Diff of the two buildlogs: -- --- b1/build.log 2024-04-14 02:27:15.181060301 +0000 +++ b2/build.log 2024-04-14 02:28:00.835127933 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 16 20:49:49 -12 2025 -I: pbuilder-time-stamp: 1747471789 +I: Current time: Sun Apr 14 16:27:18 +14 2024 +I: pbuilder-time-stamp: 1713061638 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,54 +31,86 @@ dpkg-source: info: applying arm64.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/122622/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/22800/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 14 02:27 /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/22800/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/22800/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="i686-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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='47e69d2806494f578ed6d54a5b189d7c' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='122622' - PS1='# ' - PS2='> ' + INVOCATION_ID=78ab1fa238624e6cbcc32bac0fbf2967 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=22800 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.K2hWiUQ3/pbuilderrc_VJKa --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.K2hWiUQ3/b1 --logfile b1/build.log segemehl_0.3.4-5.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.K2hWiUQ3/pbuilderrc_YbOl --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.K2hWiUQ3/b2 --logfile b2/build.log segemehl_0.3.4-5.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos16-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-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 15 17:46 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/122622/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 10 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/22800/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -175,7 +207,7 @@ Get: 51 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-1+b2 [30.2 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-1+b2 [26.2 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 pkg-config i386 1.8.1-1+b2 [14.0 kB] -Fetched 25.5 MB in 0s (61.2 MB/s) +Fetched 25.5 MB in 0s (55.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19874 files and directories currently installed.) @@ -402,7 +434,11 @@ 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/22800/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/22800/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 @@ -412,7 +448,7 @@ debian/rules clean dh clean dh_auto_clean - make -j22 clean + make -j10 clean make[1]: Entering directory '/build/reproducible-path/segemehl-0.3.4' Cleaning... rm -f -r build segemehl haarz @@ -426,52 +462,28 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/segemehl-0.3.4' dh_auto_build -- all - make -j22 "INSTALL=install --strip-program=true" all + make -j10 "INSTALL=install --strip-program=true" all make[2]: Entering directory '/build/reproducible-path/segemehl-0.3.4' -Building... library for source build/haarz.o -Building... library for source build/manopt.o -Building... library for source build/memory.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/filebuffer.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Building... library for source build/segemehl_helper.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/samio.o -Building... library for source build/manout.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/splitalign.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/mathematics.o +Building... library for source build/info.o +Building... library for source build/match.o +Building... library for source build/segemehl.o +Building... library for source build/sw.o Building... library for source build/merge.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/queryalign.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +Building... library for source build/bitVector.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Building... library for source build/samheader.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Building... library for source build/gzidx.o -Building... library for source build/bamio.o -Building... library for source build/bitvectoralg.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/multicharseq.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Building... library for source build/intervaltree.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/stack.o -Building... library for source build/vstack.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Building... library for source build/karlin.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/gzip.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/aluruSort.o +Building... library for source build/manopt.o +Building... library for source build/samio.o +Building... library for source build/memory.o cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 libs/gzip.c: In function 'readCommonHeader': libs/gzip.c:41:56: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 41 | fprintf(stderr, "common header has a length of %ld instead of %ld - not good.\n", bytesRead, sizeof(u_CommonHeader)); @@ -485,73 +497,64 @@ | | | | long int unsigned int | %d -Building... library for source build/locus.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); - | ^~ -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/charsequence.h:43, - from include/multicharseq.h:43, - from libs/multicharseq.c:38: -libs/multicharseq.c: In function 'destructMultiCharSeq': -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/multicharseq.c:212:7: note: in expansion of macro 'FREEMEMORY' - 212 | FREEMEMORY(space, mseq->markpos); - | ^~~~~~~~~~ -libs/multicharseq.c:211:9: note: some parts of macro expansion are not guarded by this 'if' clause - 211 | if (mseq->markpos != NULL) - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/multicharseq.c:214:7: note: in expansion of macro 'FREEMEMORY' - 214 | FREEMEMORY(space, mseq->map); - | ^~~~~~~~~~ -libs/multicharseq.c:213:9: note: some parts of macro expansion are not guarded by this 'if' clause - 213 | if (mseq->map != NULL) - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/multicharseq.c:216:7: note: in expansion of macro 'FREEMEMORY' - 216 | FREEMEMORY(space, mseq->ref); - | ^~~~~~~~~~ -libs/multicharseq.c:215:5: note: some parts of macro expansion are not guarded by this 'if' clause - 215 | if (mseq->ref != NULL) - | ^~ -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); - | ^~ +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/i386-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/aluruSort.