Diff of the two buildlogs: -- --- b1/build.log 2024-01-06 13:53:35.496615727 +0000 +++ b2/build.log 2024-01-06 13:56:22.713459581 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jan 6 01:47:04 -12 2024 -I: pbuilder-time-stamp: 1704548824 +I: Current time: Sun Jan 7 03:53:49 +14 2024 +I: pbuilder-time-stamp: 1704549229 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./segemehl_0.3.4.orig.tar.xz] I: copying [./segemehl_0.3.4-5.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue Aug 24 04:51:21 2021 -12 +gpgv: Signature made Tue Aug 24 16:51:21 2021 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key @@ -30,64 +30,96 @@ dpkg-source: info: applying arm64.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/6637/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2866/tmp/hooks/D01_modify_environment starting +debug: Running on ff4a. +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 Jan 6 13:54 /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/2866/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2866/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + 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]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='0db46b7bab5e4ce68cdbfbc35b9e6c12' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='6637' - PS1='# ' - PS2='> ' + INVOCATION_ID=1fd6a43c2d4b46c19607deb6b0f57c6a + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=2866 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.9DeEZA7s/pbuilderrc_pDRS --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9DeEZA7s/b1 --logfile b1/build.log segemehl_0.3.4-5.dsc' - SUDO_GID='114' - SUDO_UID='108' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.9DeEZA7s/pbuilderrc_iepQ --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9DeEZA7s/b2 --logfile b2/build.log segemehl_0.3.4-5.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux jtx1a 6.1.0-17-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-armmp-lpae #1 SMP Debian 6.1.69-1 (2023-12-30) armv7l GNU/Linux I: ls -l /bin total 4964 -rwxr-xr-x 1 root root 838488 Apr 23 2023 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod @@ -98,67 +130,67 @@ -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 2023 dmesg + -rwxr-xr-x 1 root root 59128 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 2023 fusermount + -rwxr-xr-x 1 root root 55748 Mar 23 2023 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 2022 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 2023 login + -rwxr-xr-x 1 root root 35132 Mar 23 2023 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 2023 lsblk + -rwxr-xr-x 1 root root 136808 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 2023 more - -rwsr-xr-x 1 root root 38496 Mar 22 2023 mount - -rwxr-xr-x 1 root root 9824 Mar 22 2023 mountpoint + -rwxr-xr-x 1 root root 38504 Mar 23 2023 more + -rwsr-xr-x 1 root root 38496 Mar 23 2023 mount + -rwxr-xr-x 1 root root 9824 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 14152 Jul 28 11:46 run-parts + -rwxr-xr-x 1 root root 14152 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Jan 6 13:54 sh -> /bin/bash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 2023 su + -rwsr-xr-x 1 root root 50800 Mar 23 2023 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 2023 tar - -rwxr-xr-x 1 root root 9800 Jul 28 11:46 tempfile + -rwxr-xr-x 1 root root 9800 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 2023 umount + -rwxr-xr-x 1 root root 9768 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 2023 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 2023 wdctl + -rwxr-xr-x 1 root root 42608 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/6637/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/2866/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -171,7 +203,7 @@ Depends: debhelper-compat (= 13), pkg-config, libhts-dev, libncurses-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19288 files and directories currently installed.) +(Reading database ... 17881 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -255,10 +287,10 @@ Get: 51 http://deb.debian.org/debian bookworm/main armhf pkgconf-bin armhf 1.8.1-1 [28.5 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf pkgconf armhf 1.8.1-1 [25.9 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf pkg-config armhf 1.8.1-1 [13.7 kB] -Fetched 23.4 MB in 2s (12.5 MB/s) +Fetched 23.4 MB in 2s (14.8 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 ... 19288 files and directories currently installed.) +(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 ... 17881 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. @@ -482,7 +514,11 @@ 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/2866/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/2866/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 @@ -492,7 +528,7 @@ debian/rules clean dh clean dh_auto_clean - make -j3 clean + make -j4 clean make[1]: Entering directory '/build/reproducible-path/segemehl-0.3.4' Cleaning... rm -f -r build segemehl haarz @@ -506,27 +542,71 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/segemehl-0.3.4' dh_auto_build -- all - make -j3 "INSTALL=install --strip-program=true" all + make -j4 "INSTALL=install --strip-program=true" all make[2]: Entering directory '/build/reproducible-path/segemehl-0.3.4' -Building... library for source build/gzip.o -Building... library for source build/aluruSort.