Diff of the two buildlogs: -- --- b1/build.log 2024-11-10 09:13:36.902787539 +0000 +++ b2/build.log 2024-11-10 09:19:48.849489041 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Dec 13 03:34:12 -12 2025 -I: pbuilder-time-stamp: 1765640052 +I: Current time: Sun Nov 10 23:13:39 +14 2024 +I: pbuilder-time-stamp: 1731230019 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -31,53 +31,85 @@ dpkg-source: info: applying simd_fixes I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/470/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/18005/tmp/hooks/D01_modify_environment starting +debug: Running on infom07-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 10 09:13 /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/18005/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/18005/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='5c4fc8aee9b14763bf57120276c4ae0e' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='470' - PS1='# ' - PS2='> ' + INVOCATION_ID=fc27681591cf436c89f824b868447ea2 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=18005 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.zDBzbua4/pbuilderrc_ljZu --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zDBzbua4/b1 --logfile b1/build.log gmap_2024-10-20+ds-1.dsc' - SUDO_GID='111' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.zDBzbua4/pbuilderrc_1Ybm --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zDBzbua4/b2 --logfile b2/build.log gmap_2024-10-20+ds-1.dsc' + SUDO_GID=111 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom08-i386 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/470/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/18005/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -160,7 +192,7 @@ Get: 33 http://deb.debian.org/debian unstable/main i386 libbz2-dev i386 1.0.8-6 [32.1 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 libsimde-dev all 0.8.2-1 [465 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] -Fetched 21.7 MB in 1s (22.3 MB/s) +Fetched 21.7 MB in 2s (9963 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19956 files and directories currently installed.) @@ -315,7 +347,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/gmap-2024-10-20+ds/ && 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 > ../gmap_2024-10-20+ds-1_source.changes +I: user script /srv/workspace/pbuilder/18005/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/18005/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/gmap-2024-10-20+ds/ && 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 > ../gmap_2024-10-20+ds-1_source.changes dpkg-buildpackage: info: source package gmap dpkg-buildpackage: info: source version 2024-10-20+ds-1 dpkg-buildpackage: info: source distribution unstable @@ -719,7 +755,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/gmap-2024-10-20+ds' dh_auto_build - cd build && make -j6 + cd build && make -j5 make[2]: Entering directory '/build/reproducible-path/gmap-2024-10-20+ds/build' Making all in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-10-20+ds/build/src' @@ -736,6 +772,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -755,9 +792,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -778,6 +813,7 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c @@ -828,6 +864,7 @@ | | | size_t {aka unsigned int} ../../src/access.c: In function 'Access_mmap_and_preload': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ @@ -898,8 +935,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -999,6 +1034,7 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -1105,7 +1141,6 @@ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -1117,6 +1152,7 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c @@ -1152,6 +1188,7 @@ 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -1172,12 +1209,13 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'Access_allocate_shared': ../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", @@ -1201,7 +1239,6 @@ | | | size_t {aka unsigned int} ../../src/access.c: In function 'Access_mmap_offset': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c:1084:82: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ @@ -1293,7 +1330,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -1518,6 +1554,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -1526,7 +1563,6 @@ ../../src/compress-write.c:847:5: note: in expansion of macro 'FREAD_UINTS' 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c @@ -1706,7 +1742,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -1726,6 +1761,8 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -1746,7 +1783,6 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c @@ -1784,7 +1820,6 @@ | ~~~~~~ | | | size_t {aka unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/access.c:1084:94: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1084 | fprintf(stderr,"Error in access.c (2): Got mmap failure on fd %d, offset %jd, length %jd. Error %d: %s\n", | ~~^ @@ -1816,7 +1851,6 @@ | ~~~~~~ | | | size_t {aka unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -1867,6 +1901,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c @@ -2083,6 +2119,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb.c: In function 'Indexdb_get_filenames_bitpack': ../../src/indexdb.c:935:92: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 935 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", @@ -2094,7 +2131,6 @@ | ~~~ | | | int -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); @@ -2120,6 +2156,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -2139,7 +2176,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -2385,7 +2421,6 @@ | ~~~~~~ | | | size_t {aka unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'Access_mmap_and_preload': ../../src/access.c:1317:85: warning: format '%jd' expects argument of type 'intmax_t', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", @@ -2457,6 +2492,7 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': @@ -2557,7 +2593,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -2663,6 +2698,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c @@ -2670,6 +2706,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -2689,7 +2726,6 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -2934,7 +2970,6 @@ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -3040,6 +3075,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c @@ -3051,6 +3087,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -3070,9 +3107,7 