Diff of the two buildlogs: -- --- b1/build.log 2021-12-15 09:51:21.310537379 +0000 +++ b2/build.log 2021-12-15 09:52:08.417070548 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Dec 14 21:50:48 -12 2021 -I: pbuilder-time-stamp: 1639561848 +I: Current time: Wed Jan 18 06:14:23 +14 2023 +I: pbuilder-time-stamp: 1673972063 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Fri Jan 11 09:54:08 2019 -12 +gpgv: Signature made Sat Jan 12 11:54:08 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,136 +29,170 @@ dpkg-source: info: applying rpath.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3443219/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/570718/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/570718/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/570718/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='bdae84832ec74145926910b52e446c4a' - 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='3443219' - PS1='# ' - PS2='> ' + INVOCATION_ID=a919cde209d347d7a5f9bf36e73dd4ca + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=570718 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/tmp.lOsRIsKAPj/pbuilderrc_6Czi --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.lOsRIsKAPj/b1 --logfile b1/build.log segemehl_0.3.4-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.lOsRIsKAPj/pbuilderrc_OZJT --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.lOsRIsKAPj/b2 --logfile b2/build.log segemehl_0.3.4-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Nov 7 09:58 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/3443219/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jan 18 06:14 sh -> bash + lrwxrwxrwx 1 root root 4 Dec 11 18:20 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/570718/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -257,7 +291,7 @@ Get: 53 http://deb.debian.org/debian buster/main amd64 libhts-dev amd64 1.9-12~deb10u1 [4347 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libncurses-dev amd64 6.1+20181013-2+deb10u2 [333 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 pkg-config amd64 0.29-6 [63.5 kB] -Fetched 28.0 MB in 0s (58.5 MB/s) +Fetched 28.0 MB in 1s (53.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) @@ -500,7 +534,8 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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_0.3.4-1_source.changes +hostname: Name or service not known +I: Running cd /build/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_0.3.4-1_source.changes dpkg-buildpackage: info: source package segemehl dpkg-buildpackage: info: source version 0.3.4-1 dpkg-buildpackage: info: source distribution unstable @@ -510,7 +545,7 @@ fakeroot debian/rules clean dh clean dh_auto_clean - make -j15 clean + make -j16 clean make[1]: Entering directory '/build/segemehl-0.3.4' Cleaning... rm -f -r build segemehl haarz @@ -524,30 +559,26 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/segemehl-0.3.4' dh_auto_build -- all - make -j15 "INSTALL=install --strip-program=true" all + make -j16 "INSTALL=install --strip-program=true" all make[2]: Entering directory '/build/segemehl-0.3.4' Building... library for source build/matealign.o Building... library for source build/alignment.o Building... library for source build/nw.o Building... library for source build/mappingqual.o +Building... library for source build/mapfrag.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/matealign.o libs/matealign.c cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/alignment.o libs/alignment.c -Building... library for source build/mapfrag.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/nw.o libs/nw.c -Building... library for source build/filebuffer.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/mappingqual.o libs/mappingqual.c -Building... library for source build/multicharseq.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/mapfrag.o libs/mapfrag.c +Building... library for source build/filebuffer.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/filebuffer.o libs/filebuffer.c -Building... library for source build/mathematics.o -Building... library for source build/manopt.o +Building... library for source build/multicharseq.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/multicharseq.o libs/multicharseq.c +Building... library for source build/mathematics.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/mathematics.o libs/mathematics.c +Building... library for source build/manopt.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/manopt.o libs/manopt.c -Building... library for source build/haarz.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/haarz.o libs/haarz.c -Building... library for source build/intervaltree.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/intervaltree.o libs/intervaltree.c In file included from include/mathematics.h:117, from libs/alignment.c:38: libs/alignment.c: In function 'wrapAlignment': @@ -571,50 +602,7 @@ libs/alignment.c:98:3: note: some parts of macro expansion are not guarded by this 'if' clause if(al->rmuseq) FREEMEMORY(NULL, al->u); ^~ -Building... library for source build/bitvectoralg.o -In file included from include/mathematics.h:117, - from libs/mathematics.c:38: -libs/mathematics.c: In function 'destructVector': -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - ^~~~ -libs/mathematics.c:251:23: note: in expansion of macro 'FREEMEMORY' - if (v->elements) FREEMEMORY(space, v->elements); - ^~~~~~~~~~ -libs/mathematics.c:251:6: note: some parts of macro expansion are not guarded by this 'if' clause - if (v->elements) FREEMEMORY(space, v->elements); - ^~ -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/bitvectoralg.o libs/bitvectoralg.