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 +Building... library for source build/seqclip.o +Building... library for source build/samheader.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/seqclip.o libs/seqclip.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/samheader.o libs/samheader.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 +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 +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) + | ^~ +In file included from include/mathematics.h:117, + from libs/alignment.c:38: +libs/alignment.c: In function 'wrapAlignment': +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/alignment.c:97:18: note: in expansion of macro 'FREEMEMORY' + 97 | if(al->rmvseq) FREEMEMORY(NULL, al->v); + | ^~~~~~~~~~ +libs/alignment.c:97:3: note: some parts of macro expansion are not guarded by this 'if' clause + 97 | if(al->rmvseq) FREEMEMORY(NULL, al->v); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/alignment.c:98:18: note: in expansion of macro 'FREEMEMORY' + 98 | if(al->rmuseq) FREEMEMORY(NULL, al->u); + | ^~~~~~~~~~ +libs/alignment.c:98:3: note: some parts of macro expansion are not guarded by this 'if' clause + 98 | if(al->rmuseq) FREEMEMORY(NULL, al->u); + | ^~ +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 +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/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/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/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/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)); - | ~~^ ~~~~~~~~~ - | | | - | long int size_t {aka unsigned int} - | %d -libs/gzip.c:41:71: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'unsigned int' [-Wformat=] - 41 | fprintf(stderr, "common header has a length of %ld instead of %ld - not good.\n", bytesRead, sizeof(u_CommonHeader)); - | ~~^ ~~~~~~~~~~~~~~~~~~~~~~ - | | | - | long int unsigned int - | %d In file included from include/stringutils.h:27, from libs/annotation.c:29: libs/annotation.c: In function 'bl_annotationitemDestruct': @@ -649,278 +729,12 @@ 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/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/nw.o libs/nw.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 -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); - | ^~ -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/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) - | ^~ -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/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/sw.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/sw.o libs/sw.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 -Building... library for source build/manopt.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/manopt.o libs/manopt.c -In file included from include/stringutils.h:27, - from include/charsequence.h:43, - from include/sufarray.h:45, - from libs/sufarray.c:39: -libs/sufarray.c: In function 'destructSufArr': -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/sufarray.c:613:5: note: in expansion of macro 'FREEMEMORY' - 613 | FREEMEMORY(space, arr->lcpctab); - | ^~~~~~~~~~ -libs/sufarray.c:612:3: note: some parts of macro expansion are not guarded by this 'if' clause - 612 | if (arr->lcpctab != NULL) - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/sufarray.c:615:5: note: in expansion of macro 'FREEMEMORY' - 615 | FREEMEMORY(space, arr->inv_suftab); - | ^~~~~~~~~~ -libs/sufarray.c:614:3: note: some parts of macro expansion are not guarded by this 'if' clause - 614 | if (arr->inv_suftab != NULL) - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/sufarray.c:619:5: note: in expansion of macro 'FREEMEMORY' - 619 | FREEMEMORY(space, arr->idvtab); - | ^~~~~~~~~~ -libs/sufarray.c:618:3: note: some parts of macro expansion are not guarded by this 'if' clause - 618 | if (arr->idvtab != NULL) - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/sufarray.c:624:5: note: in expansion of macro 'FREEMEMORY' - 624 | FREEMEMORY(space, arr->suflink); - | ^~~~~~~~~~ -libs/sufarray.c:620:3: note: some parts of macro expansion are not guarded by this 'if' clause - 620 | if (arr->suflink != NULL) - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/sufarray.c:627:5: note: in expansion of macro 'FREEMEMORY' - 627 | FREEMEMORY(space, arr->chldtab); - | ^~~~~~~~~~ -libs/sufarray.c:626:3: note: some parts of macro expansion are not guarded by this 'if' clause - 626 | if (arr->chldtab != NULL) - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/sufarray.c:629:5: note: in expansion of macro 'FREEMEMORY' - 629 | FREEMEMORY(space, arr->mdfive); - | ^~~~~~~~~~ -libs/sufarray.c:628:3: note: some parts of macro expansion are not guarded by this 'if' clause - 628 | if (arr->mdfive) - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/sufarray.c:631:5: note: in expansion of macro 'FREEMEMORY' - 631 | FREEMEMORY(space, arr->llvtab); - | ^~~~~~~~~~ -libs/sufarray.c:630:3: note: some parts of macro expansion are not guarded by this 'if' clause - 630 | if(arr->llvtab != NULL) - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/sufarray.c:636:5: note: in expansion of macro 'FREEMEMORY' - 636 | FREEMEMORY(space, arr->id); - | ^~~~~~~~~~ -libs/sufarray.c:632:3: note: some parts of macro expansion are not guarded by this 'if' clause - 632 | if(arr->id != NULL) - | ^~ -libs/sufarray.c: In function 'readSuffixarray': -libs/sufarray.c:428:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 