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/i386-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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/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/i386-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 ()); + | ~~~~~~~~~~~~~~~~~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, @@ -658,192 +661,95 @@ 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); | ^~ -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/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/iupac.o +Building... library for source build/multicharseq.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/portable_endian.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 In file included from include/stringutils.h:27, - from include/biofiles.h:43, - from include/alignment.h:38, - from include/bitvectoralg.h:32, - from include/splitalign.h:29, - from libs/splitalign.c:32: -libs/splitalign.c: In function 'bl_fixSplitAlignHoffmann': -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/splitalign.c:1323:25: note: in expansion of macro 'FREEMEMORY' - 1323 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); - | ^~~~~~~~~~ -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -libs/splitalign.c:1323:7: note: some parts of macro expansion are not guarded by this 'if' clause - 1323 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/splitalign.c:1324:25: note: in expansion of macro 'FREEMEMORY' - 1324 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); - | ^~~~~~~~~~ -libs/splitalign.c:1324:7: note: some parts of macro expansion are not guarded by this 'if' clause - 1324 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); - | ^~ + 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/splitalign.c:1325:26: note: in expansion of macro 'FREEMEMORY' - 1325 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); - | ^~~~~~~~~~ -libs/splitalign.c:1325:7: note: some parts of macro expansion are not guarded by this 'if' clause - 1325 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); - | ^~ +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/splitalign.c:1326:26: note: in expansion of macro 'FREEMEMORY' - 1326 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); +libs/merge.c:1216:26: note: in expansion of macro 'FREEMEMORY' + 1216 | if(!reads && curkey) FREEMEMORY(NULL, curkey); | ^~~~~~~~~~ -libs/splitalign.c:1326:7: note: some parts of macro expansion are not guarded by this 'if' clause - 1326 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); - | ^~ +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/kdseed.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/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/splitalign.c: In function 'bl_fixSplitAlignBrendel': -Building... library for source build/fileio.o -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/splitalign.c:1565:27: note: in expansion of macro 'FREEMEMORY' - 1565 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); - | ^~~~~~~~~~ -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -libs/splitalign.c:1565:9: note: some parts of macro expansion are not guarded by this 'if' clause - 1565 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/splitalign.c:1566:27: note: in expansion of macro 'FREEMEMORY' - 1566 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); - | ^~~~~~~~~~ -libs/splitalign.c:1566:9: note: some parts of macro expansion are not guarded by this 'if' clause - 1566 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/splitalign.c:1567:28: note: in expansion of macro 'FREEMEMORY' - 1567 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); - | ^~~~~~~~~~ -libs/splitalign.c:1567:9: note: some parts of macro expansion are not guarded by this 'if' clause - 1567 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); - | ^~ + from libs/multicharseq.c:38: +libs/multicharseq.c: In function 'destructMultiCharSeq': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/splitalign.c:1568:28: note: in expansion of macro 'FREEMEMORY' - 1568 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); - | ^~~~~~~~~~ -libs/splitalign.c:1568:9: note: some parts of macro expansion are not guarded by this 'if' clause - 1568 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); +libs/multicharseq.c:212:7: note: in expansion of macro 'FREEMEMORY' + 212 | FREEMEMORY(space, mseq->markpos); + | ^~~~~~~~~~ +libs/multicharseq.c:211:9: note: some parts of macro expansion are not guarded by this 'if' clause + 211 | if (mseq->markpos != NULL) | ^~ -Building... library for source build/bitArray.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Building... library for source build/mapfrag.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/match.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/sort.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Building... library for source build/charsequence.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/charsequence.c:467:9: note: in expansion of macro 'FREEMEMORY' - 467 | FREEMEMORY(space, sequence->sequence); - | ^~~~~~~~~~ -libs/charsequence.c:466:3: note: some parts of macro expansion are not guarded by this 'if' clause - 466 | if (sequence->sequence != NULL) - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/charsequence.c:470:5: note: in expansion of macro 'FREEMEMORY' - 470 | FREEMEMORY(space, sequence->alphabetname); - | ^~~~~~~~~~ -libs/charsequence.c:469:9: note: some parts of macro expansion are not guarded by this 'if' clause - 469 | if (sequence->alphabetname != NULL) +libs/multicharseq.c:214:7: note: in expansion of macro 'FREEMEMORY' + 214 | FREEMEMORY(space, mseq->map); + | ^~~~~~~~~~ +libs/multicharseq.c:213:9: note: some parts of macro expansion are not guarded by this 'if' clause + 213 | if (mseq->map != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/charsequence.c:472:9: note: in expansion of macro 'FREEMEMORY' - 472 | FREEMEMORY(space, sequence->url); - | ^~~~~~~~~~ -libs/charsequence.c:471:5: note: some parts of macro expansion are not guarded by this 'if' clause - 471 | if (sequence->url != NULL) +libs/multicharseq.c:216:7: note: in expansion of macro 'FREEMEMORY' + 216 | FREEMEMORY(space, mseq->ref); + | ^~~~~~~~~~ +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/mappingqual.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/brendel.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/pigeon.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +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/charsequence.c:474:9: note: in expansion of macro 'FREEMEMORY' - 474 | FREEMEMORY(space, sequence->info); - | ^~~~~~~~~~ -libs/charsequence.c:473:5: note: some parts of macro expansion are not guarded by this 'if' clause - 473 | if (sequence->info != NULL) - | ^~ -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/charsequence.c:304:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 304 | fread(s->description, sizeof(char), s->descrlen+1, infile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/charsequence.c:305:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 305 | fread(s->alphabetname, sizeof(char), s->namelen+1, infile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/charsequence.c:306:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 306 | fread(s->url, sizeof(char), s->urllen+1, infile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/queryalign.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +Building... library for source build/debug.o +Building... library for source build/gzidx.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/alignment.o cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/portable_endian.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/md5.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +Building... library for source build/sufarray.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 In file included from include/mathematics.h:117, from libs/alignment.c:38: libs/alignment.c: In function 'wrapAlignment': @@ -865,85 +771,12 @@ 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); | ^~ -Building... library for source build/bedfiles.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Building... library for source build/debug.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/vtprogressbar.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/matealign.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Building... library for source build/junctions.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/segemehl.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Building... library for source build/pigeon.o +Building... library for source build/filebuffer.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/container.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/bitVector.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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': -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]); - | ^~ -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]); - | ^~ -Building... library for source build/biofiles.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/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; - | ^~ -Building... library for source build/sufarray.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/kdseed.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Building... library for source build/vqueue.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/brendel.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/segemehl_helper.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/sufarray.h:45, @@ -1037,6 +870,7 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Building... library for source build/charsequence.o 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1052,6 +886,7 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1061,89 +896,80 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Building... library for source build/radixsort.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/info.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/seqclip.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/annotation.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/i386-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/mappingqual.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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/i386-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/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/i386-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/bgzip.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -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': +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] 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/charsequence.c:467:9: note: in expansion of macro 'FREEMEMORY' + 467 | FREEMEMORY(space, sequence->sequence); | ^~~~~~~~~~ -libs/seqclip.c:528:7: note: some parts of macro expansion are not guarded by this 'if' clause - 528 | if(adapter) - | ^~ +libs/charsequence.c:466:3: note: some parts of macro expansion are not guarded by this 'if' clause + 466 | if (sequence->sequence != NULL) + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/charsequence.c:470:5: note: in expansion of macro 'FREEMEMORY' + 470 | FREEMEMORY(space, sequence->alphabetname); + | ^~~~~~~~~~ +libs/charsequence.c:469:9: note: some parts of macro expansion are not guarded by this 'if' clause + 469 | if (sequence->alphabetname != NULL) + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/charsequence.c:472:9: note: in expansion of macro 'FREEMEMORY' + 472 | FREEMEMORY(space, sequence->url); + | ^~~~~~~~~~ +libs/charsequence.c:471:5: note: some parts of macro expansion are not guarded by this 'if' clause + 471 | if (sequence->url != NULL) + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/charsequence.c:474:9: note: in expansion of macro 'FREEMEMORY' + 474 | FREEMEMORY(space, sequence->info); + | ^~~~~~~~~~ +libs/charsequence.c:473:5: note: some parts of macro expansion are not guarded by this 'if' clause + 473 | if (sequence->info != NULL) + | ^~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/charsequence.c:304:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 304 | fread(s->description, sizeof(char), s->descrlen+1, infile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/charsequence.c:305:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 305 | fread(s->alphabetname, sizeof(char), s->namelen+1, infile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/charsequence.c:306:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 306 | fread(s->url, sizeof(char), s->urllen+1, infile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Building... library for source build/intervaltree.