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] - #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - ^~~~ -libs/matealign.c:313:15: note: in expansion of macro 'FREEMEMORY' - 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 - if(npos[0]) FREEMEMORY(NULL, spos[0]); - ^~ -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: -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - ^~~~ -libs/matealign.c:314:15: note: in expansion of macro 'FREEMEMORY' - 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 - if(npos[1]) FREEMEMORY(NULL, spos[1]); - ^~ -Building... library for source build/iupac.o +Building... library for source build/haarz.o In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, @@ -655,7 +643,60 @@ libs/multicharseq.c:215:5: note: some parts of macro expansion are not guarded by this 'if' clause if (mseq->ref != NULL) ^~ +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/haarz.o libs/haarz.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] + #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + ^~~~ +libs/matealign.c:313:15: note: in expansion of macro 'FREEMEMORY' + 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 + if(npos[0]) FREEMEMORY(NULL, spos[0]); + ^~ +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: +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + ^~~~ +libs/matealign.c:314:15: note: in expansion of macro 'FREEMEMORY' + 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 + if(npos[1]) FREEMEMORY(NULL, spos[1]); + ^~ +Building... library for source build/intervaltree.o +Building... library for source build/bitvectoralg.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/intervaltree.o libs/intervaltree.c +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/bitvectoralg.o libs/bitvectoralg.c +In file included from include/mathematics.h:117, + from libs/mathematics.c:38: +libs/mathematics.c: In function 'destructVector': +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + ^~~~ +libs/mathematics.c:251:23: note: in expansion of macro 'FREEMEMORY' + if (v->elements) FREEMEMORY(space, v->elements); + ^~~~~~~~~~ +libs/mathematics.c:251:6: note: some parts of macro expansion are not guarded by this 'if' clause + if (v->elements) FREEMEMORY(space, v->elements); + ^~ +Building... library for source build/iupac.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/iupac.o libs/iupac.c +Building... library for source build/splitalign.o +Building... library for source build/fileBins.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/splitalign.o libs/splitalign.c +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/fileBins.o libs/fileBins.c +Building... library for source build/sufarray.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/sufarray.o libs/sufarray.c In file included from include/mathematics.h:117, from libs/intervaltree.c:27: libs/intervaltree.c: In function 'bl_intervaltreeDestruct': @@ -668,13 +709,117 @@ libs/intervaltree.c:443:3: note: some parts of macro expansion are not guarded by this 'if' clause if(root->ncoll) FREEMEMORY(NULL, root->collisions); ^~ -Building... library for source build/splitalign.o -Building... library for source build/fileBins.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/splitalign.o libs/splitalign.c -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/fileBins.o libs/fileBins.c -Building... library for source build/sufarray.o Building... library for source build/gzip.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/sufarray.o libs/sufarray.c +Building... library for source build/info.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/gzip.o libs/gzip.c +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/info.o libs/info.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] + #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + ^~~~ +libs/sufarray.c:613:5: note: in expansion of macro 'FREEMEMORY' + FREEMEMORY(space, arr->lcpctab); + ^~~~~~~~~~ +libs/sufarray.c:612:3: note: some parts of macro expansion are not guarded by this 'if' clause + if (arr->lcpctab != NULL) + ^~ +In file included from include/stringutils.h:27, + from include/charsequence.h:43, + from include/sufarray.h:45, + from libs/sufarray.c:39: +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + ^~~~ +libs/sufarray.c:615:5: note: in expansion of macro 'FREEMEMORY' + FREEMEMORY(space, arr->inv_suftab); + ^~~~~~~~~~ +libs/sufarray.c:614:3: note: some parts of macro expansion are not guarded by this 'if' clause + if (arr->inv_suftab != NULL) + ^~ +In file included from include/stringutils.h:27, + from include/charsequence.h:43, + from include/sufarray.h:45, + from libs/sufarray.c:39: +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + ^~~~ +libs/sufarray.c:619:5: note: in expansion of macro 