling); + | ^ +std_calculation_funcs.c:1430:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1430 | if((int)((prev_rowp+w)->labeling) == cur_address) { + | ^ +training_algorithms_multialpha.c:1639:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1639 | alphabet = (int)hmmp->alphabet; + | ^ +training_algorithms_multialpha.c:1646:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1646 | alphabet = (int)hmmp->alphabet_2; + | ^ +training_algorithms_multialpha.c:1653:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1653 | alphabet = (int)hmmp->alphabet_3; + | ^ +training_algorithms_multialpha.c:1660:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1660 | alphabet = (int)hmmp->alphabet_4; + | ^ +readseqs_multialpha.c: In function 'get_sequence_std_multi': +readseqs_multialpha.c:286:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 286 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:1784:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1784 | alphabet = (int)hmmp->alphabet; + | ^ readhmm.c: In function 'readhmm': readhmm.c:69:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:1791:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1791 | alphabet = (int)hmmp->alphabet_2; + | ^ +training_algorithms_multialpha.c:1798:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1798 | alphabet = (int)hmmp->alphabet_3; + | ^ +training_algorithms_multialpha.c:1805:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1805 | alphabet = (int)hmmp->alphabet_4; + | ^ readhmm.c: In function 'readanhmm': readhmm.c:342:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 342 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': +readseqs_multialpha.c:625:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 625 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c:754:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 754 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readhmm.c: In function 'read_module': readhmm.c:745:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 745 | fgets(s, MAX_LINE, file); @@ -603,18 +714,20 @@ readhmm.c:848:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 848 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c: In function 'read_prior_files': -readhmm.c:1225:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1225 | fgets(ps, 2048, priorfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -std_funcs.c: In function 'get_replacement_letter_index_single': -std_funcs.c:680:62: warning: comparison between pointer and integer - 680 | if(((replacement_letters->letters + a_index)->letter)[0] == c) { - | ^~ readhmm_multialpha.c: In function 'readhmm_multialpha': +readseqs_multialpha.c:874:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 874 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:326:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 326 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c:995:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 995 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readhmm.c: In function 'read_prior_files': +readhmm.c:1225:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1225 | fgets(ps, 2048, priorfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c: In function 'read_module_multi': readhmm_multialpha.c:1039:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1039 | fgets(s, MAX_LINE, file); @@ -649,63 +762,23 @@ readhmm_multialpha.c:1233:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1233 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': -training_algorithms_multialpha.c:701:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 701 | alphabet = (int)hmmp->alphabet; - | ^ -training_algorithms_multialpha.c:710:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 710 | alphabet = (int)hmmp->alphabet_2; - | ^ -training_algorithms_multialpha.c:719:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 719 | alphabet = (int)hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:728:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 728 | alphabet = (int)hmmp->alphabet_4; - | ^ -training_algorithms_multialpha.c: In function 'extended_msa_baum_welch_dirichlet_multi': -training_algorithms_multialpha.c:1639:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1639 | alphabet = (int)hmmp->alphabet; - | ^ -training_algorithms_multialpha.c:1646:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1646 | alphabet = (int)hmmp->alphabet_2; - | ^ -training_algorithms_multialpha.c:1653:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1653 | alphabet = (int)hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:1660:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1660 | alphabet = (int)hmmp->alphabet_4; - | ^ -training_algorithms_multialpha.c:1784:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1784 | alphabet = (int)hmmp->alphabet; - | ^ -training_algorithms_multialpha.c:1791:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1791 | alphabet = (int)hmmp->alphabet_2; - | ^ -training_algorithms_multialpha.c:1798:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1798 | alphabet = (int)hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:1805:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1805 | alphabet = (int)hmmp->alphabet_4; - | ^ -readseqs_multialpha.c: In function 'get_sequence_std_multi': -readseqs_multialpha.c:121:55: warning: unknown escape sequence: '\s' - 121 | if(line[0] == '<' || line[0] == '#' || line[0] == '\s' || line[0] == '\n' || line[0] == '/') { - | ^~~~ -readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': -readseqs_multialpha.c:372:18: warning: unknown escape sequence: '\s' - 372 | else if(i == '\s' && i == '\n') { - | ^~~~ training_algorithms_multialpha.c: In function 'add_to_E_multi': -std_funcs.c: In function 'get_nr_alphabets': training_algorithms_multialpha.c:3589:43: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3589 | (char*)alphabet); | ^ -std_funcs.c:2726:10: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] - 2726 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:3593:49: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3593 | (char*)alphabet); | ^ +training_algorithms_multialpha.c:3618:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] + 3618 | (char*)alphabet); + | ^ +training_algorithms_multialpha.c:3622:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] + 3622 | (char*)alphabet); + | ^ +std_funcs.c: In function 