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +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/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/junctions.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/annotation.o +Building... library for source build/bgzip.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 In file included from include/stringutils.h:27, from libs/annotation.c:29: libs/annotation.c: In function 'bl_annotationitemDestruct': @@ -1219,9 +1045,7 @@ libs/annotation.c:156:3: note: some parts of macro expansion are not guarded by this 'if' clause 156 | if(item->source) FREEMEMORY(space, item->source); | ^~ -Building... library for source build/sw.o libs/annotation.c: In function 'bl_annotationtrackDestruct': -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ @@ -1268,14 +1092,160 @@ 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) ; | ^~ -Building... library for source build/kdchain.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/stringutils.o -cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +Building... library for source build/haarz.o +Building... library for source build/mathematics.o +Building... library for source build/mapfrag.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +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); + | ^~ Building... library for source build/fileBins.o cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/sort.o +Building... library for source build/iupac.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 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); + | ^~ +Building... library for source build/bitvectoralg.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +Building... library for source build/vtprogressbar.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/splitalign.o Building... library for source build/nw.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/vqueue.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +In file included from include/stringutils.h:27, + from include/biofiles.h:43, + from include/alignment.h:38, + from include/bitvectoralg.h:32, + from include/splitalign.h:29, + from libs/splitalign.c:32: +libs/splitalign.c: In function 'bl_fixSplitAlignHoffmann': +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/splitalign.c:1323:25: note: in expansion of macro 'FREEMEMORY' + 1323 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); + | ^~~~~~~~~~ +libs/splitalign.c:1323:7: note: some parts of macro expansion are not guarded by this 'if' clause + 1323 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/splitalign.c:1324:25: note: in expansion of macro 'FREEMEMORY' + 1324 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); + | ^~~~~~~~~~ +libs/splitalign.c:1324:7: note: some parts of macro expansion are not guarded by this 'if' clause + 1324 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/splitalign.c:1325:26: note: in expansion of macro 'FREEMEMORY' + 1325 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); + | ^~~~~~~~~~ +libs/splitalign.c:1325:7: note: some parts of macro expansion are not guarded by this 'if' clause + 1325 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/splitalign.c:1326:26: note: in expansion of macro 'FREEMEMORY' + 1326 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); + | ^~~~~~~~~~ +libs/splitalign.c:1326:7: note: some parts of macro expansion are not guarded by this 'if' clause + 1326 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); + | ^~ +libs/splitalign.c: In function 'bl_fixSplitAlignBrendel': +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/splitalign.c:1565:27: note: in expansion of macro 'FREEMEMORY' + 1565 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); + | ^~~~~~~~~~ +libs/splitalign.c:1565:9: note: some parts of macro expansion are not guarded by this 'if' clause + 1565 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/splitalign.c:1566:27: note: in expansion of macro 'FREEMEMORY' + 1566 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); + | ^~~~~~~~~~ +libs/splitalign.c:1566:9: note: some parts of macro expansion are not guarded by this 'if' clause + 1566 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/splitalign.c:1567:28: note: in expansion of macro 'FREEMEMORY' + 1567 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); + | ^~~~~~~~~~ +libs/splitalign.c:1567:9: note: some parts of macro expansion are not guarded by this 'if' clause + 1567 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/splitalign.c:1568:28: note: in expansion of macro 'FREEMEMORY' + 1568 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); + | ^~~~~~~~~~ +libs/splitalign.c:1568:9: note: some parts of macro expansion are not guarded by this 'if' clause + 1568 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); + | ^~ +Building... library for source build/bitArray.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +Building... library for source build/karlin.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/locus.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/seqclip.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +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/stringutils.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +Building... library for source build/matealign.