'FREEMEMORY' + FREEMEMORY(space, arr->idvtab); + ^~~~~~~~~~ +libs/sufarray.c:618:3: note: some parts of macro expansion are not guarded by this 'if' clause + if (arr->idvtab != NULL) + ^~ +In file included from include/stringutils.h:27, + from include/charsequence.h:43, + from include/sufarray.h:45, + from libs/sufarray.c:39: +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + ^~~~ +libs/sufarray.c:624:5: note: in expansion of macro 'FREEMEMORY' + FREEMEMORY(space, arr->suflink); + ^~~~~~~~~~ +libs/sufarray.c:620:3: note: some parts of macro expansion are not guarded by this 'if' clause + if (arr->suflink != NULL) + ^~ +In file included from include/stringutils.h:27, + from include/charsequence.h:43, + from include/sufarray.h:45, + from libs/sufarray.c:39: +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + ^~~~ +libs/sufarray.c:627:5: note: in expansion of macro 'FREEMEMORY' + FREEMEMORY(space, arr->chldtab); + ^~~~~~~~~~ +libs/sufarray.c:626:3: note: some parts of macro expansion are not guarded by this 'if' clause + if (arr->chldtab != NULL) + ^~ +In file included from include/stringutils.h:27, + from include/charsequence.h:43, + from include/sufarray.h:45, + from libs/sufarray.c:39: +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + ^~~~ +libs/sufarray.c:629:5: note: in expansion of macro 'FREEMEMORY' + FREEMEMORY(space, arr->mdfive); + ^~~~~~~~~~ +libs/sufarray.c:628:3: note: some parts of macro expansion are not guarded by this 'if' clause + if (arr->mdfive) + ^~ +In file included from include/stringutils.h:27, + from include/charsequence.h:43, + from include/sufarray.h:45, + from libs/sufarray.c:39: +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + ^~~~ +libs/sufarray.c:631:5: note: in expansion of macro 'FREEMEMORY' + FREEMEMORY(space, arr->llvtab); + ^~~~~~~~~~ +libs/sufarray.c:630:3: note: some parts of macro expansion are not guarded by this 'if' clause + if(arr->llvtab != NULL) + ^~ +In file included from include/stringutils.h:27, + from include/charsequence.h:43, + from include/sufarray.h:45, + from libs/sufarray.c:39: +include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] + #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + ^~~~ +libs/sufarray.c:636:5: note: in expansion of macro 'FREEMEMORY' + FREEMEMORY(space, arr->id); + ^~~~~~~~~~ +libs/sufarray.c:632:3: note: some parts of macro expansion are not guarded by this 'if' clause + if(arr->id != NULL) + ^~ +Building... library for source build/brendel.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/brendel.o libs/brendel.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] @@ -686,7 +831,22 @@ libs/fileBins.c:901:5: note: some parts of macro expansion are not guarded by this 'if' clause if(fileSort) FREEMEMORY(space, line); ^~ -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/gzip.o libs/gzip.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=] + sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", + ^~ +libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] + sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/info.c:64:5: note: 'sprintf' output between 16 and 67 bytes into a destination of size 26 + sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + wday_name[timeptr->tm_wday], mon_name[timeptr->tm_mon], + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + timeptr->tm_mday, timeptr->tm_hour, timeptr->tm_min, + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + timeptr->tm_sec, 1900 + timeptr->tm_year); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/alignment.h:38, @@ -748,6 +908,23 @@ libs/splitalign.c:1326:7: note: some parts of macro expansion are not guarded by this 'if' clause if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); ^~ +libs/info.c: In function 'infomsg': +libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=] + sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", + ^~ +libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] + sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libs/info.c:64:5: note: 'sprintf' output between 16 and 67 bytes into a destination of size 26 + sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + wday_name[timeptr->tm_wday], mon_name[timeptr->tm_mon], + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + timeptr->tm_mday, timeptr->tm_hour, timeptr->tm_min, + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + timeptr->tm_sec, 1900 + timeptr->tm_year); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Building... library for source build/manout.o In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/alignment.h:38, @@ -809,145 +986,6 @@ libs/splitalign.c:1568:9: note: some parts of macro expansion are not guarded by this 'if' clause if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); ^~ -Building... library for source build/info.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/info.o libs/info.