Diff of the two buildlogs: -- --- b1/build.log 2024-04-30 14:24:23.045602671 +0000 +++ b2/build.log 2024-04-30 14:29:02.341711029 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 2 08:46:00 -12 2025 -I: pbuilder-time-stamp: 1748897160 +I: Current time: Wed May 1 04:24:30 +14 2024 +I: pbuilder-time-stamp: 1714487070 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying arm64.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2035838/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1306934/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 30 14:24 /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/1306934/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1306934/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='55fce497a6144d79be60884915eb788e' - 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='2035838' - PS1='# ' - PS2='> ' + INVOCATION_ID=82f8ddc368f24cfd90a8b28d420046eb + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1306934 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.asHK1YtV/pbuilderrc_a8O0 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.asHK1YtV/b1 --logfile b1/build.log segemehl_0.3.4-5.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.asHK1YtV/pbuilderrc_ZSSv --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.asHK1YtV/b2 --logfile b2/build.log segemehl_0.3.4-5.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 25 19:07 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2035838/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 22 13:10 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1306934/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -209,7 +241,7 @@ Get: 52 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] -Fetched 27.3 MB in 1s (33.1 MB/s) +Fetched 27.3 MB in 3s (9464 kB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libssl3:amd64: dependency problems, but removing anyway as you requested: libkrb5-3:amd64 depends on libssl3 (>= 3.0.0). @@ -447,7 +479,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/segemehl-0.3.4/ && 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 > ../segemehl_0.3.4-5_source.changes +I: user script /srv/workspace/pbuilder/1306934/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1306934/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/segemehl-0.3.4/ && 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 > ../segemehl_0.3.4-5_source.changes dpkg-buildpackage: info: source package segemehl dpkg-buildpackage: info: source version 0.3.4-5 dpkg-buildpackage: info: source distribution unstable @@ -457,7 +493,7 @@ debian/rules clean dh clean dh_auto_clean - make -j42 clean + make -j20 clean make[1]: Entering directory '/build/reproducible-path/segemehl-0.3.4' Cleaning... rm -f -r build segemehl haarz @@ -471,221 +507,302 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/segemehl-0.3.4' dh_auto_build -- all - make -j42 "INSTALL=install --strip-program=true" all + make -j20 "INSTALL=install --strip-program=true" all make[2]: Entering directory '/build/reproducible-path/segemehl-0.3.4' -Building... library for source build/segemehl_helper.o -Building... library for source build/matealign.o -Building... library for source build/samio.o +Building... library for source build/md5.o Building... library for source build/gzidx.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/segemehl_helper.o libs/segemehl_helper.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/matealign.o libs/matealign.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/samio.o libs/samio.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/md5.o libs/md5.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/gzidx.o libs/gzidx.c -Building... library for source build/sw.o -Building... library for source build/container.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/sw.o libs/sw.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/container.o libs/container.c -Building... library for source build/stack.o -Building... library for source build/karlin.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/stack.o libs/stack.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/karlin.o libs/karlin.c +Building... library for source build/kdseed.o +Building... library for source build/sufarray.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/kdseed.o libs/kdseed.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/sufarray.o libs/sufarray.c Building... library for source build/memory.o -Building... library for source build/stringutils.o -Building... library for source build/segemehl.o +Building... library for source build/manopt.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/memory.o libs/memory.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/stringutils.o libs/stringutils.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/manopt.o libs/manopt.c +Building... library for source build/radixsort.o +Building... library for source build/fileio.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/radixsort.o libs/radixsort.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/fileio.o libs/fileio.c +Building... library for source build/match.o +Building... library for source build/intervaltree.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/match.o libs/match.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/intervaltree.o libs/intervaltree.c +Building... library for source build/segemehl.o +Building... library for source build/sw.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/segemehl.o libs/segemehl.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/sw.o libs/sw.c +Building... library for source build/junctions.o +Building... library for source build/vqueue.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/junctions.o libs/junctions.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/vqueue.o libs/vqueue.c +Building... library for source build/haarz.o Building... library for source build/bedfiles.o -Building... library for source build/brendel.o -Building... library for source build/manout.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/brendel.o libs/brendel.c +Building... library for source build/kdchain.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/haarz.o libs/haarz.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bedfiles.o libs/bedfiles.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/manout.o libs/manout.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/kdchain.o libs/kdchain.c Building... library for source build/bitVector.o -Building... library for source build/annotation.o -Building... library for source build/radixsort.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bitVector.o libs/bitVector.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/annotation.o libs/annotation.