Diff of the two buildlogs: -- --- b1/build.log 2025-03-08 09:56:14.110627251 +0000 +++ b2/build.log 2025-03-08 09:56:58.588636269 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Mar 7 21:55:39 -12 2025 -I: pbuilder-time-stamp: 1741427739 +I: Current time: Sat Apr 11 06:19:16 +14 2026 +I: pbuilder-time-stamp: 1775837956 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying gcc-11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1078381/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/639754/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-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 Apr 10 16:19 /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/639754/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/639754/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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(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='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='f84aec2ad5a34f138dc69a94f391d43e' - 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='1078381' - PS1='# ' - PS2='> ' + INVOCATION_ID=f88dfcd0661342bcaa6985bb435a7221 + 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=639754 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.FPT8COZJ/pbuilderrc_mpwn --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.FPT8COZJ/b1 --logfile b1/build.log samtools-legacy_0.1.19+dfsg-6.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.FPT8COZJ/pbuilderrc_uZ8I --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.FPT8COZJ/b2 --logfile b2/build.log samtools-legacy_0.1.19+dfsg-6.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 codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1078381/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/639754/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -146,7 +178,7 @@ Get: 31 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5+20250216-1 [96.1 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libncurses-dev arm64 6.5+20250216-1 [341 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 21.5 MB in 0s (145 MB/s) +Fetched 21.5 MB in 0s (102 MB/s) Preconfiguring packages ... 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 ... 19914 files and directories currently installed.) @@ -293,7 +325,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/samtools-legacy-0.1.19+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 > ../samtools-legacy_0.1.19+dfsg-6_source.changes +I: user script /srv/workspace/pbuilder/639754/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/639754/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/samtools-legacy-0.1.19+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 > ../samtools-legacy_0.1.19+dfsg-6_source.changes dpkg-buildpackage: info: source package samtools-legacy dpkg-buildpackage: info: source version 0.1.19+dfsg-6 dpkg-buildpackage: info: source distribution unstable @@ -330,32 +366,109 @@ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o +make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o -make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o +bam_index.c: In function 'bam_index_load_core': +bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 335 | fread(magic, 1, 4, fp); + | ^~~~~~~~~~~~~~~~~~~~~~ +bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 342 | fread(&idx->n, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 355 | fread(&size, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~ +bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 358 | fread(&key, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~ +bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 362 | fread(&p->n, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~ +bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 366 | fread(p->list, 16, p->n, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 376 | fread(&index2->n, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 380 | fread(index2->offset, index2->n, 8, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o +razf.c: In function 'razf_flush': +razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +razf.c:234:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +razf.c: In function '_razf_write': +razf.c:201:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o +razf.c: In function 'razf_close': +razf.c:804:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +razf.c:805:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +razf.c:808:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +razf.c:810:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +razf.c: In function 'razf_end_flush': +razf.c:258:25: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +razf.c: In function 'save_zindex': +razf.c:96:19: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +razf.c:99:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 99 | write(fd, &v32, sizeof(uint32_t)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +razf.c:106:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[4]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o razip.c: In function 'main': razip.c:131:33: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | write(f_dst, buffer, c); @@ -364,6 +477,31 @@ razip.c:32:25: warning: ignoring return value of 'scanf' declared with attribute 'warn_unused_result' [-Wunused-result] 32 | scanf("%c", &c); | ^~~~~~~~~~~~~~~ +bam_index.c: In function 'bam_index_load_core': +bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 335 | fread(magic, 1, 4, fp); + | ^~~~~~~~~~~~~~~~~~~~~~ +bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 342 | fread(&idx->n, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 355 | fread(&size, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~ +bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 358 | fread(&key, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~ +bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 362 | fread(&p->n, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~ +bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 366 | fread(p->list, 16, p->n, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 376 | fread(&index2->n, 4, 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 380 | fread(index2->offset, index2->n, 8, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function 'razf_flush': razf.c:221:17: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); @@ -405,10 +543,6 @@ razf.c:107:9: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o In file included from knetfile.c:46: knetfile.c: In function 'kftp_send_cmd': knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -424,12 +558,11 @@ knetfile.c:415:9: note: in expansion of macro 'netwrite' 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o bam_index.c: In function 'bam_index_load_core': bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fread(magic, 1, 4, fp); @@ -455,53 +588,39 @@ bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o +In file included from knetfile.c:46: +knetfile.c: In function 'kftp_send_cmd': +knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) + | ^~~~~~~~~~~~~~~~~~~ +knetfile.c:236:9: note: in expansion of macro 'netwrite' + 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); + | ^~~~~~~~ +knetfile.c: In function 'khttp_connect_file': +knetfile.h:9:32: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) + | ^~~~~~~~~~~~~~~~~~~ +knetfile.c:415:9: note: in expansion of macro 'netwrite' + 415 | netwrite(fp->fd, buf, l); + | ^~~~~~~~ +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o -bam_index.c: In function 'bam_index_load_core': -bam_index.c:335:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 335 | fread(magic, 1, 4, fp); - | ^~~~~~~~~~~~~~~~~~~~~~ -bam_index.c:342:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 342 | fread(&idx->n, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -bam_index.c:355:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 355 | fread(&size, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~ -bam_index.c:358:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 358 | fread(&key, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~ -bam_index.c:362:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 362 | fread(&p->n, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~ -bam_index.c:366:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 366 | fread(p->list, 16, p->n, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bam_index.c:376:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 376 | fread(&index2->n, 4, 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -bam_index.c:380:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 380 | fread(index2->offset, index2->n, 8, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o +gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o @@ -524,11 +643,7 @@ make[4]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg' make[4]: Entering directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o -gcc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/reproducible-path/samtools-legacy-0.1.19+dfsg/bcftools' @@ -558,8 +673,8 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz @@ -629,12 +744,14 @@ 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/639754/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/639754/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/1078381 and its subdirectories -I: Current time: Fri Mar 7 21:56:13 -12 2025 -I: pbuilder-time-stamp: 1741427773 +I: removing directory /srv/workspace/pbuilder/639754 and its subdirectories +I: Current time: Sat Apr 11 06:19:56 +14 2026 +I: pbuilder-time-stamp: 1775837996