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=] - sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", - ^~ -libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] - sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/info.c:64:5: note: 'sprintf' output between 16 and 67 bytes into a destination of size 26 - sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - wday_name[timeptr->tm_wday], mon_name[timeptr->tm_mon], - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - timeptr->tm_mday, timeptr->tm_hour, timeptr->tm_min, - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - timeptr->tm_sec, 1900 + timeptr->tm_year); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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] - #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - ^~~~ -libs/sufarray.c:613:5: note: in expansion of macro 'FREEMEMORY' - FREEMEMORY(space, arr->lcpctab); - ^~~~~~~~~~ -libs/sufarray.c:612:3: note: some parts of macro expansion are not guarded by this 'if' clause - if (arr->lcpctab != NULL) - ^~ -In file included from include/stringutils.h:27, - from include/charsequence.h:43, - from include/sufarray.h:45, - from libs/sufarray.c:39: -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - ^~~~ -libs/sufarray.c:615:5: note: in expansion of macro 'FREEMEMORY' - FREEMEMORY(space, arr->inv_suftab); - ^~~~~~~~~~ -libs/sufarray.c:614:3: note: some parts of macro expansion are not guarded by this 'if' clause - if (arr->inv_suftab != NULL) - ^~ -In file included from include/stringutils.h:27, - from include/charsequence.h:43, - from include/sufarray.h:45, - from libs/sufarray.c:39: -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - ^~~~ -libs/sufarray.c:619:5: note: in expansion of macro 'FREEMEMORY' - FREEMEMORY(space, arr->idvtab); - ^~~~~~~~~~ -libs/sufarray.c:618:3: note: some parts of macro expansion are not guarded by this 'if' clause - if (arr->idvtab != NULL) - ^~ -In file included from include/stringutils.h:27, - from include/charsequence.h:43, - from include/sufarray.h:45, - from libs/sufarray.c:39: -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - ^~~~ -libs/sufarray.c:624:5: note: in expansion of macro 'FREEMEMORY' - FREEMEMORY(space, arr->suflink); - ^~~~~~~~~~ -libs/sufarray.c:620:3: note: some parts of macro expansion are not guarded by this 'if' clause - if (arr->suflink != NULL) - ^~ -In file included from include/stringutils.h:27, - from include/charsequence.h:43, - from include/sufarray.h:45, - from libs/sufarray.c:39: -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - ^~~~ -libs/sufarray.c:627:5: note: in expansion of macro 'FREEMEMORY' - FREEMEMORY(space, arr->chldtab); - ^~~~~~~~~~ -libs/sufarray.c:626:3: note: some parts of macro expansion are not guarded by this 'if' clause - if (arr->chldtab != NULL) - ^~ -In file included from include/stringutils.h:27, - from include/charsequence.h:43, - from include/sufarray.h:45, - from libs/sufarray.c:39: -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - ^~~~ -libs/sufarray.c:629:5: note: in expansion of macro 'FREEMEMORY' - FREEMEMORY(space, arr->mdfive); - ^~~~~~~~~~ -libs/sufarray.c:628:3: note: some parts of macro expansion are not guarded by this 'if' clause - if (arr->mdfive) - ^~ -In file included from include/stringutils.h:27, - from include/charsequence.h:43, - from include/sufarray.h:45, - from libs/sufarray.c:39: -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - ^~~~ -libs/sufarray.c:631:5: note: in expansion of macro 'FREEMEMORY' - FREEMEMORY(space, arr->llvtab); - ^~~~~~~~~~ -libs/sufarray.c:630:3: note: some parts of macro expansion are not guarded by this 'if' clause - if(arr->llvtab != NULL) - ^~ -In file included from include/stringutils.h:27, - from include/charsequence.h:43, - from include/sufarray.h:45, - from libs/sufarray.c:39: -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - ^~~~ -libs/sufarray.c:636:5: note: in expansion of macro 'FREEMEMORY' - FREEMEMORY(space, arr->id); - ^~~~~~~~~~ -libs/sufarray.c:632:3: note: some parts of macro expansion are not guarded by this 'if' clause - if(arr->id != NULL) - ^~ -libs/info.c: In function 'infomsg': -libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=] - sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", - ^~ -libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] - sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libs/info.c:64:5: note: 'sprintf' output between 16 and 67 bytes into a destination of size 26 - sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - wday_name[timeptr->tm_wday], mon_name[timeptr->tm_mon], - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - timeptr->tm_mday, timeptr->tm_hour, timeptr->tm_min, - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - timeptr->tm_sec, 1900 + timeptr->tm_year); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/info.c: In function 'nfolevel': libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=] sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", @@ -964,30 +1002,13 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ timeptr->tm_sec, 1900 + timeptr->tm_year); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Building... library for source build/brendel.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/brendel.o libs/brendel.c -Building... library for source build/manout.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/manout.o libs/manout.c Building... library for source build/samio.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/samio.o libs/samio.c Building... library for source build/stringutils.o -Building... library for source build/charsequence.