428 | fread(&nmemb, sizeof(Uint), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:430:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 430 | fread(suftab, sizeof(Uint), nmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:431:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 431 | fread(&flags, sizeof(char), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:436:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 436 | fread(lcpctab, sizeof(unsigned char), nmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:438:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 438 | fread(&llvmemb, sizeof(Uint), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:440:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 440 | fread(llvtab, sizeof(PairUint), llvmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:446:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 446 | fread(chldtab, sizeof(childtab), nmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:484:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 484 | fread(suflink, sizeof(Uint), nmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:508:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 508 | fread(id, sizeof(signed char), nmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:511:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 511 | fread(&idvmemb, sizeof(Uint), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:515:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 515 | fread(idvtab, sizeof(PairLSint), idvmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:519:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 519 | fread(idvutab, sizeof(PairUint), idvmemb, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/sufarray.c:530:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 530 | fread(mdfive, sizeof(unsigned char), 16, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/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/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 -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/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/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 -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/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/iupac.o libs/iupac.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/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 -In file included from include/stringutils.h:27, - from libs/stringutils.c:39: -libs/stringutils.c: In function 'destructStringset': -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/stringutils.c:274:9: note: in expansion of macro 'FREEMEMORY' - 274 | FREEMEMORY(space, s->strings[i].str); - | ^~~~~~~~~~ -libs/stringutils.c:273:7: note: some parts of macro expansion are not guarded by this 'if' clause - 273 | if(s->strings[i].str != NULL) - | ^~ -Building... library for source build/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/gzidx.o libs/gzidx.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/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/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/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/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/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/memory.o libs/memory.c +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/nw.o libs/nw.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", @@ -977,18 +791,124 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +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/samio.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 +In file included from include/stringutils.h:27, + from include/charsequence.h:43, + from include/multicharseq.h:43, + from include/samio.h:23, + from libs/samio.c:33: +libs/samio.c: In function 'bl_samDestructTag': +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/samio.c:102:15: note: in expansion of macro 'FREEMEMORY' + 102 | if(kv->tag) FREEMEMORY(NULL, kv->tag); + | ^~~~~~~~~~ +libs/samio.c:102:3: note: some parts of macro expansion are not guarded by this 'if' clause + 102 | if(kv->tag) FREEMEMORY(NULL, kv->tag); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/samio.c:103:15: note: in expansion of macro 'FREEMEMORY' + 103 | if(kv->val) FREEMEMORY(NULL, kv->val); + | ^~~~~~~~~~ +libs/samio.c:103:3: note: some parts of macro expansion are not guarded by this 'if' clause + 103 | if(kv->val) FREEMEMORY(NULL, kv->val); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/samio.c:104:16: note: in expansion of macro 'FREEMEMORY' + 104 | if(kv->type) FREEMEMORY(NULL, kv->type); + | ^~~~~~~~~~ +libs/samio.c:104:3: note: some parts of macro expansion are not guarded by this 'if' clause + 104 | if(kv->type) FREEMEMORY(NULL, kv->type); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/samio.c:105:15: note: in expansion of macro 'FREEMEMORY' + 105 | if(kv->key) FREEMEMORY(NULL, kv->key); + | ^~~~~~~~~~ +libs/samio.c:105:3: note: some parts of macro expansion are not guarded by this 'if' clause + 105 | if(kv->key) FREEMEMORY(NULL, kv->key); + | ^~ +libs/samio.c: In function 'bl_samDestruct': +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/samio.c:112:21: note: in expansion of macro 'FREEMEMORY' + 112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname); + | ^~~~~~~~~~ +libs/samio.c:112:3: note: some parts of macro expansion are not guarded by this 'if' clause + 