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/radixsort.o libs/radixsort.c -Building... library for source build/bitvectoralg.o Building... library for source build/sort.o -In file included from include/stringutils.h:27, - from libs/stringutils.c:39: -libs/stringutils.c: In function 'destructStringset': -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/stringutils.c:274:9: note: in expansion of macro 'FREEMEMORY' - 274 | FREEMEMORY(space, s->strings[i].str); - | ^~~~~~~~~~ -Building... library for source build/intervaltree.o -libs/stringutils.c:273:7: note: some parts of macro expansion are not guarded by this 'if' clause - 273 | if(s->strings[i].str != NULL) - | ^~ -Building... library for source build/vstack.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/sort.o libs/sort.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bitvectoralg.o libs/bitvectoralg.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/intervaltree.o libs/intervaltree.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/vstack.o libs/vstack.c -Building... library for source build/md5.o -Building... library for source build/vtprogressbar.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/md5.o libs/md5.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/vtprogressbar.o libs/vtprogressbar.c -Building... library for source build/match.o -Building... library for source build/aluruSort.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bitVector.o libs/bitVector.c +Building... library for source build/debug.o +Building... library for source build/samheader.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/debug.o libs/debug.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/samheader.o libs/samheader.c In file included from include/stringutils.h:27, from include/charsequence.h:43, - from include/multicharseq.h:43, - from include/samio.h:23, - from libs/samio.c:33: -libs/samio.c: In function 'bl_samDestructTag': + from include/sufarray.h:45, + from libs/sufarray.c:39: +libs/sufarray.c: In function 'destructSufArr': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:102:15: note: in expansion of macro 'FREEMEMORY' - 102 | if(kv->tag) FREEMEMORY(NULL, kv->tag); - | ^~~~~~~~~~ -libs/samio.c:102:3: note: some parts of macro expansion are not guarded by this 'if' clause - 102 | if(kv->tag) FREEMEMORY(NULL, kv->tag); +libs/sufarray.c:613:5: note: in expansion of macro 'FREEMEMORY' + 613 | FREEMEMORY(space, arr->lcpctab); + | ^~~~~~~~~~ +libs/sufarray.c:612:3: note: some parts of macro expansion are not guarded by this 'if' clause + 612 | if (arr->lcpctab != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:103:15: note: in expansion of macro 'FREEMEMORY' - 103 | if(kv->val) FREEMEMORY(NULL, kv->val); - | ^~~~~~~~~~ -libs/samio.c:103:3: note: some parts of macro expansion are not guarded by this 'if' clause - 103 | if(kv->val) FREEMEMORY(NULL, kv->val); +libs/sufarray.c:615:5: note: in expansion of macro 'FREEMEMORY' + 615 | FREEMEMORY(space, arr->inv_suftab); + | ^~~~~~~~~~ +libs/sufarray.c:614:3: note: some parts of macro expansion are not guarded by this 'if' clause + 614 | if (arr->inv_suftab != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:104:16: note: in expansion of macro 'FREEMEMORY' - 104 | if(kv->type) FREEMEMORY(NULL, kv->type); - | ^~~~~~~~~~ -libs/samio.c:104:3: note: some parts of macro expansion are not guarded by this 'if' clause - 104 | if(kv->type) FREEMEMORY(NULL, kv->type); +libs/sufarray.c:619:5: note: in expansion of macro 'FREEMEMORY' + 619 | FREEMEMORY(space, arr->idvtab); + | ^~~~~~~~~~ +libs/sufarray.c:618:3: note: some parts of macro expansion are not guarded by this 'if' clause + 618 | if (arr->idvtab != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:105:15: note: in expansion of macro 'FREEMEMORY' - 105 | if(kv->key) FREEMEMORY(NULL, kv->key); - | ^~~~~~~~~~ -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/match.o libs/match.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/aluruSort.o libs/aluruSort.c -libs/samio.c:105:3: note: some parts of macro expansion are not guarded by this 'if' clause - 105 | if(kv->key) FREEMEMORY(NULL, kv->key); +libs/sufarray.c:624:5: note: in expansion of macro 'FREEMEMORY' + 624 | FREEMEMORY(space, arr->suflink); + | ^~~~~~~~~~ +libs/sufarray.c:620:3: note: some parts of macro expansion are not guarded by this 'if' clause + 620 | if (arr->suflink != NULL) | ^~ -libs/samio.c: In function 'bl_samDestruct': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:112:21: note: in expansion of macro 'FREEMEMORY' - 112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname); - | ^~~~~~~~~~ -libs/samio.c:112:3: note: some parts of macro expansion are not guarded by this 'if' clause - 112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname); +libs/sufarray.c:627:5: note: in expansion of macro 'FREEMEMORY' + 627 | FREEMEMORY(space, arr->chldtab); + | ^~~~~~~~~~ +libs/sufarray.c:626:3: note: some parts of macro expansion are not guarded by this 'if' clause + 626 | if (arr->chldtab != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:113:21: note: in expansion of macro 'FREEMEMORY' - 113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname); - | ^~~~~~~~~~ -libs/samio.c:113:3: note: some parts of macro expansion are not guarded by this 'if' clause - 113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname); +libs/sufarray.c:629:5: note: in expansion of macro 'FREEMEMORY' + 629 | FREEMEMORY(space, arr->mdfive); + | ^~~~~~~~~~ +libs/sufarray.c:628:3: note: some parts of macro expansion are not guarded by this 'if' clause + 628 | if (arr->mdfive) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:114:21: note: in expansion of macro 'FREEMEMORY' - 114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar); - | ^~~~~~~~~~ -libs/samio.c:114:3: note: some parts of macro expansion are not guarded by this 'if' clause - 114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar); +libs/sufarray.c:631:5: note: in expansion of macro 'FREEMEMORY' + 631 | FREEMEMORY(space, arr->llvtab); + | ^~~~~~~~~~ +libs/sufarray.c:630:3: note: some parts of macro expansion are not guarded by this 'if' clause + 630 | if(arr->llvtab != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:115:21: note: in expansion of macro 'FREEMEMORY' - 115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext); - | ^~~~~~~~~~ -libs/samio.c:115:3: note: some parts of macro expansion are not guarded by this 'if' clause - 115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext); +libs/sufarray.c:636:5: note: in expansion of macro 'FREEMEMORY' + 636 | FREEMEMORY(space, arr->id); + | ^~~~~~~~~~ +libs/sufarray.c:632:3: note: some parts of macro expansion are not guarded by this 'if' clause + 632 | if(arr->id != NULL) | ^~ +libs/fileio.c: In function 'bl_rm': +libs/sufarray.c: In function 'readSuffixarray': +libs/sufarray.c:428:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 428 | fread(&nmemb, sizeof(Uint), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:430:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 430 | fread(suftab, sizeof(Uint), nmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/fileio.c:220:3: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 220 | system(cmd); + | ^~~~~~~~~~~ +libs/sufarray.c:431:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 431 | fread(&flags, sizeof(char), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:436:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 436 | fread(lcpctab, sizeof(unsigned char), nmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:438:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 438 | fread(&llvmemb, sizeof(Uint), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:440:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 440 | fread(llvtab, sizeof(PairUint), llvmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:446:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 446 | fread(chldtab, sizeof(childtab), nmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:484:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | fread(suflink, sizeof(Uint), nmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:508:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 508 | fread(id, sizeof(signed char), nmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:511:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 511 | fread(&idvmemb, sizeof(Uint), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:515:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 515 | fread(idvtab, sizeof(PairLSint), idvmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:519:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 519 | fread(idvutab, sizeof(PairUint), idvmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:530:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(mdfive, sizeof(unsigned char), 16, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from include/mathematics.h:117, + from libs/intervaltree.c:27: +libs/intervaltree.c: In function 'bl_intervaltreeDestruct': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:116:21: note: in expansion of macro 'FREEMEMORY' - 116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq); - | ^~~~~~~~~~ -libs/samio.c:116:3: note: some parts of macro expansion are not guarded by this 'if' clause - 116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq); +libs/intervaltree.c:443:19: note: in expansion of macro 'FREEMEMORY' + 443 | if(root->ncoll) FREEMEMORY(NULL, root->collisions); + | ^~~~~~~~~~ +libs/intervaltree.c:443:3: note: some parts of macro expansion are not guarded by this 'if' clause + 443 | if(root->ncoll) FREEMEMORY(NULL, root->collisions); | ^~ +Building... library for source build/mathematics.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/mathematics.o libs/mathematics.c +Building... library for source build/merge.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/merge.o libs/merge.c +Building... library for source build/manout.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/manout.o libs/manout.c +Building... library for source build/stack.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/stack.o libs/stack.c +In file included from include/mathematics.h:117, + from libs/mathematics.c:38: +libs/mathematics.c: In function 'destructVector': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:117:21: note: in expansion of macro 'FREEMEMORY' - 117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual); - | ^~~~~~~~~~ -libs/samio.c:117:3: note: some parts of macro expansion are not guarded by this 'if' clause - 117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual); - | ^~ +libs/mathematics.c:251:26: note: in expansion of macro 'FREEMEMORY' + 251 | if (v->elements) FREEMEMORY(space, v->elements); + | ^~~~~~~~~~ +libs/mathematics.c:251:9: note: some parts of macro expansion are not guarded by this 'if' clause + 251 | if (v->elements) FREEMEMORY(space, v->elements); + | ^~ +Building... library for source build/stringutils.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/stringutils.o libs/stringutils.c +In file included from include/stringutils.h:27, + from libs/stringutils.c:39: +libs/stringutils.c: In function 'destructStringset': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:121:20: note: in expansion of macro 'FREEMEMORY' - 121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags); +libs/stringutils.c:274:9: note: in expansion of macro 'FREEMEMORY' + 274 | FREEMEMORY(space, s->strings[i].str); + | ^~~~~~~~~~ +libs/stringutils.c:273:7: note: some parts of macro expansion are not guarded by this 'if' clause + 273 | if(s->strings[i].str != NULL) + | ^~ +Building... library for source build/queryalign.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/queryalign.o libs/queryalign.c +In file included from include/stringutils.h:27, + from libs/merge.c:34: +libs/merge.c: In function 'se_mergeWorker': +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/merge.c:1096:20: note: in expansion of macro 'FREEMEMORY' + 1096 | if(curkey) FREEMEMORY(NULL, curkey); | ^~~~~~~~~~ -libs/samio.c:121:3: note: some parts of macro expansion are not guarded by this 'if' clause - 121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags); - | ^~ -Building... library for source build/filebuffer.o -Building... library for source build/gzip.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/filebuffer.o libs/filebuffer.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/gzip.o libs/gzip.c -Building... library for source build/haarz.o -Building... library for source build/info.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/haarz.o libs/haarz.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/info.o libs/info.c -Building... library for source build/pigeon.o -Building... library for source build/sufarray.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/pigeon.o libs/pigeon.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/sufarray.o libs/sufarray.c +libs/merge.c:1096:9: note: some parts of macro expansion are not guarded by this 'if' clause + 1096 | if(curkey) FREEMEMORY(NULL, curkey); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/merge.c:1216:26: note: in expansion of macro 'FREEMEMORY' + 1216 | if(!reads && curkey) FREEMEMORY(NULL, curkey); + | ^~~~~~~~~~ +libs/merge.c:1216:5: note: some parts of macro expansion are not guarded by this 'if' clause + 1216 | if(!reads && curkey) FREEMEMORY(NULL, curkey); + | ^~ +Building... library for source build/brendel.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/brendel.o libs/brendel.c +Building... library for source build/portable_endian.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/portable_endian.o libs/portable_endian.c Building... library for source build/bitArray.o -Building... library for source build/seqclip.