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -3093,12 +3128,12 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'Access_allocate_shared': ../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", @@ -3153,6 +3188,7 @@ | ~~~~ | | | size_t {aka unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c:1317:101: warning: format '%jd' expects argument of type 'intmax_t', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 1317 | fprintf(stderr,"Error in access.c (5): Got mmap failure on file %s with len %jd from length %jd. Error %d: %s\n", | ~~^ @@ -3436,7 +3472,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb.c: In function 'Indexdb_get_filenames_bitpack': ../../src/indexdb.c:935:92: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 935 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", @@ -3452,13 +3487,9 @@ ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -3470,6 +3501,11 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c @@ -3639,7 +3675,6 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -3739,6 +3774,8 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -3844,7 +3881,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': @@ -3872,11 +3908,11 @@ | ~~~ | | | int -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c @@ -3926,7 +3962,6 @@ 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -3947,11 +3982,11 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/access.c: In function 'Access_allocate_shared': ../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", @@ -4066,6 +4101,7 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c @@ -4168,7 +4204,6 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -4274,10 +4309,11 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function 'Compress_cat': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/littleendian.h:26:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -4290,7 +4326,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb.c: In function 'Indexdb_get_filenames_bitpack': ../../src/indexdb.c:935:92: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 935 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", @@ -4306,8 +4341,10 @@ ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -4319,7 +4356,6 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c @@ -4335,7 +4371,27 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 14 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 27 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 60 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -4356,31 +4412,12 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 14 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:27:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 27 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:45:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:60:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 60 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'Access_allocate_shared': ../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", @@ -4445,7 +4482,6 @@ | ~~~~~~ | | | size_t {aka unsigned int} -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/access.c: In function 'copy_memory_from_file': ../../src/access.c:525:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -4497,7 +4533,6 @@ 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -4603,6 +4638,7 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c In file included from ../../src/iit-read-univ.c:12: @@ -4711,7 +4747,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -4726,6 +4761,7 @@ ../../src/transcriptome.c:184:5: note: in expansion of macro 'FREAD_INT' 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c @@ -4758,7 +4794,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -4779,8 +4814,11 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'Access_allocate_shared': ../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", @@ -4895,10 +4933,7 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -5103,6 +5138,11 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -5114,10 +5154,6 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c @@ -5198,6 +5234,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -5205,7 +5242,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c @@ -5220,7 +5256,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:14:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 14 | write(fd,buf,1); @@ -5240,6 +5275,8 @@ ../../src/littleendian.c:66:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -5260,13 +5297,11 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c ../../src/access.c: In function 'Access_allocate_shared': ../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", @@ -5381,7 +5416,7 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -5481,6 +5516,7 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -5587,8 +5623,6 @@ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In function 'update', inlined from 'finish' at ../../src/md5.c:241:3, inlined from 'MD5_compute' at ../../src/md5.c:273:10: @@ -5600,6 +5634,8 @@ ../../src/md5.c:104:1: note: in a call to function 'transform' 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c @@ -5727,8 +5763,6 @@ 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -5749,6 +5783,8 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c @@ -5868,7 +5904,6 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -5968,6 +6003,9 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -6073,8 +6111,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c @@ -6111,6 +6147,9 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c ../../src/indexdb.c: In function 'Indexdb_get_filenames_bitpack': ../../src/indexdb.c:935:92: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] 935 | fprintf(stderr,"Cannot parse part between %s and offsets in filename %s: found %ld characters, expecting %d\n", @@ -6126,9 +6165,6 @@ ../../src/indexdb.c:1953:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c @@ -6137,9 +6173,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -6148,6 +6181,9 @@ /usr/include/i386-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c @@ -6225,7 +6261,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -6246,8 +6281,10 @@ /usr/include/i386-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -6255,7 +6292,6 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c @@ -6293,8 +6329,6 @@ | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:16:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 