112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/samio.c:113:21: note: in expansion of macro 'FREEMEMORY' + 113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname); + | ^~~~~~~~~~ +libs/samio.c:113:3: note: some parts of macro expansion are not guarded by this 'if' clause + 113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/samio.c:114:21: note: in expansion of macro 'FREEMEMORY' + 114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar); + | ^~~~~~~~~~ +libs/samio.c:114:3: note: some parts of macro expansion are not guarded by this 'if' clause + 114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/samio.c:115:21: note: in expansion of macro 'FREEMEMORY' + 115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext); + | ^~~~~~~~~~ +libs/samio.c:115:3: note: some parts of macro expansion are not guarded by this 'if' clause + 115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/samio.c:116:21: note: in expansion of macro 'FREEMEMORY' + 116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq); + | ^~~~~~~~~~ +libs/samio.c:116:3: note: some parts of macro expansion are not guarded by this 'if' clause + 116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/samio.c:117:21: note: in expansion of macro 'FREEMEMORY' + 117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual); + | ^~~~~~~~~~ +libs/samio.c:117:3: note: some parts of macro expansion are not guarded by this 'if' clause + 117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual); + | ^~ +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/samio.c:121:20: note: in expansion of macro 'FREEMEMORY' + 121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags); + | ^~~~~~~~~~ +libs/samio.c:121:3: note: some parts of macro expansion are not guarded by this 'if' clause + 121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags); + | ^~ Building... library for source build/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/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/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/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/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/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/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/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 In file included from include/stringutils.h:27, @@ -1023,12 +943,126 @@ 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/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/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 +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/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/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/memory.o libs/memory.c +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/gzidx.o libs/gzidx.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); + | ^~ +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/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/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/container.o libs/container.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/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/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/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/radixsort.o +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/radixsort.o libs/radixsort.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/kdseed.o libs/kdseed.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/aluruSort.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/aluruSort.o libs/aluruSort.c +In file included from include/stringutils.h:27, + from libs/stringutils.c:39: +libs/stringutils.c: In function 'destructStringset': +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + | ^~~~ +libs/stringutils.c:274:9: note: in expansion of macro 'FREEMEMORY' + 274 | FREEMEMORY(space, s->strings[i].str); + | ^~~~~~~~~~ +libs/stringutils.c:273:7: note: some parts of macro expansion are not guarded by this 'if' clause + 273 | if(s->strings[i].str != NULL) + | ^~ +Building... library for source build/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/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 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/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/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/iupac.o libs/iupac.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/splitalign.o libs/splitalign.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/biofiles.h:43, from include/alignment.h:38, @@ -1109,27 +1143,15 @@ 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/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/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 -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/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 -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/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/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/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/mathematics.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/bgzip.o In file included from include/mathematics.h:117, from libs/mathematics.c:38: libs/mathematics.c: In function 'destructVector': -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 include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ @@ -1139,34 +1161,14 @@ 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/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/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/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/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/haarz.