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bitArray.o libs/bitArray.c -In file included from include/stringutils.h:27, - from include/charsequence.h:43, - from include/locus.h:41, - from include/mapfrag.h:39, - from libs/matealign.c:32: -libs/matealign.c: In function 'bl_matealign': +Building... library for source build/mapfrag.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/mapfrag.o libs/mapfrag.c +Building... library for source build/mappingqual.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/mappingqual.o libs/mappingqual.c +Building... library for source build/pigeon.o +Building... library for source build/filebuffer.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/pigeon.o libs/pigeon.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/filebuffer.o libs/filebuffer.c +Building... library for source build/alignment.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/alignment.o libs/alignment.c +Building... library for source build/iupac.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/iupac.o libs/iupac.c +In file included from include/mathematics.h:117, + from libs/alignment.c:38: +libs/alignment.c: In function 'wrapAlignment': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/matealign.c:313:15: note: in expansion of macro 'FREEMEMORY' - 313 | if(npos[0]) FREEMEMORY(NULL, spos[0]); - | ^~~~~~~~~~ -libs/matealign.c:313:3: note: some parts of macro expansion are not guarded by this 'if' clause - 313 | if(npos[0]) FREEMEMORY(NULL, spos[0]); +libs/alignment.c:97:18: note: in expansion of macro 'FREEMEMORY' + 97 | if(al->rmvseq) FREEMEMORY(NULL, al->v); + | ^~~~~~~~~~ +libs/alignment.c:97:3: note: some parts of macro expansion are not guarded by this 'if' clause + 97 | if(al->rmvseq) FREEMEMORY(NULL, al->v); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/matealign.c:314:15: note: in expansion of macro 'FREEMEMORY' - 314 | if(npos[1]) FREEMEMORY(NULL, spos[1]); - | ^~~~~~~~~~ -libs/matealign.c:314:3: note: some parts of macro expansion are not guarded by this 'if' clause - 314 | if(npos[1]) FREEMEMORY(NULL, spos[1]); +libs/alignment.c:98:18: note: in expansion of macro 'FREEMEMORY' + 98 | if(al->rmuseq) FREEMEMORY(NULL, al->u); + | ^~~~~~~~~~ +libs/alignment.c:98:3: note: some parts of macro expansion are not guarded by this 'if' clause + 98 | if(al->rmuseq) FREEMEMORY(NULL, al->u); | ^~ -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/seqclip.o libs/seqclip.c -Building... library for source build/alignment.o +Building... library for source build/container.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/container.o libs/container.c +Building... library for source build/locus.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/locus.o libs/locus.c +In file included from include/stringutils.h:27, + from include/biofiles.h:43, + from include/segemehl.h:44, + from libs/pigeon.c:35: +libs/pigeon.c: In function 'pigeon': +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/pigeon.c:352:13: note: in expansion of macro 'FREEMEMORY' + 352 | if(check) FREEMEMORY(space, check); + | ^~~~~~~~~~ +libs/pigeon.c:352:3: note: some parts of macro expansion are not guarded by this 'if' clause + 352 | if(check) FREEMEMORY(space, check); + | ^~ +Building... library for source build/annotation.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/annotation.o libs/annotation.c In file included from include/stringutils.h:27, from libs/annotation.c:29: libs/annotation.c: In function 'bl_annotationitemDestruct': -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/alignment.o libs/alignment.c include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ @@ -695,7 +812,6 @@ libs/annotation.c:149:3: note: some parts of macro expansion are not guarded by this 'if' clause 149 | if(item->chromname) FREEMEMORY(space, item->chromname); | ^~ -Building... library for source build/junctions.o include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ @@ -806,21 +922,101 @@ libs/annotation.c:455:3: note: some parts of macro expansion are not guarded by this 'if' clause 455 | if(track->items) FREEMEMORY(space, track->items) ; | ^~ -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/junctions.o libs/junctions.c -Building... library for source build/mathematics.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/mathematics.o libs/mathematics.c +Building... library for source build/bgzip.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bgzip.o libs/bgzip.c +Building... library for source build/karlin.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/karlin.o libs/karlin.c +Building... library for source build/seqclip.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/seqclip.o libs/seqclip.c +Building... library for source build/vstack.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/vstack.o libs/vstack.c +Building... library for source build/vtprogressbar.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/vtprogressbar.o libs/vtprogressbar.c +In file included from include/stringutils.h:27, + from include/biofiles.h:43, + from include/alignment.h:38, + from include/sw.h:38, + from libs/seqclip.c:44: +libs/seqclip.c: In function 'bl_Find3PrimeGreedy': +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/seqclip.c:529:9: note: in expansion of macro 'FREEMEMORY' + 529 | FREEMEMORY(space, adapter); + | ^~~~~~~~~~ +libs/seqclip.c:528:7: note: some parts of macro expansion are not guarded by this 'if' clause + 528 | if(adapter) + | ^~ +Building... library for source build/info.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/info.o libs/info.c +Building... library for source build/fileBins.o +Building... library for source build/bamio.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/fileBins.o libs/fileBins.c +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bamio.o libs/bamio.c +libs/info.c: In function 'timestr_r': +libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=] + 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", + | ^~ +libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] + 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:906, + from libs/info.c:41: +In function 'sprintf', + inlined from 'timestr_r' at libs/info.c:64:5: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 67 bytes into a destination of size 26 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +Building... library for source build/bitvectoralg.o Building... library for source build/charsequence.o -Building... library for source build/iupac.o +libs/info.c: In function 'infomsg': +libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=] + 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", + | ^~ +In function 'timestr_r', + inlined from 'infomsg' at libs/info.c:93:4: +libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] + 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'sprintf', + inlined from 'timestr_r' at libs/info.c:64:5, + inlined from 'infomsg' at libs/info.c:93:4: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 67 bytes into a destination of size 26 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bitvectoralg.o libs/bitvectoralg.