Diff of the two buildlogs: -- --- b1/build.log 2025-10-10 10:35:20.302414618 +0000 +++ b2/build.log 2025-10-10 10:38:00.098600448 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Oct 9 22:29:34 -12 2025 -I: pbuilder-time-stamp: 1760092174 +I: Current time: Fri Nov 13 06:58:24 +14 2026 +I: pbuilder-time-stamp: 1794502704 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -26,53 +26,85 @@ dpkg-source: info: applying simd_fixes I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4053389/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1574342/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 12 16:58 /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/1574342/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1574342/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='d8a523e9e40e4841ac99578507bca9ae' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='4053389' - PS1='# ' - PS2='> ' + INVOCATION_ID=f87e98ac11d2411bb49cd58f70ce9734 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1574342 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.wOQLN87Q/pbuilderrc_GEsw --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.wOQLN87Q/b1 --logfile b1/build.log gmap_2025-07-31+ds-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wOQLN87Q/pbuilderrc_0oQp --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.wOQLN87Q/b2 --logfile b2/build.log gmap_2025-07-31+ds-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4053389/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1574342/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -155,7 +187,7 @@ Get: 33 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libsimde-dev all 0.8.2-3 [467 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 12.6 MB in 0s (121 MB/s) +Fetched 12.6 MB in 0s (94.7 MB/s) Preconfiguring packages ... 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 ... 19958 files and directories currently installed.) @@ -315,7 +347,11 @@ fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/gmap-2025-07-31+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_2025-07-31+ds-1_source.changes +I: user script /srv/workspace/pbuilder/1574342/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1574342/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/gmap-2025-07-31+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_2025-07-31+ds-1_source.changes dpkg-buildpackage: info: source package gmap dpkg-buildpackage: info: source version 2025-07-31+ds-1 dpkg-buildpackage: info: source distribution unstable @@ -724,26 +760,6 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -../../src/littleendian.c: In function 'Littleendian_write_char': -../../src/littleendian.c:13:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 13 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint': -../../src/littleendian.c:26:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 26 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8': -../../src/littleendian.c:44:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 44 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': -../../src/littleendian.c:59:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 59 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/littleendian.c:65:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 65 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 15 | write(fd,buf,1); @@ -761,14 +777,37 @@ 366 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/bigendian.c:483:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 483 | read(fd,buf,8); | ^~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_char': +../../src/littleendian.c:13:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 13 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint': +../../src/littleendian.c:26:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 26 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8': +../../src/littleendian.c:44:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 44 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': +../../src/littleendian.c:59:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 59 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/littleendian.c:65:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 65 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../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); @@ -819,14 +858,20 @@ ../../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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': +In file included from ../../src/iit-read.c:11: +../../src/iit-read.c: In function 'IIT_read_divint': +../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:2587:5: note: in expansion of macro 'FREAD_INT' + 2587 | FREAD_INT(&version,fp); + | ^~~~~~~~~ ../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -857,6 +902,13 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ +../../src/iit-read.c: In function 'IIT_read': +../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read.c:3102:5: note: in expansion of macro 'FREAD_INT' + 3102 | FREAD_INT(&new->version,fp); + | ^~~~~~~~~ ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:28:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -917,30 +969,6 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c -In file included from ../../src/iit-read.c:11: -../../src/iit-read.c: In function 'IIT_read_divint': -../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:2587:5: note: in expansion of macro 'FREAD_INT' - 2587 | FREAD_INT(&version,fp); - | ^~~~~~~~~ -../../src/iit-read.c: In function 'IIT_read': -../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read.c:3102:5: note: in expansion of macro 'FREAD_INT' - 3102 | FREAD_INT(&new->version,fp); - | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1759:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1759 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -957,6 +985,13 @@ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1888:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1888 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); @@ -1031,6 +1066,7 @@ ../../src/iit-read.c:2292:5: note: in expansion of macro 'FREAD_UINT' 2292 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c @@ -1054,10 +1090,14 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:13:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 13 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 15 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:26:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | write(fd,buf,4); @@ -1073,10 +1113,6 @@ ../../src/littleendian.c:65:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 65 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 15 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/bigendian.c:214:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 