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/stringutils.o libs/stringutils.c +Building... library for source build/charsequence.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/charsequence.o libs/charsequence.c -Building... library for source build/match.o -In file included from include/stringutils.h:27, - from libs/stringutils.c:39: -libs/stringutils.c: In function 'destructStringset': -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - ^~~~ -libs/stringutils.c:274:9: note: in expansion of macro 'FREEMEMORY' - FREEMEMORY(space, s->strings[i].str); - ^~~~~~~~~~ -libs/stringutils.c:273:7: note: some parts of macro expansion are not guarded by this 'if' clause - if(s->strings[i].str != NULL) - ^~ -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/match.o libs/match.c In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, @@ -1144,8 +1165,18 @@ libs/samio.c:121:3: note: some parts of macro expansion are not guarded by this 'if' clause if(samrec->tags) FREEMEMORY(NULL, samrec->tags); ^~ -Building... library for source build/sort.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/sort.o libs/sort.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] + #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + ^~~~ +libs/stringutils.c:274:9: note: in expansion of macro 'FREEMEMORY' + FREEMEMORY(space, s->strings[i].str); + ^~~~~~~~~~ +libs/stringutils.c:273:7: note: some parts of macro expansion are not guarded by this 'if' clause + if(s->strings[i].str != NULL) + ^~ 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] @@ -1187,6 +1218,10 @@ libs/charsequence.c:473:5: note: some parts of macro expansion are not guarded by this 'if' clause if (sequence->info != NULL) ^~ +Building... library for source build/match.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/match.o libs/match.c +Building... library for source build/sort.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/sort.o libs/sort.c Building... library for source build/radixsort.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/radixsort.o libs/radixsort.c Building... library for source build/pigeon.o @@ -1195,10 +1230,6 @@ cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/junctions.o libs/junctions.c Building... library for source build/memory.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/memory.o libs/memory.c -Building... library for source build/segemehl.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/segemehl.o libs/segemehl.c -Building... library for source build/bedfiles.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/bedfiles.o libs/bedfiles.c In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/segemehl.h:44, @@ -1213,6 +1244,10 @@ libs/pigeon.c:352:3: note: some parts of macro expansion are not guarded by this 'if' clause if(check) FREEMEMORY(space, check); ^~ +Building... library for source build/segemehl.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/segemehl.o libs/segemehl.c +Building... library for source build/bedfiles.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/bedfiles.o libs/bedfiles.c Building... library for source build/container.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/container.o libs/container.c Building... library for source build/portable_endian.o @@ -1224,14 +1259,14 @@ Building... library for source build/karlin.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/karlin.o libs/karlin.c Building... library for source build/vtprogressbar.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/vtprogressbar.o libs/vtprogressbar.c Building... library for source build/kdchain.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/vtprogressbar.o libs/vtprogressbar.c cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/kdchain.o libs/kdchain.c Building... library for source build/fileio.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/fileio.o libs/fileio.c Building... library for source build/sw.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/sw.o libs/sw.c Building... library for source build/samheader.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/sw.o libs/sw.c cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/samheader.o libs/samheader.c Building... library for source build/bitArray.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/bitArray.o libs/bitArray.c @@ -1244,9 +1279,15 @@ Building... library for source build/bamio.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/bamio.o libs/bamio.c Building... library for source build/stack.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/stack.o libs/stack.c Building... library for source build/kdseed.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/stack.o libs/stack.c cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/kdseed.o libs/kdseed.c +Building... library for source build/merge.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/merge.o libs/merge.c +Building... library for source build/debug.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/debug.o libs/debug.c +Building... library for source build/seqclip.