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/charsequence.o libs/charsequence.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/iupac.o libs/iupac.c -Building... library for source build/queryalign.o -Building... library for source build/mapfrag.o -Building... library for source build/debug.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/queryalign.o libs/queryalign.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/mapfrag.o libs/mapfrag.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/debug.o libs/debug.c -Building... library for source build/merge.o -Building... library for source build/vqueue.o +Building... library for source build/biofiles.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/biofiles.o libs/biofiles.c +libs/info.c: In function 'nfolevel': +libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=] + 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", + | ^~ +In function 'timestr_r', + inlined from 'nfolevel' at libs/info.c:139:5: +libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] + 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'sprintf', + inlined from 'timestr_r' at libs/info.c:64:5, + inlined from 'nfolevel' at libs/info.c:139:5: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 67 bytes into a destination of size 26 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +Building... library for source build/samio.o +Building... library for source build/nw.o In file included from libs/charsequence.c:26: libs/charsequence.c: In function 'destructSequence': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] @@ -859,6 +1055,7 @@ libs/charsequence.c:473:5: note: some parts of macro expansion are not guarded by this 'if' clause 473 | if (sequence->info != NULL) | ^~ +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/samio.o libs/samio.c libs/charsequence.c: In function 'loadSequence': libs/charsequence.c:296:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 296 | fread(s, sizeof(CharSequence), 1, infile); @@ -875,296 +1072,150 @@ libs/charsequence.c:307:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 307 | fread(sequence, sizeof(char), s->length, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/merge.o libs/merge.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/vqueue.o libs/vqueue.c -Building... library for source build/multicharseq.o -Building... library for source build/bgzip.o -In file included from include/mathematics.h:117, - from libs/alignment.c:38: -libs/alignment.c: In function 'wrapAlignment': +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/nw.o libs/nw.c +In file included from libs/fileBins.c:51: +libs/fileBins.c: In function 'bl_fileBinsSortLine': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/alignment.c:97:18: note: in expansion of macro 'FREEMEMORY' - 97 | if(al->rmvseq) FREEMEMORY(NULL, al->v); +libs/fileBins.c:901:18: note: in expansion of macro 'FREEMEMORY' + 901 | if(fileSort) FREEMEMORY(space, line); | ^~~~~~~~~~ -libs/alignment.c:97:3: note: some parts of macro expansion are not guarded by this 'if' clause - 97 | if(al->rmvseq) FREEMEMORY(NULL, al->v); - | ^~ +libs/fileBins.c:901:5: note: some parts of macro expansion are not guarded by this 'if' clause + 901 | if(fileSort) FREEMEMORY(space, line); + | ^~ +Building... library for source build/aluruSort.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/aluruSort.o libs/aluruSort.c +In file included from include/stringutils.h:27, + from include/charsequence.h:43, + from include/multicharseq.h:43, + from include/samio.h:23, + from include/bamio.h:21, + from libs/bamio.c:32: +libs/bamio.c: In function 'bl_bamCrossSectionDestruct': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/alignment.c:98:18: note: in expansion of macro 'FREEMEMORY' - 98 | if(al->rmuseq) FREEMEMORY(NULL, al->u); - | ^~~~~~~~~~ -libs/alignment.c:98:3: note: some parts of macro expansion are not guarded by this 'if' clause - 98 | if(al->rmuseq) FREEMEMORY(NULL, al->u); - | ^~ -In file included from include/mathematics.h:117, - from libs/intervaltree.c:27: -libs/intervaltree.c: In function 'bl_intervaltreeDestruct': +libs/bamio.c:468:20: note: in expansion of macro 'FREEMEMORY' + 468 | if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d); + | ^~~~~~~~~~ +libs/bamio.c:468:5: note: some parts of macro expansion are not guarded by this 'if' clause + 468 | if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d); + | ^~ +In file included from include/stringutils.h:27, + from include/charsequence.h:43, + from include/multicharseq.h:43, + from include/samio.h:23, + from libs/samio.c:33: +libs/samio.c: In function 'bl_samDestructTag': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/intervaltree.c:443:19: note: in expansion of macro 'FREEMEMORY' - 443 | if(root->ncoll) FREEMEMORY(NULL, root->collisions); - | ^~~~~~~~~~ -libs/info.c: In function 'timestr_r': -libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=] - 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", - | ^~ -libs/intervaltree.c:443:3: note: some parts of macro expansion are not guarded by this 'if' clause - 443 | if(root->ncoll) FREEMEMORY(NULL, root->collisions); +libs/samio.c:102:15: note: in expansion of macro 'FREEMEMORY' + 102 | if(kv->tag) FREEMEMORY(NULL, kv->tag); + | ^~~~~~~~~~ +libs/samio.c:102:3: note: some parts of macro expansion are not guarded by this 'if' clause + 102 | if(kv->tag) FREEMEMORY(NULL, kv->tag); | ^~ -libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] - 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:906, - from libs/info.c:41: -In function 'sprintf', - inlined from 'timestr_r' at libs/info.c:64:5: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 67 bytes into a destination of size 26 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -libs/matealign.c: In function 'bl_greedypairMappingSets': -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/multicharseq.o libs/multicharseq.c -libs/matealign.c:76:15: warning: 'm3' may be used uninitialized [-Wmaybe-uninitialized] - 76 | s->elem = bl_concatMapping(m3, m4); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -libs/matealign.c:56:24: note: 'm3' was declared here - 56 | mapping_t *m1, *m2, *m3, *m4; - | ^~ -libs/matealign.c:76:15: warning: 'm4' may be used uninitialized [-Wmaybe-uninitialized] - 76 | s->elem = bl_concatMapping(m3, m4); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -libs/matealign.c:56:29: note: 'm4' was declared here - 56 | mapping_t *m1, *m2, *m3, *m4; - | ^~ -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bgzip.o libs/bgzip.c -Building... library for source build/samheader.