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 +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/sw.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/sw.o libs/sw.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/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/merge.o libs/merge.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/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 In file included from include/stringutils.h:27, from libs/merge.c:34: libs/merge.c: In function 'se_mergeWorker': @@ -1188,188 +1190,222 @@ libs/merge.c:1216:5: note: some parts of macro expansion are not guarded by this 'if' clause 1216 | if(!reads && curkey) FREEMEMORY(NULL, curkey); | ^~ -In file included from include/mathematics.h:117, - from libs/alignment.c:38: -libs/alignment.c: In function 'wrapAlignment': +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/alignment.c:97:18: note: in expansion of macro 'FREEMEMORY' - 97 | if(al->rmvseq) FREEMEMORY(NULL, al->v); - | ^~~~~~~~~~ -libs/alignment.c:97:3: note: some parts of macro expansion are not guarded by this 'if' clause - 97 | if(al->rmvseq) FREEMEMORY(NULL, al->v); +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/alignment.c:98:18: note: in expansion of macro 'FREEMEMORY' - 98 | if(al->rmuseq) FREEMEMORY(NULL, al->u); - | ^~~~~~~~~~ -libs/alignment.c:98:3: note: some parts of macro expansion are not guarded by this 'if' clause - 98 | if(al->rmuseq) FREEMEMORY(NULL, al->u); - | ^~ -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/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 libs/fileBins.c:51: -libs/fileBins.c: In function 'bl_fileBinsSortLine': +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/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/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) | ^~ -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 -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/samio.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 +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/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/charsequence.h:43, - from include/multicharseq.h:43, - from include/samio.h:23, - from libs/samio.c:33: -libs/samio.c: In function 'bl_samDestructTag': -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/samio.c:102:15: note: in expansion of macro 'FREEMEMORY' - 102 | if(kv->tag) FREEMEMORY(NULL, kv->tag); - | ^~~~~~~~~~ -libs/samio.c:102:3: note: some parts of macro expansion are not guarded by this 'if' clause - 102 | if(kv->tag) FREEMEMORY(NULL, kv->tag); - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/samio.c:103:15: note: in expansion of macro 'FREEMEMORY' - 103 | if(kv->val) FREEMEMORY(NULL, kv->val); - | ^~~~~~~~~~ -libs/samio.c:103:3: note: some parts of macro expansion are not guarded by this 'if' clause - 103 | if(kv->val) FREEMEMORY(NULL, kv->val); - | ^~ -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - | ^~~~ -libs/samio.c:104:16: note: in expansion of macro 'FREEMEMORY' - 104 | if(kv->type) FREEMEMORY(NULL, kv->type); - | ^~~~~~~~~~ -libs/samio.c:104:3: note: some parts of macro expansion are not guarded by this 'if' clause - 104 | if(kv->type) FREEMEMORY(NULL, kv->type); - | ^~ + from include/sufarray.h:45, + from libs/sufarray.c:39: +libs/sufarray.c: In function 'destructSufArr': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:105:15: note: in expansion of macro 'FREEMEMORY' - 105 | if(kv->key) FREEMEMORY(NULL, kv->key); - | ^~~~~~~~~~ -libs/samio.c:105:3: note: some parts of macro expansion are not guarded by this 'if' clause - 105 | if(kv->key) FREEMEMORY(NULL, kv->key); +libs/sufarray.c:613:5: note: in expansion of macro 'FREEMEMORY' + 613 | FREEMEMORY(space, arr->lcpctab); + | ^~~~~~~~~~ +libs/sufarray.c:612:3: note: some parts of macro expansion are not guarded by this 'if' clause + 612 | if (arr->lcpctab != NULL) | ^~ -libs/samio.c: In function 'bl_samDestruct': include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:112:21: note: in expansion of macro 'FREEMEMORY' - 112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname); - | ^~~~~~~~~~ -libs/samio.c:112:3: note: some parts of macro expansion are not guarded by this 'if' clause - 112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname); +libs/sufarray.c:615:5: note: in expansion of macro 'FREEMEMORY' + 615 | FREEMEMORY(space, arr->inv_suftab); + | ^~~~~~~~~~ +libs/sufarray.c:614:3: note: some parts of macro expansion are not guarded by this 'if' clause + 614 | if (arr->inv_suftab != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:113:21: note: in expansion of macro 'FREEMEMORY' - 113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname); - | ^~~~~~~~~~ -libs/samio.c:113:3: note: some parts of macro expansion are not guarded by this 'if' clause - 113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname); +libs/sufarray.c:619:5: note: in expansion of macro 'FREEMEMORY' + 619 | FREEMEMORY(space, arr->idvtab); + | ^~~~~~~~~~ +libs/sufarray.c:618:3: note: some parts of macro expansion are not guarded by this 'if' clause + 618 | if (arr->idvtab != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:114:21: note: in expansion of macro 'FREEMEMORY' - 114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar); - | ^~~~~~~~~~ -libs/samio.c:114:3: note: some parts of macro expansion are not guarded by this 'if' clause - 114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar); +libs/sufarray.c:624:5: note: in expansion of macro 'FREEMEMORY' + 624 | FREEMEMORY(space, arr->suflink); + | ^~~~~~~~~~ +libs/sufarray.c:620:3: note: some parts of macro expansion are not guarded by this 'if' clause + 620 | if (arr->suflink != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:115:21: note: in expansion of macro 'FREEMEMORY' - 115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext); - | ^~~~~~~~~~ -libs/samio.c:115:3: note: some parts of macro expansion are not guarded by this 'if' clause - 115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext); +libs/sufarray.c:627:5: note: in expansion of macro 'FREEMEMORY' + 627 | FREEMEMORY(space, arr->chldtab); + | ^~~~~~~~~~ +libs/sufarray.c:626:3: note: some parts of macro expansion are not guarded by this 'if' clause + 626 | if (arr->chldtab != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:116:21: note: in expansion of macro 'FREEMEMORY' - 116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq); - | ^~~~~~~~~~ -libs/samio.c:116:3: note: some parts of macro expansion are not guarded by this 'if' clause - 116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq); +libs/sufarray.c:629:5: note: in expansion of macro 'FREEMEMORY' + 629 | FREEMEMORY(space, arr->mdfive); + | ^~~~~~~~~~ +libs/sufarray.c:628:3: note: some parts of macro expansion are not guarded by this 'if' clause + 628 | if (arr->mdfive) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:117:21: note: in expansion of macro 'FREEMEMORY' - 117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual); - | ^~~~~~~~~~ -libs/samio.c:117:3: note: some parts of macro expansion are not guarded by this 'if' clause - 117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual); +libs/sufarray.c:631:5: note: in expansion of macro 'FREEMEMORY' + 631 | FREEMEMORY(space, arr->llvtab); + | ^~~~~~~~~~ +libs/sufarray.c:630:3: note: some parts of macro expansion are not guarded by this 'if' clause + 630 | if(arr->llvtab != NULL) | ^~ include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ -libs/samio.c:121:20: note: in expansion of macro 'FREEMEMORY' - 121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags); - | ^~~~~~~~~~ -libs/samio.c:121:3: note: some parts of macro expansion are not guarded by this 'if' clause - 121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags); +libs/sufarray.c:636:5: note: in expansion of macro 'FREEMEMORY' + 636 | FREEMEMORY(space, arr->id); + | ^~~~~~~~~~ +libs/sufarray.c:632:3: note: some parts of macro expansion are not guarded by this 'if' clause + 632 | if(arr->id != NULL) | ^~ -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/container.o libs/container.c +libs/sufarray.c: In function 'readSuffixarray': +libs/sufarray.c:428:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 428 | fread(&nmemb, sizeof(Uint), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:430:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 430 | fread(suftab, sizeof(Uint), nmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:431:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 431 | fread(&flags, sizeof(char), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:436:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 436 | fread(lcpctab, sizeof(unsigned char), nmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:438:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 438 | fread(&llvmemb, sizeof(Uint), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:440:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 440 | fread(llvtab, sizeof(PairUint), llvmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:446:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 446 | fread(chldtab, sizeof(childtab), nmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:484:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 484 | fread(suflink, sizeof(Uint), nmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:508:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 508 | fread(id, sizeof(signed char), nmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:511:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 511 | fread(&idvmemb, sizeof(Uint), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:515:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 515 | fread(idvtab, sizeof(PairLSint), idvmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:519:7: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 519 | fread(idvutab, sizeof(PairUint), idvmemb, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/sufarray.c:530:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fread(mdfive, sizeof(unsigned char), 16, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/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 +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/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 +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/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 +Building... library for source build/haarz.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 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/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/gzip.o libs/gzip.