214 | write(fd,buf,4); @@ -1101,6 +1137,8 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-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); @@ -1151,9 +1189,8 @@ ../../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 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -1253,18 +1290,7 @@ ../../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 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c -In function 'update', - inlined from 'finish' at ../../src/md5.c:240:3, - inlined from 'MD5_compute' at ../../src/md5.c:272:10: -../../src/md5.c:211:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 211 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:211:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:103:1: note: in a call to function 'transform' - 103 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In file included from ../../src/iit-read.c:11: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -1370,8 +1396,18 @@ ../../src/iit-read.c:2292:5: note: in expansion of macro 'FREAD_UINT' 2292 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c +In function 'update', + inlined from 'finish' at ../../src/md5.c:240:3, + inlined from 'MD5_compute' at ../../src/md5.c:272:10: +../../src/md5.c:211:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 211 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:211:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:103:1: note: in a call to function 'transform' + 103 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 @@ -1405,6 +1441,12 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-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 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-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 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5395:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5395 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -1623,13 +1665,6 @@ | ~~~~~~~~ | | | UINT8 {aka long 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.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 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-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 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:786:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 786 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -1655,6 +1690,7 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c @@ -1664,6 +1700,8 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c In file included from ../../src/sarray-write.c:33: ../../src/sarray-write.c: In function 'Sarray_write_csa': ../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -1801,8 +1839,6 @@ ../../src/sarray-write.c:2442:5: note: in expansion of macro 'FREAD_UINT' 2442 | FREAD_UINT(&SA_i,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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c @@ -1829,6 +1865,8 @@ ../../src/littleendian.c:65:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 65 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 15 | write(fd,buf,1); @@ -1849,10 +1887,11 @@ ../../src/bigendian.c:483:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 483 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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); @@ -1903,9 +1942,6 @@ ../../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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 @@ -1913,6 +1949,106 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:28:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 28 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:28:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 28 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ In file included from ../../src/iit-read.c:11: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -2018,109 +2154,10 @@ ../../src/iit-read.c:2292:5: note: in expansion of macro 'FREAD_UINT' 2292 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': -../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ -../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:28:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 28 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:28:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 28 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5395:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5395 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -2339,12 +2376,12 @@ | ~~~~~~~~ | | | UINT8 {aka long 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:786:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 786 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -2370,7 +2407,6 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:320:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 320 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -2433,7 +2469,6 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:13:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 13 | write(fd,buf,1); @@ -2453,6 +2488,7 @@ ../../src/littleendian.c:65:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 65 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 15 | write(fd,buf,1); @@ -2482,7 +2518,6 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c ../../src/access.c: In function 'copy_memory_from_file': -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c ../../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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2532,6 +2567,7 @@ ../../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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c @@ -2540,6 +2576,8 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/iit_store.c: In function 'parse_fasta': ../../src/iit_store.c:688:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 688 | fprintf(stderr,"Assigning %llu to end\n",end); @@ -2548,31 +2586,9 @@ | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 15 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:214:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 214 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': -../../src/bigendian.c:298:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 298 | read(fd,buf,4); - | ^~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint8': -../../src/bigendian.c:366:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 366 | write(fd,buf,8); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': -../../src/bigendian.c:483:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 483 | read(fd,buf,8); - | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:13:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 13 | write(fd,buf,1); @@ -2594,13 +2610,33 @@ | ^~~~~~~~~~~~~~~ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 15 