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +Building... library for source build/vstack.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 In file included from include/stringutils.h:27, from libs/stringutils.c:39: libs/stringutils.c: In function 'destructStringset': @@ -1288,21 +1258,87 @@ 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) | ^~ -In file included from libs/fileBins.c:51: -libs/fileBins.c: In function 'bl_fileBinsSortLine': +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': 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/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]); + | ^~ +Building... library for source build/samheader.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/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; + | ^~ +Building... library for source build/md5.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +Building... library for source build/fileio.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +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/bedfiles.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +Building... library for source build/biofiles.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +Building... library for source build/stack.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +Building... library for source build/manout.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/kdchain.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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/bamio.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +Building... library for source build/radixsort.o +cc -g -O2 -ffile-prefix-map=/build/reproducible-path/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 +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/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); | ^~ Linking segemehl -cc build/manopt.o build/memory.o build/filebuffer.o build/segemehl_helper.o build/samio.o build/manout.o build/splitalign.o build/mathematics.o build/merge.o build/queryalign.o build/samheader.o build/gzidx.o build/bamio.o build/bitvectoralg.o build/multicharseq.o build/intervaltree.o build/stack.o build/vstack.o build/karlin.o build/gzip.o build/aluruSort.o build/locus.o build/iupac.o build/fileio.o build/bitArray.o build/mapfrag.o build/match.o build/sort.o build/charsequence.o build/alignment.o build/portable_endian.o build/md5.o build/bedfiles.o build/debug.o build/vtprogressbar.o build/matealign.o build/junctions.o build/pigeon.o build/container.o build/bitVector.o build/biofiles.o build/sufarray.o build/kdseed.o build/vqueue.o build/brendel.o build/radixsort.o build/info.o build/seqclip.o build/annotation.o build/mappingqual.o build/bgzip.o build/sw.o build/kdchain.o build/stringutils.o build/fileBins.o build/nw.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/info.o build/match.o build/sw.o build/merge.o build/bitVector.o build/gzip.o build/manopt.o build/samio.o build/memory.o build/aluruSort.o build/multicharseq.o build/portable_endian.o build/kdseed.o build/mappingqual.o build/brendel.o build/pigeon.o build/queryalign.o build/debug.o build/gzidx.o build/alignment.o build/sufarray.o build/filebuffer.o build/container.o build/segemehl_helper.o build/charsequence.o build/intervaltree.o build/junctions.o build/annotation.o build/bgzip.o build/mathematics.o build/mapfrag.o build/fileBins.o build/sort.o build/iupac.o build/bitvectoralg.o build/vtprogressbar.o build/splitalign.o build/nw.o build/vqueue.o build/bitArray.o build/karlin.o build/locus.o build/seqclip.o build/stringutils.o build/matealign.o build/vstack.o build/samheader.o build/md5.o build/fileio.o build/bedfiles.o build/biofiles.o build/stack.o build/manout.o build/kdchain.o build/bamio.o build/radixsort.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/manopt.o build/memory.o build/filebuffer.o build/segemehl_helper.o build/samio.o build/manout.o build/splitalign.o build/mathematics.o build/merge.o build/queryalign.o build/samheader.o build/gzidx.o build/bamio.o build/bitvectoralg.o build/multicharseq.o build/intervaltree.o build/stack.o build/vstack.o build/karlin.o build/gzip.o build/aluruSort.o build/locus.o build/iupac.o build/fileio.o build/bitArray.o build/mapfrag.o build/match.o build/sort.o build/charsequence.o build/alignment.o build/portable_endian.o build/md5.o build/bedfiles.o build/debug.o build/vtprogressbar.o build/matealign.o build/junctions.o build/pigeon.o build/container.o build/bitVector.o build/biofiles.o build/sufarray.o build/kdseed.o build/vqueue.o build/brendel.o build/radixsort.o build/info.o build/seqclip.o build/annotation.o build/mappingqual.o build/bgzip.o build/sw.o build/kdchain.o build/stringutils.o build/fileBins.o build/nw.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/info.o build/match.o build/sw.o build/merge.o build/bitVector.o build/gzip.o build/manopt.o build/samio.o build/memory.o build/aluruSort.o build/multicharseq.o build/portable_endian.o build/kdseed.o build/mappingqual.o build/brendel.o build/pigeon.o build/queryalign.o build/debug.o build/gzidx.o build/alignment.o build/sufarray.o build/filebuffer.o build/container.o build/segemehl_helper.o build/charsequence.o build/intervaltree.o build/junctions.o build/annotation.o build/bgzip.o build/mathematics.o build/mapfrag.o build/fileBins.o build/sort.o build/iupac.o build/bitvectoralg.o build/vtprogressbar.o build/splitalign.o build/nw.o build/vqueue.o build/bitArray.o build/karlin.o build/locus.o build/seqclip.o build/stringutils.o build/matealign.o build/vstack.o build/samheader.o build/md5.o build/fileio.o build/bedfiles.o build/biofiles.o build/stack.o build/manout.o build/kdchain.o build/bamio.o build/radixsort.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 @@ -1343,12 +1379,14 @@ 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/22800/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/22800/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/122622 and its subdirectories -I: Current time: Fri May 16 20:50:14 -12 2025 -I: pbuilder-time-stamp: 1747471814 +I: removing directory /srv/workspace/pbuilder/22800 and its subdirectories +I: Current time: Sun Apr 14 16:28:00 +14 2024 +I: pbuilder-time-stamp: 1713061680