Diff of the two buildlogs: -- --- b1/build.log 2024-05-06 17:09:09.125867571 +0000 +++ b2/build.log 2024-05-06 17:10:11.939195140 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 6 05:05:39 -12 2024 -I: pbuilder-time-stamp: 1715015139 +I: Current time: Mon Jun 9 13:32:14 +14 2025 +I: pbuilder-time-stamp: 1749425534 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying fix-implicit-declaration.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/508934/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1680172/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 8 23:32 /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/1680172/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1680172/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + 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]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='e3a36f22b5494cfdb6c66e859079d6d2' - 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='508934' - PS1='# ' - PS2='> ' + INVOCATION_ID=d1d93b9b46dd401088340d5e3ab739f5 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1680172 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.KO2pBqqT/pbuilderrc_6T5Y --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.KO2pBqqT/b1 --logfile b1/build.log libpsortb_1.0+dfsg-6.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.KO2pBqqT/pbuilderrc_m8tp --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.KO2pBqqT/b2 --logfile b2/build.log libpsortb_1.0+dfsg-6.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 5 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/508934/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 7 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1680172/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: 37 http://deb.debian.org/debian trixie/main amd64 libsvm-dev amd64 3.24+ds-6+b1 [62.1 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] -Fetched 19.6 MB in 6s (3128 kB/s) +Fetched 19.6 MB in 0s (64.3 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 ... 19698 files and directories currently installed.) @@ -332,7 +364,11 @@ 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-6_source.changes +I: user script /srv/workspace/pbuilder/1680172/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1680172/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-6_source.changes dpkg-buildpackage: info: source package libpsortb dpkg-buildpackage: info: source version 1.0+dfsg-6 dpkg-buildpackage: info: source distribution unstable @@ -516,19 +552,19 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j20 + make -j42 make[1]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' make all-recursive 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c binding.cpp -fPIC -DPIC -o .libs/binding.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/x86_64-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 -fcf-protection -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/x86_64-linux-gnu binding.lo svmloc.lo -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o .libs/binding.o .libs/svmloc.o -lsvm -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -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") @@ -538,22 +574,105 @@ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c core_algorithms_multialpha.c -fPIC -DPIC -o .libs/core_algorithms_multialpha.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.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); + | ^~~~~~~~~~~ +debug_funcs.c:7:40: warning: 'struct emission_dirichlet_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); + | ^~~~~~~~~~~~~~~~~~~~ +readhmm.c: In function 'readhmm': +readhmm.c:121:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] + 121 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + | ^ +readhmm.c: In function 'readanhmm': +readhmm.c:394:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] + 394 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + | ^ +readhmm_multialpha.c: In function 'copy_hmm_struct': +readhmm_multialpha.c:273:34: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] + 273 | retrain_hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + | ^ +readseqs_multialpha.c: In function 'get_sequence_fasta_multi': +readseqs_multialpha.c:83:39: warning: assignment to 'char' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 83 | (seq_infop->seqs + seq_nr)->name[0] = "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: In function 'get_scores': +hmmsearch.c:535:19: warning: assignment to 'struct helix_site *' from incompatible pointer type 'helix_sites *' [-Wincompatible-pointer-types] + 535 | hSites->helix = (helix_sites *) malloc(sizeof (helix_sites) * helices); + | ^ +readhmm_multialpha.c: In function 'readhmm_multialpha': +readhmm_multialpha.c:469:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] + 469 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_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') { + | ^~~~ +hmmsearch.c: In function 'get_nullmodel_score_multi': +hmmsearch.c:656:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 656 | printf("Could not find letter %s when scoring null model\n", &seq[l]); + | ~^ ~~~~~~~ + | | | + | char * struct letter_s * +hmmsearch.c:674:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 674 | printf("Could not find letter %s when scoring null model\n", &seq_2[l]); + | ~^ ~~~~~~~~~ + | | | + | char * struct letter_s * +training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': +hmmsearch.c:693:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 693 | printf("Could not find letter %s when scoring null model\n", &seq_3[l]); + | ~^ ~~~~~~~~~ + | | | + | char * struct letter_s * +training_algorithms_multialpha.c:701:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 701 | alphabet = hmmp->alphabet; + | ^ +training_algorithms_multialpha.c:710:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 710 | alphabet = hmmp->alphabet_2; + | ^ +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 * +training_algorithms_multialpha.c:719:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 719 | alphabet = hmmp->alphabet_3; + | ^ +training_algorithms_multialpha.c:728:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 728 | alphabet = hmmp->alphabet_4; + | ^ +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) { + | ^~ core_algorithms_multialpha.c: In function 'msa_forward_multi': +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1190:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1190 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -563,6 +682,7 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +std_calculation_funcs.c: In function 'update_labelings': core_algorithms_multialpha.c:1197:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1197 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -587,15 +707,40 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c: In function 'extended_msa_baum_welch_dirichlet_multi': +readhmm.c: In function 'readanhmm': +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); + | ^ +readhmm.c:342:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 342 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +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:1639:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1639 | alphabet = hmmp->alphabet; + | ^ +training_algorithms_multialpha.c:1646:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1646 | alphabet = hmmp->alphabet_2; + | ^ core_algorithms_multialpha.c: In function 'msa_backward_multi': core_algorithms_multialpha.c:1417:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1417 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * +std_calculation_funcs.c: In function 'deallocate_row_labelings': funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +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); + | ^ +readhmm.c: In function 'read_module': +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) { + | ^ core_algorithms_multialpha.c:1424:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1424 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -604,6 +749,9 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:1653:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1653 | alphabet = hmmp->alphabet_3; + | ^ core_algorithms_multialpha.c:1433:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1433 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -612,16 +760,37 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +readhmm.c:745:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 745 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1442:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1442 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * -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 -fcf-protection -c std_funcs.c -fPIC -DPIC -o .libs/std_funcs.o funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:1660:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1660 | alphabet = hmmp->alphabet_4; + | ^ +readhmm.c:780:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 780 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readhmm.c:815:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 815 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readhmm.c:844:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 844 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readhmm.c:848:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 848 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:1784:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1784 | alphabet = hmmp->alphabet; + | ^ core_algorithms_multialpha.c: In function 'msa_viterbi_multi': +std_funcs.c: In function 'get_reverse_msa_seq': core_algorithms_multialpha.c:1606:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1606 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -630,11 +799,17 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +std_funcs.c:2071:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] + 2071 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; + | ^ core_algorithms_multialpha.c:1613:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1613 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * +training_algorithms_multialpha.c:1791:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1791 | alphabet = hmmp->alphabet_2; + | ^ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ @@ -646,6 +821,13 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +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:1798:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1798 | alphabet = hmmp->alphabet_3; + | ^ core_algorithms_multialpha.c:1631:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1631 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -654,7 +836,18 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +std_funcs.c: In function 'get_reverse_msa_seq_multi': +training_algorithms_multialpha.c:1805:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 1805 | alphabet = hmmp->alphabet_4; + | ^ +std_funcs.c:2179:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] + 2179 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; + | ^ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c: In function 'msa_one_best_multi': +readhmm.c: In function 'read_prior_files': core_algorithms_multialpha.c:1890:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1890 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -663,6 +856,9 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +readhmm.c:1225:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1225 | fgets(ps, 2048, priorfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1897:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1897 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -671,6 +867,7 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +std_funcs.c: In function 'update_shares_prior_multi': core_algorithms_multialpha.c:1906:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1906 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -679,6 +876,11 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +readhmm_multialpha.c: In function 'read_module_multi': +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1915:93: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1915 