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': +../../src/bigendian.c:214:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 214 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': +../../src/bigendian.c:298:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 298 | read(fd,buf,4); + | ^~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint8': +../../src/bigendian.c:366:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 366 | write(fd,buf,8); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint8': +../../src/bigendian.c:483:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 483 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/access.c: In function 'copy_memory_from_file': +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2650,6 +2686,9 @@ ../../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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -2749,8 +2788,6 @@ ../../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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 In file included from ../../src/iit-read.c:11: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -2795,7 +2832,6 @@ ../../src/iit-read.c:1895:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1895 | fread(&(new->intervals[divno][i].type),sizeof(int),1,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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:28:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -2844,6 +2880,7 @@ ../../src/iit-read.c:3523:5: note: in expansion of macro 'FREAD_INT' 3523 | FREAD_INT(&new->version,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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:28:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -2857,13 +2894,13 @@ ../../src/iit-read.c:2292:5: note: in expansion of macro 'FREAD_UINT' 2292 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:13:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 13 | write(fd,buf,1); @@ -2884,6 +2921,7 @@ 65 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_write_char': +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 15 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -2903,8 +2941,6 @@ ../../src/bigendian.c:483:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 483 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c @@ -2913,42 +2949,11 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -In file included from ../../src/iit-read-univ.c:12: -../../src/iit-read-univ.c: In function 'read_tree_univ': +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/access.c: In function 'copy_memory_from_file': -../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' - 1068 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' - 1070 | FREAD_INT(&(new->nodes[i].a),fp); - | ^~~~~~~~~ -../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' - 1071 | FREAD_INT(&(new->nodes[i].b),fp); - | ^~~~~~~~~ -../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' - 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); - | ^~~~~~~~~ ../../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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' - 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); - | ^~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2970,73 +2975,6 @@ ../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_intervals_univ': -../../src/littleendian.h:28:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 28 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' - 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:28:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 28 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' - 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); - | ^~~~~~~~~~~ -../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' - 1123 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' - 1132 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' - 1134 | FREAD_UINT(&uint4,fp); - | ^~~~~~~~~~ -../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' - 1136 | FREAD_INT(&(new->intervals[i].type),fp); - | ^~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words': -../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' - 1196 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' - 1278 | FREAD_UINT(&length,fp); - | ^~~~~~~~~~ ../../src/access.c: In function 'copy_limited_from_file': ../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); @@ -3062,7 +3000,7 @@ ../../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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 In file included from ../../src/iit-read.c:11: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -3078,7 +3016,6 @@ ../../src/iit-read.c:3102:5: note: in expansion of macro 'FREAD_INT' 3102 | FREAD_INT(&new->version,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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/iit-read.c: In function 'read_tree': ../../src/iit-read.c:1759:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1759 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); @@ -3092,6 +3029,7 @@ ../../src/iit-read.c:1762:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3169,7 +3107,105 @@ ../../src/iit-read.c:2292:5: note: in expansion of macro 'FREAD_UINT' 2292 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c +In file included from ../../src/iit-read-univ.c:12: +../../src/iit-read-univ.c: In function 'read_tree_univ': +../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' + 1068 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1070:9: note: in expansion of macro 'FREAD_INT' + 1070 | FREAD_INT(&(new->nodes[i].a),fp); + | ^~~~~~~~~ +../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1071:9: note: in expansion of macro 'FREAD_INT' + 1071 | FREAD_INT(&(new->nodes[i].b),fp); + | ^~~~~~~~~ +../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1072:9: note: in expansion of macro 'FREAD_INT' + 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); + | ^~~~~~~~~ +../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' + 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_intervals_univ': +../../src/littleendian.h:28:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 28 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1121:7: note: in expansion of macro 'FREAD_UINT8' + 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:28:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 28 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1122:7: note: in expansion of macro 'FREAD_UINT8' + 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); + | ^~~~~~~~~~~ +../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1123:7: note: in expansion of macro 'FREAD_INT' + 1123 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1132:7: note: in expansion of macro 'FREAD_UINT' + 1132 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1134:7: note: in