16 | write(fd,buf,1); @@ -6315,9 +6349,10 @@ ../../src/bigendian.c:484:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function 'Access_allocate_shared': ../../src/access.c:884:93: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 884 | fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n", @@ -6432,8 +6467,8 @@ ../../src/access.c:615:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:24:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -6533,6 +6568,8 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:23:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -6625,6 +6662,7 @@ ../../src/iit-read.c:3524:5: note: in expansion of macro 'FREAD_INT' 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:29:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -6638,8 +6676,6 @@ ../../src/iit-read.c:2293:5: note: in expansion of macro 'FREAD_UINT' 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c @@ -6710,10 +6746,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: @@ -6722,6 +6754,10 @@ /usr/include/i386-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c @@ -6748,7 +6784,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:124:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", @@ -6797,6 +6832,7 @@ | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long long unsigned int} +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c @@ -6841,7 +6877,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1314:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long long unsigned int'} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -6889,12 +6924,11 @@ | | | | unsigned int Univcoord_T {aka long long unsigned int} | %llu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, @@ -6915,10 +6949,10 @@ /usr/include/i386-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:236:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); @@ -6926,6 +6960,8 @@ ../../src/samheader.c:241:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2024-10-20+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c @@ -6982,42 +7018,42 @@ Making all in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-10-20+ds/build/util' cp gmap_process.pl gmap_process +chmod +x gmap_process cp gmap_build.pl gmap_build -cp gmap_cat.pl gmap_cat -cp md_coords.pl md_coords -cp fa_coords.pl fa_coords -cp psl_splicesites.pl psl_splicesites chmod +x gmap_build -chmod +x gmap_process +cp gmap_cat.pl gmap_cat chmod +x gmap_cat +cp md_coords.pl md_coords chmod +x md_coords +cp fa_coords.pl fa_coords chmod +x fa_coords +cp psl_splicesites.pl psl_splicesites chmod +x psl_splicesites cp psl_introns.pl psl_introns +chmod +x psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes -cp gtf_splicesites.pl gtf_splicesites -chmod +x psl_introns chmod +x psl_genes -cp gtf_introns.pl gtf_introns chmod +x ensembl_genes +cp gtf_splicesites.pl gtf_splicesites chmod +x gtf_splicesites -cp gtf_genes.pl gtf_genes +cp gtf_introns.pl gtf_introns chmod +x gtf_introns +cp gtf_genes.pl gtf_genes chmod +x gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites -cp gff3_splicesites.pl gff3_splicesites -cp gff3_introns.pl gff3_introns -cp gff3_genes.pl gff3_genes chmod +x gtf_transcript_splicesites +cp gff3_splicesites.pl gff3_splicesites chmod +x gff3_splicesites +cp gff3_introns.pl gff3_introns chmod +x gff3_introns +cp gff3_genes.pl gff3_genes +chmod +x gff3_genes cp dbsnp_iit.pl dbsnp_iit +chmod +x dbsnp_iit cp gvf_iit.pl gvf_iit -chmod +x gff3_genes -cp vcf_iit.pl vcf_iit chmod +x gvf_iit -chmod +x dbsnp_iit +cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2024-10-20+ds/build/util' Making all in tests @@ -7086,21 +7122,21 @@ /usr/bin/help2man --no-info --version-string=2024-10-20+ds-1 --name='Tool for genome database creation for GMAP or GSNAP' \ /build/reproducible-path/gmap-2024-10-20+ds/build/util/gmap_build |debian/filter.pl >/build/reproducible-path/gmap-2024-10-20+ds/debian/gmap/usr/share/man/man1/gmap_build.1 dh_auto_install - cd build && make -j6 install DESTDIR=/build/reproducible-path/gmap-2024-10-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no + cd build && make -j5 install DESTDIR=/build/reproducible-path/gmap-2024-10-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/gmap-2024-10-20+ds/build' Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2024-10-20+ds/build/src' make[4]: Entering directory '/build/reproducible-path/gmap-2024-10-20+ds/build/src' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-10-20+ds/debian/gmap/usr/lib/gmap' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd '/build/reproducible-path/gmap-2024-10-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-10-20+ds/build/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-10-20+ds/build/src' Making install in util make[3]: Entering directory '/build/reproducible-path/gmap-2024-10-20+ds/build/util' make[4]: Entering directory '/build/reproducible-path/gmap-2024-10-20+ds/build/util' -make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/gmap-2024-10-20+ds/debian/gmap/usr/lib/gmap' +make[4]: Nothing to be done for 'install-data-am'. /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/reproducible-path/gmap-2024-10-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2024-10-20+ds/build/util' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-10-20+ds/build/util' @@ -7114,7 +7150,7 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2024-10-20+ds/build' make[4]: Entering directory '/build/reproducible-path/gmap-2024-10-20+ds/build' make[4]: Nothing to be done for 'install-exec-am'. -/bin/bash /build/reproducible-path/gmap-2024-10-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-10-20+ds/debian/gmap/var/cache/gmap +/bin/sh /build/reproducible-path/gmap-2024-10-20+ds/config/install-sh -d /build/reproducible-path/gmap-2024-10-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2024-10-20+ds/build' make[3]: Leaving directory '/build/reproducible-path/gmap-2024-10-20+ds/build' make[2]: Leaving directory '/build/reproducible-path/gmap-2024-10-20+ds/build' @@ -7172,12 +7208,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/18005/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/18005/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/470 and its subdirectories -I: Current time: Sat Dec 13 03:36:35 -12 2025 -I: pbuilder-time-stamp: 1765640195 +I: removing directory /srv/workspace/pbuilder/18005 and its subdirectories +I: Current time: Sun Nov 10 23:19:47 +14 2024 +I: pbuilder-time-stamp: 1731230387