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/samheader.o libs/samheader.c -libs/info.c: In function 'infomsg': -libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=] - 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", - | ^~ -In function 'timestr_r', - inlined from 'infomsg' at libs/info.c:93:4: -libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] - 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'sprintf', - inlined from 'timestr_r' at libs/info.c:64:5, - inlined from 'infomsg' at libs/info.c:93:4: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 67 bytes into a destination of size 26 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -Building... library for source build/nw.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/nw.o libs/nw.c -Building... library for source build/kdchain.o -In file included from include/mathematics.h:117, - from libs/mathematics.c:38: -libs/mathematics.c: In function 'destructVector': -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/mathematics.c:251:26: note: in expansion of macro 'FREEMEMORY' - 251 | if (v->elements) FREEMEMORY(space, v->elements); - | ^~~~~~~~~~ -libs/mathematics.c:251:9: note: some parts of macro expansion are not guarded by this 'if' clause - 251 | if (v->elements) FREEMEMORY(space, v->elements); - | ^~ -In file included from include/stringutils.h:27, - from include/charsequence.h:43, - from include/sufarray.h:45, - from libs/sufarray.c:39: -libs/sufarray.c: In function 'destructSufArr': -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/kdchain.o libs/kdchain.c include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/sufarray.c:613:5: note: in expansion of macro 'FREEMEMORY' - 613 | FREEMEMORY(space, arr->lcpctab); - | ^~~~~~~~~~ -libs/sufarray.c:612:3: note: some parts of macro expansion are not guarded by this 'if' clause - 612 | if (arr->lcpctab != NULL) +libs/samio.c:103:15: note: in expansion of macro 'FREEMEMORY' + 103 | if(kv->val) FREEMEMORY(NULL, kv->val); + | ^~~~~~~~~~ +libs/samio.c:103:3: note: some parts of macro expansion are not guarded by this 'if' clause + 103 | if(kv->val) FREEMEMORY(NULL, kv->val); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/sufarray.c:615:5: note: in expansion of macro 'FREEMEMORY' - 615 | FREEMEMORY(space, arr->inv_suftab); - | ^~~~~~~~~~ -libs/sufarray.c:614:3: note: some parts of macro expansion are not guarded by this 'if' clause - 614 | if (arr->inv_suftab != NULL) +libs/samio.c:104:16: note: in expansion of macro 'FREEMEMORY' + 104 | if(kv->type) FREEMEMORY(NULL, kv->type); + | ^~~~~~~~~~ +libs/samio.c:104:3: note: some parts of macro expansion are not guarded by this 'if' clause + 104 | if(kv->type) FREEMEMORY(NULL, kv->type); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/sufarray.c:619:5: note: in expansion of macro 'FREEMEMORY' - 619 | FREEMEMORY(space, arr->idvtab); - | ^~~~~~~~~~ -libs/sufarray.c:618:3: note: some parts of macro expansion are not guarded by this 'if' clause - 618 | if (arr->idvtab != NULL) +libs/samio.c:105:15: note: in expansion of macro 'FREEMEMORY' + 105 | if(kv->key) FREEMEMORY(NULL, kv->key); + | ^~~~~~~~~~ +libs/samio.c:105:3: note: some parts of macro expansion are not guarded by this 'if' clause + 105 | if(kv->key) FREEMEMORY(NULL, kv->key); | ^~ +libs/samio.c: In function 'bl_samDestruct': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/sufarray.c:624:5: note: in expansion of macro 'FREEMEMORY' - 624 | FREEMEMORY(space, arr->suflink); - | ^~~~~~~~~~ -libs/sufarray.c:620:3: note: some parts of macro expansion are not guarded by this 'if' clause - 620 | if (arr->suflink != NULL) +libs/samio.c:112:21: note: in expansion of macro 'FREEMEMORY' + 112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname); + | ^~~~~~~~~~ +libs/samio.c:112:3: note: some parts of macro expansion are not guarded by this 'if' clause + 112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/sufarray.c:627:5: note: in expansion of macro 'FREEMEMORY' - 627 | FREEMEMORY(space, arr->chldtab); - | ^~~~~~~~~~ -libs/sufarray.c:626:3: note: some parts of macro expansion are not guarded by this 'if' clause - 626 | if (arr->chldtab != NULL) +libs/samio.c:113:21: note: in expansion of macro 'FREEMEMORY' + 113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname); + | ^~~~~~~~~~ +libs/samio.c:113:3: note: some parts of macro expansion are not guarded by this 'if' clause + 113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/sufarray.c:629:5: note: in expansion of macro 'FREEMEMORY' - 629 | FREEMEMORY(space, arr->mdfive); - | ^~~~~~~~~~ -libs/sufarray.c:628:3: note: some parts of macro expansion are not guarded by this 'if' clause - 628 | if (arr->mdfive) +libs/samio.c:114:21: note: in expansion of macro 'FREEMEMORY' + 114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar); + | ^~~~~~~~~~ +libs/samio.c:114:3: note: some parts of macro expansion are not guarded by this 'if' clause + 114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/sufarray.c:631:5: note: in expansion of macro 'FREEMEMORY' - 631 | FREEMEMORY(space, arr->llvtab); - | ^~~~~~~~~~ -libs/sufarray.c:630:3: note: some parts of macro expansion are not guarded by this 'if' clause - 630 | if(arr->llvtab != NULL) +libs/samio.c:115:21: note: in expansion of macro 'FREEMEMORY' + 115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext); + | ^~~~~~~~~~ +libs/samio.c:115:3: note: some parts of macro expansion are not guarded by this 'if' clause + 115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext); | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/sufarray.c:636:5: note: in expansion of macro 'FREEMEMORY' - 636 | FREEMEMORY(space, arr->id); - | ^~~~~~~~~~ -libs/sufarray.c:632:3: note: some parts of macro expansion are not guarded by this 'if' clause - 632 | if(arr->id != NULL) +libs/samio.c:116:21: note: in expansion of macro 'FREEMEMORY' + 116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq); + | ^~~~~~~~~~ +libs/samio.c:116:3: note: some parts of macro expansion are not guarded by this 'if' clause + 116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq); | ^~ -libs/info.c: In function 'nfolevel': -libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=] - 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", - | ^~ -In function 'timestr_r', - inlined from 'nfolevel' at libs/info.c:139:5: -libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] - 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'sprintf', - inlined from 'timestr_r' at libs/info.c:64:5, - inlined from 'nfolevel' at libs/info.c:139:5: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 16 and 67 bytes into a destination of size 26 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -Building... library for source build/portable_endian.