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/seqclip.o libs/seqclip.c In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, @@ -1263,16 +1304,27 @@ libs/bamio.c:468:5: note: some parts of macro expansion are not guarded by this 'if' clause if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d); ^~ -Building... library for source build/merge.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/merge.o libs/merge.c -Building... library for source build/debug.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/debug.o libs/debug.c -Building... library for source build/seqclip.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/seqclip.o libs/seqclip.c Building... library for source build/locus.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/locus.o libs/locus.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] + #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL + ^~~~ +libs/seqclip.c:529:9: note: in expansion of macro 'FREEMEMORY' + FREEMEMORY(space, adapter); + ^~~~~~~~~~ +libs/seqclip.c:528:7: note: some parts of macro expansion are not guarded by this 'if' clause + if(adapter) + ^~ Building... library for source build/bitVector.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/bitVector.o libs/bitVector.c +Building... library for source build/biofiles.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/biofiles.o libs/biofiles.c In file included from include/stringutils.h:27, from libs/merge.c:34: libs/merge.c: In function 'se_mergeWorker': @@ -1296,27 +1348,12 @@ libs/merge.c:1216:5: note: some parts of macro expansion are not guarded by this 'if' clause if(!reads && curkey) FREEMEMORY(NULL, curkey); ^~ -Building... library for source build/biofiles.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/biofiles.o libs/biofiles.c -In file included from include/stringutils.h:27, - from include/biofiles.h:43, - from include/alignment.h:38, - from include/sw.h:38, - from libs/seqclip.c:44: -libs/seqclip.c: In function 'bl_Find3PrimeGreedy': -include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] - #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL - ^~~~ -libs/seqclip.c:529:9: note: in expansion of macro 'FREEMEMORY' - FREEMEMORY(space, adapter); - ^~~~~~~~~~ -libs/seqclip.c:528:7: note: some parts of macro expansion are not guarded by this 'if' clause - if(adapter) - ^~ Building... library for source build/annotation.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/annotation.o libs/annotation.c Building... library for source build/queryalign.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/queryalign.o libs/queryalign.c +Building... library for source build/vstack.o +cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/vstack.o libs/vstack.c In file included from include/stringutils.h:27, from libs/annotation.c:29: libs/annotation.c: In function 'bl_annotationitemDestruct': @@ -1463,8 +1500,6 @@ libs/annotation.c:455:3: note: some parts of macro expansion are not guarded by this 'if' clause if(track->items) FREEMEMORY(space, track->items) ; ^~ -Building... library for source build/vstack.o -cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/vstack.o libs/vstack.c Building... library for source build/md5.o cc -g -O2 -ffile-prefix-map=/build/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 -c -o build/md5.o libs/md5.c Linking segemehl @@ -1500,16 +1535,16 @@ dh_strip dh_makeshlibs dh_shlibdeps -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/segemehl debian/segemehl/usr/bin/haarz were not linked against libtinfo.so.6 (they use none of the library's symbols) -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/segemehl debian/segemehl/usr/bin/haarz were not linked against libncurses.so.6 (they use none of the library's symbols) -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/segemehl debian/segemehl/usr/bin/haarz were not linked against libform.so.6 (they use none of the library's symbols) -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/segemehl debian/segemehl/usr/bin/haarz were not linked against libmenu.so.6 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/haarz debian/segemehl/usr/bin/segemehl were not linked against libmenu.so.6 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/haarz debian/segemehl/usr/bin/segemehl were not linked against libform.so.6 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/haarz debian/segemehl/usr/bin/segemehl were not linked against libncurses.so.6 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/haarz debian/segemehl/usr/bin/segemehl were not linked against libtinfo.so.6 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'segemehl' in '../segemehl_0.3.4-1_amd64.deb'. dpkg-deb: building package 'segemehl-dbgsym' in '../segemehl-dbgsym_0.3.4-1_amd64.deb'. +dpkg-deb: building package 'segemehl' in '../segemehl_0.3.4-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../segemehl_0.3.4-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1517,12 +1552,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/570718/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/570718/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/3443219 and its subdirectories -I: Current time: Tue Dec 14 21:51:21 -12 2021 -I: pbuilder-time-stamp: 1639561881 +I: removing directory /srv/workspace/pbuilder/570718 and its subdirectories +I: Current time: Wed Jan 18 06:15:08 +14 2023 +I: pbuilder-time-stamp: 1673972108