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)); + | ~~^ ~~~~~~~~~ + | | | + | long int size_t {aka unsigned int} + | %d +libs/gzip.c:41:71: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'unsigned int' [-Wformat=] + 41 | fprintf(stderr, "common header has a length of %ld instead of %ld - not good.\n", bytesRead, sizeof(u_CommonHeader)); + | ~~^ ~~~~~~~~~~~~~~~~~~~~~~ + | | | + | long int unsigned int + | %d +Building... library for source build/manopt.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/manopt.o libs/manopt.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/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 Linking segemehl -cc build/gzip.o build/aluruSort.o build/annotation.o build/nw.o build/bamio.o build/mapfrag.o build/charsequence.o build/sw.o build/sufarray.o build/manopt.o build/portable_endian.o build/biofiles.o build/match.o build/sort.o build/kdseed.o build/segemehl_helper.o build/seqclip.o build/iupac.o build/stringutils.o build/locus.o build/gzidx.o build/intervaltree.o build/filebuffer.o build/info.o build/memory.o build/manout.o build/fileio.o build/debug.o build/vqueue.o build/multicharseq.o build/bedfiles.o build/brendel.o build/splitalign.o build/mappingqual.o build/bitVector.o build/junctions.o build/vstack.o build/md5.o build/queryalign.o build/samheader.o build/mathematics.o build/bgzip.o build/stack.o build/kdchain.o build/pigeon.o build/merge.o build/alignment.o build/bitvectoralg.o build/fileBins.o build/radixsort.o build/matealign.o build/samio.o build/container.o build/bitArray.o build/karlin.o build/vtprogressbar.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/seqclip.o build/samheader.o build/mapfrag.o build/alignment.o build/fileBins.o build/filebuffer.o build/annotation.o build/kdchain.o build/info.o build/nw.o build/sort.o build/samio.o build/manout.o build/queryalign.o build/junctions.o build/bitvectoralg.o build/multicharseq.o build/portable_endian.o build/match.o build/stack.o build/bamio.o build/memory.o build/gzidx.o build/pigeon.o build/container.o build/matealign.o build/debug.o build/vqueue.o build/radixsort.o build/kdseed.o build/stringutils.o build/aluruSort.o build/intervaltree.o build/bgzip.o build/bedfiles.o build/iupac.o build/splitalign.o build/bitVector.o build/vstack.o build/vtprogressbar.o build/mathematics.o build/mappingqual.o build/sw.o build/md5.o build/merge.o build/charsequence.o build/sufarray.o build/brendel.o build/fileio.o build/biofiles.o build/locus.o build/segemehl_helper.o build/bitArray.o build/gzip.o build/manopt.o build/karlin.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/gzip.o build/aluruSort.o build/annotation.o build/nw.o build/bamio.o build/mapfrag.o build/charsequence.o build/sw.o build/sufarray.o build/manopt.o build/portable_endian.o build/biofiles.o build/match.o build/sort.o build/kdseed.o build/segemehl_helper.o build/seqclip.o build/iupac.o build/stringutils.o build/locus.o build/gzidx.o build/intervaltree.o build/filebuffer.o build/info.o build/memory.o build/manout.o build/fileio.o build/debug.o build/vqueue.o build/multicharseq.o build/bedfiles.o build/brendel.o build/splitalign.o build/mappingqual.o build/bitVector.o build/junctions.o build/vstack.o build/md5.o build/queryalign.o build/samheader.o build/mathematics.o build/bgzip.o build/stack.o build/kdchain.o build/pigeon.o build/merge.o build/alignment.o build/bitvectoralg.o build/fileBins.o build/radixsort.o build/matealign.o build/samio.o build/container.o build/bitArray.o build/karlin.o build/vtprogressbar.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/seqclip.o build/samheader.o build/mapfrag.o build/alignment.o build/fileBins.o build/filebuffer.o build/annotation.o build/kdchain.o build/info.o build/nw.o build/sort.o build/samio.o build/manout.o build/queryalign.o build/junctions.o build/bitvectoralg.o build/multicharseq.o build/portable_endian.o build/match.o build/stack.o build/bamio.o build/memory.o build/gzidx.o build/pigeon.o build/container.o build/matealign.o build/debug.o build/vqueue.o build/radixsort.o build/kdseed.o build/stringutils.o build/aluruSort.o build/intervaltree.o build/bgzip.o build/bedfiles.o build/iupac.o build/splitalign.o build/bitVector.o build/vstack.o build/vtprogressbar.o build/mathematics.o build/mappingqual.o build/sw.o build/md5.o build/merge.o build/charsequence.o build/sufarray.o build/brendel.o build/fileio.o build/biofiles.o build/locus.o build/segemehl_helper.o build/bitArray.o build/gzip.o build/manopt.o build/karlin.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 @@ -1401,8 +1437,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'segemehl-dbgsym' in '../segemehl-dbgsym_0.3.4-5_armhf.deb'. dpkg-deb: building package 'segemehl' in '../segemehl_0.3.4-5_armhf.deb'. +dpkg-deb: building package 'segemehl-dbgsym' in '../segemehl-dbgsym_0.3.4-5_armhf.deb'. dpkg-genbuildinfo --build=binary -O../segemehl_0.3.4-5_armhf.buildinfo dpkg-genchanges --build=binary -O../segemehl_0.3.4-5_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1410,12 +1446,14 @@ 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/2866/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2866/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/6637 and its subdirectories -I: Current time: Sat Jan 6 01:53:27 -12 2024 -I: pbuilder-time-stamp: 1704549207 +I: removing directory /srv/workspace/pbuilder/2866 and its subdirectories +I: Current time: Sun Jan 7 03:56:18 +14 2024 +I: pbuilder-time-stamp: 1704549378