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/portable_endian.o libs/portable_endian.c -Building... library for source build/biofiles.o -libs/sufarray.c: In function 'readSuffixarray': -libs/sufarray.c:428:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 428 | fread(&nmemb, sizeof(Uint), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:430:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 430 | fread(suftab, sizeof(Uint), nmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:431:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 431 | fread(&flags, sizeof(char), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:436:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 436 | fread(lcpctab, sizeof(unsigned char), nmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:438:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 438 | fread(&llvmemb, sizeof(Uint), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:440:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 440 | fread(llvtab, sizeof(PairUint), llvmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:446:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 446 | fread(chldtab, sizeof(childtab), nmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:484:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | fread(suflink, sizeof(Uint), nmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:508:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 508 | fread(id, sizeof(signed char), nmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:511:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 511 | fread(&idvmemb, sizeof(Uint), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:515:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 515 | fread(idvtab, sizeof(PairLSint), idvmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:519:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 519 | fread(idvutab, sizeof(PairUint), idvmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:530:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(mdfive, sizeof(unsigned char), 16, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/biofiles.o libs/biofiles.c -In file included from include/stringutils.h:27, - from include/biofiles.h:43, - from include/alignment.h:38, - from include/sw.h:38, - from libs/seqclip.c:44: -libs/seqclip.c: In function 'bl_Find3PrimeGreedy': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/seqclip.c:529:9: note: in expansion of macro 'FREEMEMORY' - 529 | FREEMEMORY(space, adapter); - | ^~~~~~~~~~ -In file included from include/stringutils.h:27, - from include/biofiles.h:43, - from include/segemehl.h:44, - from libs/pigeon.c:35: -libs/pigeon.c: In function 'pigeon': +libs/samio.c:117:21: note: in expansion of macro 'FREEMEMORY' + 117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual); + | ^~~~~~~~~~ +libs/samio.c:117:3: note: some parts of macro expansion are not guarded by this 'if' clause + 117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual); + | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/pigeon.c:352:13: note: in expansion of macro 'FREEMEMORY' - 352 | if(check) FREEMEMORY(space, check); - | ^~~~~~~~~~ -libs/pigeon.c:352:3: note: some parts of macro expansion are not guarded by this 'if' clause - 352 | if(check) FREEMEMORY(space, check); +libs/samio.c:121:20: note: in expansion of macro 'FREEMEMORY' + 121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags); + | ^~~~~~~~~~ +libs/samio.c:121:3: note: some parts of macro expansion are not guarded by this 'if' clause + 121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags); | ^~ -libs/seqclip.c:528:7: note: some parts of macro expansion are not guarded by this 'if' clause - 528 | if(adapter) - | ^~ -Building... library for source build/manopt.o -Building... library for source build/fileBins.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/manopt.o libs/manopt.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/fileBins.o libs/fileBins.c +Building... library for source build/segemehl_helper.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/segemehl_helper.o libs/segemehl_helper.c +Building... library for source build/multicharseq.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/multicharseq.o libs/multicharseq.c Building... library for source build/splitalign.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/splitalign.o libs/splitalign.c -Building... library for source build/bamio.o -Building... library for source build/locus.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bamio.o libs/bamio.c -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/locus.o libs/locus.c -Building... library for source build/fileio.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/fileio.o libs/fileio.c -Building... library for source build/mappingqual.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/mappingqual.o libs/mappingqual.c +Building... library for source build/gzip.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/gzip.o libs/gzip.c In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, @@ -1197,44 +1248,8 @@ libs/multicharseq.c:215:5: note: some parts of macro expansion are not guarded by this 'if' clause 215 | if (mseq->ref != NULL) | ^~ -Building... library for source build/kdseed.o -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/kdseed.o libs/kdseed.c -In file included from include/stringutils.h:27, - from libs/merge.c:34: -libs/merge.c: In function 'se_mergeWorker': -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/merge.c:1096:20: note: in expansion of macro 'FREEMEMORY' - 1096 | if(curkey) FREEMEMORY(NULL, curkey); - | ^~~~~~~~~~ -libs/merge.c:1096:9: note: some parts of macro expansion are not guarded by this 'if' clause - 1096 | if(curkey) FREEMEMORY(NULL, curkey); - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/merge.c:1216:26: note: in expansion of macro 'FREEMEMORY' - 1216 | if(!reads && curkey) FREEMEMORY(NULL, curkey); - | ^~~~~~~~~~ -libs/merge.c:1216:5: note: some parts of macro expansion are not guarded by this 'if' clause - 1216 | if(!reads && curkey) FREEMEMORY(NULL, curkey); - | ^~ -In file included from libs/fileBins.c:51: -libs/fileBins.c: In function 'bl_fileBinsSortLine': -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/fileBins.c:901:18: note: in expansion of macro 'FREEMEMORY' - 901 | if(fileSort) FREEMEMORY(space, line); - | ^~~~~~~~~~ -libs/fileBins.c:901:5: note: some parts of macro expansion are not guarded by this 'if' clause - 901 | if(fileSort) FREEMEMORY(space, line); - | ^~ -libs/fileio.c: In function 'bl_rm': -libs/fileio.c:220:3: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 220 | system(cmd); - | ^~~~~~~~~~~ +Building... library for source build/matealign.o +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/matealign.o libs/matealign.c In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/alignment.h:38, @@ -1317,24 +1332,45 @@ | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, - from include/multicharseq.h:43, - from include/samio.h:23, - from include/bamio.h:21, - from libs/bamio.c:32: -libs/bamio.c: In function 'bl_bamCrossSectionDestruct': + from include/locus.h:41, + from include/mapfrag.h:39, + from libs/matealign.c:32: +libs/matealign.c: In function 'bl_matealign': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/bamio.c:468:20: note: in expansion of macro 'FREEMEMORY' - 468 | if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d); - | ^~~~~~~~~~ -libs/bamio.c:468:5: note: some parts of macro expansion are not guarded by this 'if' clause - 468 | if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d); - | ^~ +libs/matealign.c:313:15: note: in expansion of macro 'FREEMEMORY' + 313 | if(npos[0]) FREEMEMORY(NULL, spos[0]); + | ^~~~~~~~~~ +libs/matealign.c:313:3: note: some parts of macro expansion are not guarded by this 'if' clause + 313 | if(npos[0]) FREEMEMORY(NULL, spos[0]); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/matealign.c:314:15: note: in expansion of macro 'FREEMEMORY' + 314 | if(npos[1]) FREEMEMORY(NULL, spos[1]); + | ^~~~~~~~~~ +libs/matealign.c:314:3: note: some parts of macro expansion are not guarded by this 'if' clause + 314 | if(npos[1]) FREEMEMORY(NULL, spos[1]); + | ^~ +libs/matealign.c: In function 'bl_greedypairMappingSets': +libs/matealign.c:76:15: warning: 'm3' may be used uninitialized [-Wmaybe-uninitialized] + 76 | s->elem = bl_concatMapping(m3, m4); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +libs/matealign.c:56:24: note: 'm3' was declared here + 56 | mapping_t *m1, *m2, *m3, *m4; + | ^~ +libs/matealign.c:76:15: warning: 'm4' may be used uninitialized [-Wmaybe-uninitialized] + 76 | s->elem = bl_concatMapping(m3, m4); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +libs/matealign.c:56:29: note: 'm4' was declared here + 56 | mapping_t *m1, *m2, *m3, *m4; + | ^~ Linking segemehl -cc build/segemehl_helper.o build/matealign.o build/samio.o build/gzidx.o build/sw.o build/container.o build/stack.o build/karlin.o build/memory.o build/stringutils.o build/brendel.o build/bedfiles.o build/manout.o build/bitVector.o build/annotation.o build/radixsort.o build/bitvectoralg.o build/sort.o build/intervaltree.o build/vstack.o build/md5.o build/vtprogressbar.o build/match.o build/aluruSort.o build/filebuffer.o build/gzip.o build/info.o build/pigeon.o build/sufarray.o build/bitArray.o build/seqclip.o build/alignment.o build/junctions.o build/mathematics.o build/charsequence.o build/iupac.o build/queryalign.o build/mapfrag.o build/debug.o build/merge.o build/vqueue.o build/multicharseq.o build/bgzip.o build/samheader.o build/nw.o build/kdchain.o build/portable_endian.o build/biofiles.o build/manopt.o build/fileBins.o build/splitalign.o build/bamio.o build/locus.o build/fileio.o build/mappingqual.o build/kdseed.o build/segemehl.o -o ./segemehl.x -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/ `pkg-config --libs htslib` -Wl,-z,relro -Wl,-z,now Linking haarz -cc build/segemehl_helper.o build/matealign.o build/samio.o build/gzidx.o build/sw.o build/container.o build/stack.o build/karlin.o build/memory.o build/stringutils.o build/brendel.o build/bedfiles.o build/manout.o build/bitVector.o build/annotation.o build/radixsort.o build/bitvectoralg.o build/sort.o build/intervaltree.o build/vstack.o build/md5.o build/vtprogressbar.o build/match.o build/aluruSort.o build/filebuffer.o build/gzip.o build/info.o build/pigeon.o build/sufarray.o build/bitArray.o build/seqclip.o build/alignment.o build/junctions.o build/mathematics.o build/charsequence.o build/iupac.o build/queryalign.o build/mapfrag.o build/debug.o build/merge.o build/vqueue.o build/multicharseq.o build/bgzip.o build/samheader.o build/nw.o build/kdchain.o build/portable_endian.o build/biofiles.o build/manopt.o build/fileBins.o build/splitalign.o build/bamio.o build/locus.o build/fileio.o build/mappingqual.o build/kdseed.o build/haarz.o -o ./haarz.x -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/ `pkg-config --libs htslib` -Wl,-z,relro -Wl,-z,now +cc build/md5.o build/gzidx.o build/kdseed.o build/sufarray.o build/memory.o build/manopt.o build/radixsort.o build/fileio.o build/match.o build/intervaltree.o build/sw.o build/junctions.o build/vqueue.o build/bedfiles.o build/kdchain.o build/bitVector.o build/sort.o build/debug.o build/samheader.o build/mathematics.o build/merge.o build/manout.o build/stack.o build/stringutils.o build/queryalign.o build/brendel.o build/portable_endian.o build/bitArray.o build/mapfrag.o build/mappingqual.o build/pigeon.o build/filebuffer.o build/alignment.o build/iupac.o build/container.o build/locus.o build/annotation.o build/bgzip.o build/karlin.o build/seqclip.o build/vstack.o build/vtprogressbar.o build/info.o build/fileBins.o build/bamio.o build/bitvectoralg.o build/charsequence.o build/biofiles.o build/samio.o build/nw.o build/aluruSort.o build/segemehl_helper.o build/multicharseq.o build/splitalign.o build/gzip.o build/matealign.o build/segemehl.o -o ./segemehl.x -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/ `pkg-config --libs htslib` -Wl,-z,relro -Wl,-z,now +cc build/md5.o build/gzidx.o build/kdseed.o build/sufarray.o build/memory.o build/manopt.o build/radixsort.o build/fileio.o build/match.o build/intervaltree.o build/sw.o build/junctions.o build/vqueue.o build/bedfiles.o build/kdchain.o build/bitVector.o build/sort.o build/debug.o build/samheader.o build/mathematics.o build/merge.o build/manout.o build/stack.o build/stringutils.o build/queryalign.o build/brendel.o build/portable_endian.o build/bitArray.o build/mapfrag.o build/mappingqual.o build/pigeon.o build/filebuffer.o build/alignment.o build/iupac.o build/container.o build/locus.o build/annotation.o build/bgzip.o build/karlin.o build/seqclip.o build/vstack.o build/vtprogressbar.o build/info.o build/fileBins.o build/bamio.o build/bitvectoralg.o build/charsequence.o build/biofiles.o build/samio.o build/nw.o build/aluruSort.o build/segemehl_helper.o build/multicharseq.o build/splitalign.o build/gzip.o build/matealign.o build/haarz.o -o ./haarz.x -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/ `pkg-config --libs htslib` -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/segemehl-0.3.4' make[1]: Leaving directory '/build/reproducible-path/segemehl-0.3.4' dh_auto_test @@ -1375,12 +1411,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1306934/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1306934/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/2035838 and its subdirectories -I: Current time: Mon Jun 2 08:47:22 -12 2025 -I: pbuilder-time-stamp: 1748897242 +I: removing directory /srv/workspace/pbuilder/1306934 and its subdirectories +I: Current time: Wed May 1 04:29:00 +14 2024 +I: pbuilder-time-stamp: 1714487340