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -687,77 +889,39 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ -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 -fcf-protection -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o -readhmm_multialpha.c: In function 'copy_hmm_struct': -readhmm_multialpha.c:273:34: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] - 273 | retrain_hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); - | ^ -readhmm_multialpha.c: In function 'readhmm_multialpha': -readhmm_multialpha.c:469:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] - 469 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); - | ^ -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); - | ^~~~~~~~~~~ -debug_funcs.c:7:40: warning: 'struct emission_dirichlet_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); - | ^~~~~~~~~~~~~~~~~~~~ -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 -fcf-protection -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c: In function 'readhmm': -readhmm_multialpha.c: In function 'read_module_multi': -readhmm.c:121:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] - 121 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); - | ^ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~ +std_funcs.c:2466:5: warning: 'return' with no value, in function returning non-void + 2466 | return; + | ^~~~~~ +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_multialpha.c:1074:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1074 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ +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:1108:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1108 | 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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +std_funcs.c:2452:5: note: declared here + 2452 | int update_shares_prior_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ readhmm_multialpha.c:1137:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1137 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c: In function 'readanhmm': -readhmm.c:394:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] - 394 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); - | ^ -hmmsearch.c: In function 'get_scores': -hmmsearch.c:535:19: warning: assignment to 'struct helix_site *' from incompatible pointer type 'helix_sites *' [-Wincompatible-pointer-types] - 535 | hSites->helix = (helix_sites *) malloc(sizeof (helix_sites) * helices); - | ^ -hmmsearch.c: In function 'get_nullmodel_score_multi': readhmm_multialpha.c:1140:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1140 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -hmmsearch.c:656:42: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 656 | printf("Could not find letter %s when scoring null model\n", &seq[l]); - | ~^ ~~~~~~~ - | | | - | char * struct letter_s * -hmmsearch.c:674:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 674 | printf("Could not find letter %s when scoring null model\n", &seq_2[l]); - | ~^ ~~~~~~~~~ - | | | - | char * struct letter_s * -hmmsearch.c:693:44: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 693 | printf("Could not find letter %s when scoring null model\n", &seq_3[l]); - | ~^ ~~~~~~~~~ - | | | - | char * struct letter_s * readhmm_multialpha.c:1166:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1166 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -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 * readhmm_multialpha.c:1169:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1169 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ @@ -773,72 +937,6 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c:780:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 780 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c:815:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 815 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c:844:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 844 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': -training_algorithms_multialpha.c:701:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 701 | alphabet = hmmp->alphabet; - | ^ -training_algorithms_multialpha.c:710:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 710 | alphabet = hmmp->alphabet_2; - | ^ -training_algorithms_multialpha.c:719:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 719 | alphabet = hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:728:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 728 | alphabet = hmmp->alphabet_4; - | ^ -training_algorithms_multialpha.c: In function 'extended_msa_baum_welch_dirichlet_multi': -training_algorithms_multialpha.c:1639:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1639 | alphabet = hmmp->alphabet; - | ^ -training_algorithms_multialpha.c:1646:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1646 | alphabet = hmmp->alphabet_2; - | ^ -training_algorithms_multialpha.c:1653:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1653 | alphabet = hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:1660:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1660 | alphabet = hmmp->alphabet_4; - | ^ -training_algorithms_multialpha.c:1784:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1784 | alphabet = hmmp->alphabet; - | ^ -training_algorithms_multialpha.c:1791:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1791 | alphabet = hmmp->alphabet_2; - | ^ -training_algorithms_multialpha.c:1798:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1798 | alphabet = hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:1805:26: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 1805 | alphabet = hmmp->alphabet_4; - | ^ training_algorithms_multialpha.c: In function 'add_to_E_multi': training_algorithms_multialpha.c:3589:43: warning: passing argument 9 of 'add_to_E_subst_mtx_dot_product_nr_occ' makes pointer from integer without a cast [-Wint-conversion] 3589 | alphabet); @@ -857,10 +955,6 @@ funcs.h:262:102: note: expected 'char *' but argument is of type 'int' 262 | int k, int a_size, int normalize, double *subst_mtx, char *alphabet); | ~~~~~~^~~~~~~~ -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:3618:36: warning: passing argument 9 of 'add_to_E_subst_mtx_dot_product' makes pointer from integer without a cast [-Wint-conversion] 3618 | alphabet); | ^~~~~~~~ @@ -877,64 +971,6 @@ funcs.h:243:102: note: expected 'char *' but argument is of type 'int' 243 | int k, int a_size, int normalize, double *subst_mtx, char *alphabet); | ~~~~~~^~~~~~~~ -std_funcs.c: In function 'get_reverse_msa_seq': -std_funcs.c:2071:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] - 2071 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; - | ^ -std_funcs.c: In function 'get_reverse_msa_seq_multi': -std_funcs.c:2179:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] - 2179 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; - | ^ -std_funcs.c: In function 'update_shares_prior_multi': -std_funcs.c:2466:5: warning: 'return' with no value, in function returning non-void - 2466 | return; - | ^~~~~~ -std_funcs.c:2452:5: note: declared here - 2452 | int update_shares_prior_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -readseqs_multialpha.c: In function 'get_sequence_fasta_multi': -readseqs_multialpha.c:83:39: warning: assignment to 'char' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 83 | (seq_infop->seqs + seq_nr)->name[0] = "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] == '/') { - | ^~~~ -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_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) { - | ^ -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_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) { @@ -960,8 +996,8 @@ 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 -fcf-protection -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 -fcf-protection -c readhmm.c -o readhmm.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 -fcf-protection -c std_calculation_funcs.c -o std_calculation_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 -fcf-protection -c readseqs_multialpha.c -o readseqs_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 -fcf-protection -c readhmm_multialpha.c -o readhmm_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 -fcf-protection -c readseqs_multialpha.c -o readseqs_multialpha.o >/dev/null 2>&1 In function 'fgets', inlined from 'get_nr_alphabets' at std_funcs.c:2726:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:201:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] @@ -972,10 +1008,10 @@ /usr/include/x86_64-linux-gnu/bits/stdio2.h:201:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 201 | return __fgets_chk_warn (__s, sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -fcf-protection -c training_algorithms_multialpha.c -o training_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 -fcf-protection -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 -fcf-protection -c core_algorithms_multialpha.c -o core_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 -fcf-protection -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/x86_64-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: 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 -fcf-protection -c training_algorithms_multialpha.c -o training_algorithms_multialpha.o >/dev/null 2>&1 +/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 -fcf-protection -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/x86_64-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 -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") @@ -988,7 +1024,7 @@ make[2]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/libpsortb-1.0+dfsg' dh_auto_test - make -j20 check "TESTSUITEFLAGS=-j20 --verbose" VERBOSE=1 + make -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg' Making check in svmloc make[2]: Entering directory '/build/reproducible-path/libpsortb-1.0+dfsg/svmloc' @@ -1012,7 +1048,7 @@ 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/x86_64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-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/x86_64-linux-gnu/libsvmloc.so.0.0.0 libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-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/x86_64-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; }; }) @@ -1028,7 +1064,7 @@ 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/x86_64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-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/x86_64-linux-gnu/libmodhmm.so.0.0.0 libtool: install: (cd /build/reproducible-path/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-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/x86_64-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; }; }) @@ -1096,11 +1132,11 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'libmodhmm0' in '../libmodhmm0_1.0+dfsg-6_amd64.deb'. +dpkg-deb: building package 'libmodhmm0-dbgsym' in '../libmodhmm0-dbgsym_1.0+dfsg-6_amd64.deb'. dpkg-deb: building package 'libmodhmm-dev' in '../libmodhmm-dev_1.0+dfsg-6_amd64.deb'. dpkg-deb: building package 'libsvmloc0' in '../libsvmloc0_1.0+dfsg-6_amd64.deb'. -dpkg-deb: building package 'libmodhmm0-dbgsym' in '../libmodhmm0-dbgsym_1.0+dfsg-6_amd64.deb'. dpkg-deb: building package 'libsvmloc-dev' in '../libsvmloc-dev_1.0+dfsg-6_amd64.deb'. -dpkg-deb: building package 'libmodhmm0' in '../libmodhmm0_1.0+dfsg-6_amd64.deb'. dpkg-deb: building package 'libsvmloc0-dbgsym' in '../libsvmloc0-dbgsym_1.0+dfsg-6_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libpsortb_1.0+dfsg-6_amd64.buildinfo dpkg-genchanges --build=binary -O../libpsortb_1.0+dfsg-6_amd64.changes @@ -1109,12 +1145,14 @@ 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/1680172/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1680172/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/508934 and its subdirectories -I: Current time: Mon May 6 05:09:08 -12 2024 -I: pbuilder-time-stamp: 1715015348 +I: removing directory /srv/workspace/pbuilder/1680172 and its subdirectories +I: Current time: Mon Jun 9 13:33:10 +14 2025 +I: pbuilder-time-stamp: 1749425590