expansion of macro 'FREAD_UINT' + 1134 | FREAD_UINT(&uint4,fp); + | ^~~~~~~~~~ +../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1136:7: note: in expansion of macro 'FREAD_INT' + 1136 | FREAD_INT(&(new->intervals[i].type),fp); + | ^~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words': +../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' + 1196 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c @@ -3179,19 +3215,7 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/littleendian.c: In function 'Littleendian_write_char': -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 15 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:214:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 214 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/littleendian.c:13:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 13 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -3210,6 +3234,18 @@ ../../src/littleendian.c:65:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 65 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 15 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_uint': +../../src/bigendian.c:214:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 214 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:298:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 298 | read(fd,buf,4); | ^~~~~~~~~~~~~~ @@ -3227,6 +3263,8 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.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); @@ -3277,10 +3315,10 @@ ../../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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-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:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -3357,30 +3395,6 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_annotations': -../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] - 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/iit-read-univ.c: In function 'read_words_debug': -../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:320:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 320 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -3388,21 +3402,7 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:587:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 587 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:20: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:25:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 25 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:846:5: note: in expansion of macro 'FREAD_UINTS' - 846 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_annotations': In file included from ../../src/iit-read.c:11: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -3411,6 +3411,13 @@ ../../src/iit-read.c:2587:5: note: in expansion of macro 'FREAD_INT' 2587 | FREAD_INT(&version,fp); | ^~~~~~~~~ +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:587:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 587 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -3447,6 +3454,21 @@ ../../src/iit-read.c:1895:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1895 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1393:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1397:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1401:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] + 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function 'read_words': ../../src/littleendian.h:28:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -3460,6 +3482,13 @@ ../../src/iit-read.c:2149:5: note: in expansion of macro 'FREAD_UINT' 2149 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/iit-read-univ.c: In function 'read_words_debug': +../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' + 1278 | FREAD_UINT(&length,fp); + | ^~~~~~~~~~ ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2481:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2481 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -3508,7 +3537,14 @@ ../../src/iit-read.c:2292:5: note: in expansion of macro 'FREAD_UINT' 2292 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +In file included from ../../src/compress-write.c:20: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:25:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 25 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:846:5: note: in expansion of macro 'FREAD_UINTS' + 846 | FREAD_UINTS(Buffer,3,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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 @@ -3737,7 +3773,6 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:786:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 786 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -3763,9 +3798,8 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In function 'update', inlined from 'finish' at ../../src/md5.c:240:3, inlined from 'MD5_compute' at ../../src/md5.c:272:10: @@ -3777,6 +3811,8 @@ ../../src/md5.c:103:1: note: in a call to function 'transform' 103 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c @@ -3788,7 +3824,6 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function 'Littleendian_write_char': -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c:13:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 13 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -3807,6 +3842,7 @@ ../../src/littleendian.c:65:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 65 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c ../../src/bigendian.c: In function 'Bigendian_write_char': @@ -3832,6 +3868,7 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.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); @@ -3882,11 +3919,8 @@ ../../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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -3986,6 +4020,8 @@ ../../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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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:11: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -4092,7 +4128,6 @@ 2292 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:320:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 320 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -4107,7 +4142,6 @@ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c In file included from ../../src/compress-write.c:20: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:25:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -4116,6 +4150,8 @@ ../../src/compress-write.c:846:5: note: in expansion of macro 'FREAD_UINTS' 846 | FREAD_UINTS(Buffer,3,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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c @@ -4339,6 +4375,10 @@ | | | UINT8 {aka long 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c @@ -4349,7 +4389,6 @@ | | | | long long unsigned int long unsigned int | %lu -../../src/indexdb.c: In function 'positions_read_multiple': ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1178:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1178 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -4357,9 +4396,6 @@ | | | | long long unsigned int long unsigned int | %lu -../../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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function 'Indexdb_write_positions_huge_offsets': ../../src/indexdb-write.c:2866:43: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Hugepositionsptr_T' {aka 'long unsigned int'} [-Wformat=] 2866 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", @@ -4374,6 +4410,8 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c In function 'update', inlined from 'finish' at ../../src/md5.c:240:3, inlined from 'MD5_compute' at ../../src/md5.c:272:10: @@ -4385,8 +4423,6 @@ ../../src/md5.c:103:1: note: in a call to function 'transform' 103 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c @@ -4398,6 +4434,8 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:13:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 13 | write(fd,buf,1); @@ -4417,12 +4455,7 @@ ../../src/littleendian.c:65:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 65 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 15 | write(fd,buf,1); @@ -4443,9 +4476,9 @@ ../../src/bigendian.c:483:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 483 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.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); @@ -4496,6 +4529,9 @@ ../../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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-univ.c:12: @@ -4597,31 +4633,6 @@ ../../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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c -../../src/compress-write.c: In function 'put_compressed_one': -../../src/compress-write.c:320:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 320 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); - | ~~~^ ~~~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -../../src/compress-write.c: In function 'Compress_compress': -../../src/compress-write.c:587:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 587 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); - | ~~~^ ~~~~~~~~ - | | | - | long long unsigned int Univcoord_T {aka long unsigned int} - | %lu -In file included from ../../src/compress-write.c:20: -../../src/compress-write.c: In function 'Compress_cat': -../../src/littleendian.h:25:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 25 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/compress-write.c:846:5: note: in expansion of macro 'FREAD_UINTS' - 846 | FREAD_UINTS(Buffer,3,fp); - | ^~~~~~~~~~~ In file included from ../../src/iit-read.c:11: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -4727,6 +4738,31 @@ ../../src/iit-read.c:2292:5: note: in expansion of macro 'FREAD_UINT' 2292 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c +../../src/compress-write.c: In function 'put_compressed_one': +../../src/compress-write.c:320:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 320 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); + | ~~~^ ~~~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +../../src/compress-write.c: In function 'Compress_compress': +../../src/compress-write.c:587:73: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 587 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); + | ~~~^ ~~~~~~~~ + | | | + | long long unsigned int Univcoord_T {aka long unsigned int} + | %lu +In file included from ../../src/compress-write.c:20: +../../src/compress-write.c: In function 'Compress_cat': +../../src/littleendian.h:25:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 25 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/compress-write.c:846:5: note: in expansion of macro 'FREAD_UINTS' + 846 | FREAD_UINTS(Buffer,3,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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 @@ -4950,12 +4986,11 @@ | | | UINT8 {aka long 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 '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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets': ../../src/indexdb-write.c:786:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 786 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -4963,7 +4998,6 @@ | | | | long long unsigned int long unsigned int | %lu -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c ../../src/indexdb-write.c: In function 'Indexdb_write_offsets_huge': ../../src/indexdb-write.c:1178:30: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 1178 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); @@ -4982,8 +5016,11 @@ | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c In function 'update', inlined from 'finish' at ../../src/md5.c:240:3, inlined from 'MD5_compute' at ../../src/md5.c:272:10: @@ -4995,7 +5032,6 @@ ../../src/md5.c:103:1: note: in a call to function 'transform' 103 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c @@ -5010,18 +5046,27 @@ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c +../../src/bigendian.c: In function 'Bigendian_write_char': +../../src/bigendian.c:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 15 | write(fd,buf,1); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:13:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 13 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/littleendian.c: In function 'Littleendian_write_uint': ../../src/littleendian.c:26:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c: In function 'Bigendian_write_uint': ../../src/littleendian.c: In function 'Littleendian_write_uint8': ../../src/littleendian.c:44:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 44 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ +../../src/bigendian.c:214:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] + 214 | write(fd,buf,4); + | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function 'Littleendian_write_uint8_as_uint': ../../src/littleendian.c:59:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | write(fd,buf,4); @@ -5029,14 +5074,6 @@ ../../src/littleendian.c:65:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 65 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_char': -../../src/bigendian.c:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 15 | write(fd,buf,1); - | ^~~~~~~~~~~~~~~ -../../src/bigendian.c: In function 'Bigendian_write_uint': -../../src/bigendian.c:214:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] - 214 | write(fd,buf,4); - | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function 'Bigendian_fileio_read_uint': ../../src/bigendian.c:298:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 298 | read(fd,buf,4); @@ -5049,11 +5086,14 @@ ../../src/bigendian.c:483:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 483 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.