'get_nr_alphabets': +std_funcs.c:2726:10: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] + 2726 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ std_funcs.c:2719:8: note: destination object 's' of size 1000 2719 | char s[1000]; | ^ @@ -717,49 +790,12 @@ std_funcs.c:2733:8: warning: 'fgets' writing 4000 bytes into a region of size 1000 overflows the destination [-Wstringop-overflow=] 2733 | if(fgets(s, MAX_LINE, hmmfile) != NULL) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -training_algorithms_multialpha.c:3618:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] - 3618 | (char*)alphabet); - | ^ std_funcs.c:2719:8: note: destination object 's' of size 1000 2719 | char s[1000]; | ^ /usr/include/aarch64-linux-gnu/bits/stdio2.h:305:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 305 | fgets (__fortify_clang_overload_arg (char *, __restrict, __s), int __n, | ^~~~~ -training_algorithms_multialpha.c:3622:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] - 3622 | (char*)alphabet); - | ^ -readseqs_multialpha.c: In function 'get_sequence_std_multi': -readseqs_multialpha.c:286:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 286 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': -readseqs_multialpha.c:625:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 625 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c:754:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 754 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c:874:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 874 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c:995:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 995 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -std_calculation_funcs.c: In function 'update_labelings': -std_calculation_funcs.c:1295:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1295 | cur_address = (int)((cur_rowp+v)->labeling); - | ^ -std_calculation_funcs.c:1309:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1309 | if((int)((cur_rowp+w)->labeling) == cur_address && (cur_rowp + w)->is_updated == NO) { - | ^ -std_calculation_funcs.c: In function 'deallocate_row_labelings': -std_calculation_funcs.c:1425:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1425 | cur_address = (int)((prev_rowp+v)->labeling); - | ^ -std_calculation_funcs.c:1430:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1430 | if((int)((prev_rowp+w)->labeling) == cur_address) { - | ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c hmmsearch.c -o hmmsearch.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c debug_funcs.c -o debug_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readseqs_multialpha.c -o readseqs_multialpha.o >/dev/null 2>&1 @@ -779,7 +815,7 @@ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c std_funcs.c -o std_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c core_algorithms_multialpha.c -o core_algorithms_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c training_algorithms_multialpha.c -o training_algorithms_multialpha.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/aarch64-linux-gnu core_algorithms_multialpha.lo debug_funcs.lo hmmsearch.lo readhmm.lo readhmm_multialpha.lo readseqs_multialpha.lo std_calculation_funcs.lo std_funcs.lo training_algorithms_multialpha.lo -lm +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libpsortb-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/aarch64-linux-gnu core_algorithms_multialpha.lo debug_funcs.lo hmmsearch.lo readhmm.lo readhmm_multialpha.lo readseqs_multialpha.lo std_calculation_funcs.lo std_funcs.lo training_algorithms_multialpha.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/core_algorithms_multialpha.o .libs/debug_funcs.o .libs/hmmsearch.o .libs/readhmm.o .libs/readhmm_multialpha.o .libs/readseqs_multialpha.o .libs/std_calculation_funcs.o .libs/std_funcs.o .libs/training_algorithms_multialpha.o -lm -g -O2 -fstack-protector-strong -mbranch-protection=standard -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libmodhmm.so.0 -o .libs/libmodhmm.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libmodhmm.so.0" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so.0") libtool: link: (cd ".libs" && rm -f "libmodhmm.so" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so") @@ -816,7 +852,7 @@ make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' make[4]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' /usr/bin/mkdir -p '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libsvmloc.so.0.0.0 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libsvmloc.so.0.0.0 libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so.0 || { rm -f libsvmloc.so.0 && ln -s libsvmloc.so.0.0.0 libsvmloc.so.0; }; }) libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so || { rm -f libsvmloc.so && ln -s libsvmloc.so.0.0.0 libsvmloc.so; }; }) @@ -832,7 +868,7 @@ make[3]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' make[4]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/modhmm0.92b' /usr/bin/mkdir -p '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libmodhmm.so.0.0.0 /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libmodhmm.so.0.0.0 libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so.0 || { rm -f libmodhmm.so.0 && ln -s libmodhmm.so.0.0.0 libmodhmm.so.0; }; }) libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so || { rm -f libmodhmm.so && ln -s libmodhmm.so.0.0.0 libmodhmm.so; }; }) @@ -908,8 +944,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libmodhmm0' in '../libmodhmm0_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libmodhmm0-dbgsym' in '../libmodhmm0-dbgsym_1.0+dfsg-7_arm64.deb'. +dpkg-deb: building package 'libmodhmm0' in '../libmodhmm0_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libmodhmm-dev' in '../libmodhmm-dev_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libsvmloc0' in '../libsvmloc0_1.0+dfsg-7_arm64.deb'. dpkg-deb: building package 'libsvmloc0-dbgsym' in '../libsvmloc0-dbgsym_1.0+dfsg-7_arm64.deb'. @@ -921,12 +957,14 @@ 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/2083236/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2083236/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/4181860 and its subdirectories -I: Current time: Mon Nov 18 01:54:02 -12 2024 -I: pbuilder-time-stamp: 1731938042 +I: removing directory /srv/workspace/pbuilder/2083236 and its subdirectories +I: Current time: Tue Nov 19 03:54:56 +14 2024 +I: pbuilder-time-stamp: 1731938096