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); @@ -5104,12 +5144,6 @@ ../../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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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.c:11: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -5215,8 +5249,11 @@ ../../src/iit-read.c:2292:5: note: in expansion of macro 'FREAD_UINT' 2292 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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: ../../src/iit-read-univ.c: In function 'read_tree_univ': +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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -5247,7 +5284,6 @@ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro 'FREAD_INT' 1073 | FREAD_INT(&(new->nodes[i].rightindex),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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c ../../src/iit-read-univ.c: In function 'read_intervals_univ': ../../src/littleendian.h:28:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -5317,6 +5353,9 @@ | ^~~~~~~~~~ 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/bitpack64-write.c: In function 'Bitpack64_write_differential_huge': ../../src/bitpack64-write.c:5395:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'Oligospace_T' {aka 'long unsigned int'} [-Wformat=] 5395 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", @@ -5535,11 +5574,7 @@ | ~~~~~~~~ | | | UINT8 {aka long 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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:28: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -5554,6 +5589,7 @@ ../../src/transcriptome.c:183:5: note: in expansion of macro 'FREAD_INT' 183 | 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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c @@ -5566,6 +5602,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/littleendian.c: In function 'Littleendian_write_char': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/littleendian.c:13:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 13 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ @@ -5584,7 +5621,6 @@ ../../src/littleendian.c:65:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 65 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 15 | write(fd,buf,1); @@ -5613,58 +5649,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -../../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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c: In function 'copy_limited_from_file': -../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -5741,6 +5725,7 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/access.c: In function 'copy_memory_from_file': ../../src/iit-read-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -5757,6 +5742,31 @@ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:530:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:536:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:541:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:547:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:552:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:558:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:563:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/iit-read-univ.c: In function 'read_words_debug': ../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 23 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) @@ -5764,6 +5774,33 @@ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro 'FREAD_UINT' 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +../../src/access.c: In function 'copy_limited_from_file': +../../src/access.c:589:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:591:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:597:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:599:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:605:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:607:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/access.c:613:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 In file included from ../../src/iit-read.c:11: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -5772,7 +5809,6 @@ ../../src/iit-read.c:2587:5: note: in expansion of macro 'FREAD_INT' 2587 | FREAD_INT(&version,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/iit-read.c: In function 'IIT_read': ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -5871,6 +5907,10 @@ 2292 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In function 'update', inlined from 'finish' at ../../src/md5.c:240:3, inlined from 'MD5_compute' at ../../src/md5.c:272:10: @@ -5882,9 +5922,6 @@ ../../src/md5.c:103:1: note: in a call to function 'transform' 103 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 In file included from ../../src/compress-write.c:20: ../../src/compress-write.c: In function 'Compress_cat': ../../src/littleendian.h:25:29: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -5893,7 +5930,6 @@ ../../src/compress-write.c:846:5: note: in expansion of macro 'FREAD_UINTS' 846 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c @@ -5904,11 +5940,11 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.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 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c @@ -5951,7 +5987,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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:235:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 235 | fread(buffer,sizeof(char),CHUNK,input); @@ -5959,6 +5994,7 @@ ../../src/samheader.c:240:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 240 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 @@ -5973,6 +6009,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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:13:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 13 | write(fd,buf,1); @@ -5992,7 +6029,6 @@ ../../src/littleendian.c:65:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 65 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -6019,6 +6055,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../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); @@ -6069,8 +6107,6 @@ ../../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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': @@ -6080,6 +6116,7 @@ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro 'FREAD_UINT' 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6202,6 +6239,17 @@ ../../src/iit-read.c:1763:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'update', + inlined from 'finish' at ../../src/md5.c:240:3, + inlined from 'MD5_compute' at ../../src/md5.c:272:10: +../../src/md5.c:211:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] + 211 | transform(state,&(input[i])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/md5.c:211:7: note: referencing argument 2 of type 'unsigned char[64]' +../../src/md5.c: In function 'MD5_compute': +../../src/md5.c:103:1: note: in a call to function 'transform' + 103 | transform (UINT4 state[4], unsigned char block[64]) { + | ^~~~~~~~~ ../../src/iit-read.c: In function 'read_intervals': ../../src/iit-read.c:1888:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1888 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); @@ -6256,6 +6304,7 @@ ../../src/iit-read.c:2534:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2534 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/iit-read.c: In function 'IIT_debug': ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) @@ -6276,26 +6325,12 @@ ../../src/iit-read.c:2292:5: note: in expansion of macro 'FREAD_UINT' 2292 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -In function 'update', - inlined from 'finish' at ../../src/md5.c:240:3, - inlined from 'MD5_compute' at ../../src/md5.c:272:10: -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -../../src/md5.c:211:7: warning: 'transform' accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] - 211 | transform(state,&(input[i])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/md5.c:211:7: note: referencing argument 2 of type 'unsigned char[64]' -../../src/md5.c: In function 'MD5_compute': -../../src/md5.c:103:1: note: in a call to function 'transform' - 103 | transform (UINT4 state[4], unsigned char block[64]) { - | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-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 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c ../../src/compress-write.c: In function 'put_compressed_one': ../../src/compress-write.c:320:69: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 320 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); @@ -6318,6 +6353,7 @@ ../../src/compress-write.c:846:5: note: in expansion of macro 'FREAD_UINTS' 846 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c @@ -6378,8 +6414,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:235:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 235 | fread(buffer,sizeof(char),CHUNK,input); @@ -6387,6 +6421,8 @@ ../../src/samheader.c:240:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 240 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c @@ -6607,7 +6643,6 @@ 2587 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function 'IIT_read': -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 22 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ @@ -6656,7 +6691,6 @@ ../../src/iit-read.c:2149:5: note: in expansion of macro 'FREAD_UINT' 2149 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/iit-read.c: In function 'read_annotations': ../../src/iit-read.c:2481:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 2481 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); @@ -6692,6 +6726,7 @@ ../../src/iit-read.c:3523:5: note: in expansion of macro 'FREAD_INT' 3523 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/iit-read.c: In function 'read_words_debug': ../../src/littleendian.h:28:27: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 28 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) @@ -6705,6 +6740,7 @@ ../../src/iit-read.c:2292:5: note: in expansion of macro 'FREAD_UINT' 2292 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:28: @@ -6857,9 +6893,6 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': ../../src/samheader.c:235:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 235 | fread(buffer,sizeof(char),CHUNK,input); @@ -6867,6 +6900,9 @@ ../../src/samheader.c:240:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 240 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c @@ -6881,6 +6917,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/littleendian.c: In function 'Littleendian_write_char': ../../src/littleendian.c:13:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 13 | write(fd,buf,1); @@ -6900,7 +6937,6 @@ ../../src/littleendian.c:65:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 65 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/bigendian.c: In function 'Bigendian_write_char': ../../src/bigendian.c:15:3: warning: ignoring return value of 'write' declared with attribute 'warn_unused_result' [-Wunused-result] 15 | write(fd,buf,1); @@ -6927,7 +6963,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../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); @@ -6978,8 +7013,12 @@ ../../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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function 'read_tree_univ': ../../src/littleendian.h:23:26: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -7056,7 +7095,6 @@ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro 'FREAD_UINT' 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-univ.c: In function 'read_annotations': ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); @@ -7080,9 +7118,10 @@ ../../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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c In file included from ../../src/iit-read.c:11: ../../src/iit-read.c: In function 'IIT_read_divint': ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -7188,7 +7227,6 @@ ../../src/iit-read.c:2292:5: note: in expansion of macro 'FREAD_UINT' 2292 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:28: ../../src/transcriptome.c: In function 'Transcriptome_new': ../../src/littleendian.h:22:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -7203,8 +7241,6 @@ ../../src/transcriptome.c:183:5: note: in expansion of macro 'FREAD_INT' 183 | FREAD_INT(&divint,fp); | ^~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c @@ -7225,18 +7261,18 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c ../../src/indexdb.c: In function 'positions_read_multiple_large': +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c ../../src/indexdb.c:1897:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c @@ -7259,6 +7295,7 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c ../../src/knownindels.c: In function 'Knownindels_new_from_dump': ../../src/knownindels.c:313:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) @@ -7267,6 +7304,7 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c ../../src/knownsplicing.c: In function 'Knownsplicing_new_from_dump': ../../src/knownsplicing.c:498:25: warning: format '%llu' expects argument of type 'long long unsigned int *', but argument 3 has type 'Univcoord_T *' {aka 'long unsigned int *'} [-Wformat=] 498 | sscanf(line,"%llu %llu",&startpoint,&partner) @@ -7324,8 +7362,6 @@ | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c @@ -7338,14 +7374,6 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -../../src/path.c: In function 'Path_print': -../../src/path.c:3212:26: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] - 3212 | printf(">> Path %p (%u): ",this,this->main_univdiagonal); - | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | unsigned int Univcoord_T {aka long unsigned int} - | %lu ../../src/altsplice.c: In function 'Altsplice_print': ../../src/altsplice.c:118:24: warning: format '%d' expects argument of type 'int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 118 | printf(":%u,len:%d,%llu(%d,%d)", @@ -7367,8 +7395,16 @@ | ~~~~~~~~~~~~~ | | | int +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 +../../src/path.c: In function 'Path_print': +../../src/path.c:3212:26: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] + 3212 | printf(">> Path %p (%u): ",this,this->main_univdiagonal); + | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | unsigned int Univcoord_T {aka long unsigned int} + | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c @@ -7414,6 +7450,8 @@ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ../../src/stage1hr.c: In function 'Stage1_list_extension': ../../src/stage1hr.c:1313:14: warning: format '%u' expects argument of type 'unsigned int', but argument 2 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 1313 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); @@ -7461,20 +7499,9 @@ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -../../src/samheader.c: In function 'SAM_header_change_HD_tosorted': -../../src/samheader.c:235:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 235 | fread(buffer,sizeof(char),CHUNK,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../../src/samheader.c:240:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 240 | fread(buffer,sizeof(char),headerlen,input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:4, from ../../src/single-cell.h:9, @@ -7495,14 +7522,22 @@ /usr/include/aarch64-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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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:235:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 235 | fread(buffer,sizeof(char),CHUNK,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../../src/samheader.c:240:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 240 | fread(buffer,sizeof(char),headerlen,input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c -gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c ../../src/support.c: In function 'Support_dump': ../../src/support.c:955:20: warning: format '%u' expects argument of type 'unsigned int', but argument 3 has type 'Univcoord_T' {aka 'long unsigned int'} [-Wformat=] 955 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ @@ -7528,6 +7563,7 @@ | | | unsigned int | %lu +gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm @@ -7540,11 +7576,11 @@ gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm -gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm +gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"aarch64-unknown-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/gmap-2025-07-31+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm @@ -7557,42 +7593,42 @@ cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords cp fa_coords.pl fa_coords +chmod +x gmap_build +chmod +x gmap_process cp psl_splicesites.pl psl_splicesites -cp psl_introns.pl psl_introns -cp psl_genes.pl psl_genes -cp ensembl_genes.pl ensembl_genes -cp gtf_splicesites.pl gtf_splicesites chmod +x gmap_cat +cp psl_introns.pl psl_introns chmod +x md_coords chmod +x fa_coords -chmod +x psl_introns -chmod +x psl_genes -chmod +x gmap_build -chmod +x gmap_process chmod +x psl_splicesites -chmod +x ensembl_genes -chmod +x gtf_splicesites +cp psl_genes.pl psl_genes +cp ensembl_genes.pl ensembl_genes +chmod +x psl_introns +cp gtf_splicesites.pl gtf_splicesites cp gtf_exons.pl gtf_exons cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes +chmod +x psl_genes +chmod +x ensembl_genes +chmod +x gtf_splicesites chmod +x gtf_exons -chmod +x gtf_introns -chmod +x gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites +chmod +x gtf_introns cp gff3_splicesites.pl gff3_splicesites +chmod +x gtf_genes cp gff3_exons.pl gff3_exons -chmod +x gtf_transcript_splicesites cp gff3_introns.pl gff3_introns +cp gff3_genes.pl gff3_genes +chmod +x gtf_transcript_splicesites chmod +x gff3_splicesites +cp dbsnp_iit.pl dbsnp_iit +cp gvf_iit.pl gvf_iit chmod +x gff3_exons +cp vcf_iit.pl vcf_iit chmod +x gff3_introns -cp gff3_genes.pl gff3_genes -cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_genes -cp gvf_iit.pl gvf_iit chmod +x dbsnp_iit chmod +x gvf_iit -cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/reproducible-path/gmap-2025-07-31+ds/build/util' Making all in tests @@ -7666,8 +7702,8 @@ Making install in src make[3]: Entering directory '/build/reproducible-path/gmap-2025-07-31+ds/build/src' make[4]: Entering directory '/build/reproducible-path/gmap-2025-07-31+ds/build/src' - /usr/bin/mkdir -p '/build/reproducible-path/gmap-2025-07-31+ds/debian/gmap/usr/lib/gmap' make[4]: Nothing to be done for 'install-data-am'. + /usr/bin/mkdir -p '/build/reproducible-path/gmap-2025-07-31+ds/debian/gmap/usr/lib/gmap' /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-2025-07-31+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/reproducible-path/gmap-2025-07-31+ds/build/src' make[3]: Leaving directory '/build/reproducible-path/gmap-2025-07-31+ds/build/src' @@ -7689,7 +7725,7 @@ make[3]: Entering directory '/build/reproducible-path/gmap-2025-07-31+ds/build' make[4]: Entering directory '/build/reproducible-path/gmap-2025-07-31+ds/build' make[4]: Nothing to be done for 'install-exec-am'. -/bin/bash /build/reproducible-path/gmap-2025-07-31+ds/config/install-sh -d /build/reproducible-path/gmap-2025-07-31+ds/debian/gmap/var/cache/gmap +/bin/sh /build/reproducible-path/gmap-2025-07-31+ds/config/install-sh -d /build/reproducible-path/gmap-2025-07-31+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/reproducible-path/gmap-2025-07-31+ds/build' make[3]: Leaving directory '/build/reproducible-path/gmap-2025-07-31+ds/build' make[2]: Leaving directory '/build/reproducible-path/gmap-2025-07-31+ds/build' @@ -7751,12 +7787,14 @@ 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/1574342/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1574342/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/4053389 and its subdirectories -I: Current time: Thu Oct 9 22:35:19 -12 2025 -I: pbuilder-time-stamp: 1760092519 +I: removing directory /srv/workspace/pbuilder/1574342 and its subdirectories +I: Current time: Fri Nov 13 07:00:58 +14 2026 +I: pbuilder-time-stamp: 1794502858