Diff of the two buildlogs: -- --- b1/build.log 2022-01-10 01:14:45.340943445 +0000 +++ b2/build.log 2022-01-10 01:17:41.375484657 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Feb 11 19:36:44 -12 2023 -I: pbuilder-time-stamp: 1676187404 +I: Current time: Mon Jan 10 15:14:48 +14 2022 +I: pbuilder-time-stamp: 1641777288 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./sniffles_1.0.12b+ds-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.NC8tDAVn/trustedkeys.kbx': General error -gpgv: Signature made Fri Nov 27 10:37:57 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.yD8t8Hld/trustedkeys.kbx': General error +gpgv: Signature made Sat Nov 28 12:37:57 2020 +14 gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key @@ -31,135 +31,169 @@ dpkg-source: info: applying stoppingRecursion.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1777030/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2062006/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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/2062006/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2062006/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,-fixfilepath parallel=16' - 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]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(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,-fixfilepath parallel=15' + 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='83b668d597e24f8d80149595e6d1e134' - 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='1777030' - PS1='# ' - PS2='> ' + INVOCATION_ID=fdd20c6e0f5c4aaf8511da8a429b7f82 + 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=2062006 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.rkrkjhynDX/pbuilderrc_kQ8q --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.rkrkjhynDX/b1 --logfile b1/build.log sniffles_1.0.12b+ds-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.rkrkjhynDX/pbuilderrc_NpdS --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.rkrkjhynDX/b2 --logfile b2/build.log sniffles_1.0.12b+ds-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://78.137.99.97:3128 I: uname -a - Linux ionos5-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jul 28 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jul 28 2021 more - -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount - -rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Feb 9 03:46 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jul 28 2021 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jul 28 2021 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jul 28 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/1777030/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jul 29 09:09 more + -rwsr-xr-x 1 root root 55528 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 18664 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jan 10 15:15 sh -> bash + lrwxrwxrwx 1 root root 4 Jan 7 23:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jul 29 09:09 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/2062006/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -263,7 +297,7 @@ Get: 56 http://deb.debian.org/debian bullseye/main amd64 pandoc-data all 2.9.2.1-1 [376 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 pandoc amd64 2.9.2.1-1+b1 [18.5 MB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] -Fetched 48.2 MB in 1s (76.6 MB/s) +Fetched 48.2 MB in 1s (40.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) @@ -511,7 +545,8 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/sniffles-1.0.12b+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../sniffles_1.0.12b+ds-1_source.changes +hostname: Name or service not known +I: Running cd /build/sniffles-1.0.12b+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../sniffles_1.0.12b+ds-1_source.changes dpkg-buildpackage: info: source package sniffles dpkg-buildpackage: info: source version 1.0.12b+ds-1 dpkg-buildpackage: info: source distribution unstable @@ -571,7 +606,7 @@ -- Build files have been written to: /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/sniffles-1.0.12b+ds' dh_auto_build - cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/sniffles-1.0.12b+ds -B/build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/CMakeFiles /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -586,38 +621,36 @@ make[3]: Leaving directory '/build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu' make -f src/CMakeFiles/sniffles.dir/build.make src/CMakeFiles/sniffles.dir/build make[3]: Entering directory '/build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu' -[ 4%] Building CXX object src/CMakeFiles/sniffles.dir/Genotyper/Genotyper.cpp.o -cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/Genotyper/Genotyper.cpp.o -c /build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp -[ 8%] Building CXX object src/CMakeFiles/sniffles.dir/tree/Breakpoint_Tree.cpp.o +[ 4%] Building CXX object src/CMakeFiles/sniffles.dir/tree/Breakpoint_Tree.cpp.o +[ 8%] Building CXX object src/CMakeFiles/sniffles.dir/Genotyper/Genotyper.cpp.o [ 13%] Building CXX object src/CMakeFiles/sniffles.dir/Alignment.cpp.o cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/tree/Breakpoint_Tree.cpp.o -c /build/sniffles-1.0.12b+ds/src/tree/Breakpoint_Tree.cpp +cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/Genotyper/Genotyper.cpp.o -c /build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp [ 17%] Building CXX object src/CMakeFiles/sniffles.dir/BamParser.cpp.o -[ 21%] Building CXX object src/CMakeFiles/sniffles.dir/Sniffles.cpp.o cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/Alignment.cpp.o -c /build/sniffles-1.0.12b+ds/src/Alignment.cpp +[ 21%] Building CXX object src/CMakeFiles/sniffles.dir/Sniffles.cpp.o cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/BamParser.cpp.o -c /build/sniffles-1.0.12b+ds/src/BamParser.cpp -[ 26%] Building CXX object src/CMakeFiles/sniffles.dir/Ignore_Regions.cpp.o cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/Sniffles.cpp.o -c /build/sniffles-1.0.12b+ds/src/Sniffles.cpp -cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/Ignore_Regions.cpp.o -c /build/sniffles-1.0.12b+ds/src/Ignore_Regions.cpp +[ 26%] Building CXX object src/CMakeFiles/sniffles.dir/Ignore_Regions.cpp.o [ 30%] Building CXX object src/CMakeFiles/sniffles.dir/tree/Intervall_bed.cpp.o +cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/Ignore_Regions.cpp.o -c /build/sniffles-1.0.12b+ds/src/Ignore_Regions.cpp cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/tree/Intervall_bed.cpp.o -c /build/sniffles-1.0.12b+ds/src/tree/Intervall_bed.cpp [ 34%] Building CXX object src/CMakeFiles/sniffles.dir/sub/Detect_Breakpoints.cpp.o -cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/sub/Detect_Breakpoints.cpp.o -c /build/sniffles-1.0.12b+ds/src/sub/Detect_Breakpoints.cpp [ 39%] Building CXX object src/CMakeFiles/sniffles.dir/sub/Breakpoint.cpp.o -cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/sub/Breakpoint.cpp.o -c /build/sniffles-1.0.12b+ds/src/sub/Breakpoint.cpp [ 43%] Building CXX object src/CMakeFiles/sniffles.dir/tree/IntervallTree.cpp.o +cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/sub/Detect_Breakpoints.cpp.o -c /build/sniffles-1.0.12b+ds/src/sub/Detect_Breakpoints.cpp +cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/sub/Breakpoint.cpp.o -c /build/sniffles-1.0.12b+ds/src/sub/Breakpoint.cpp cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/tree/IntervallTree.cpp.o -c /build/sniffles-1.0.12b+ds/src/tree/IntervallTree.cpp [ 47%] Building CXX object src/CMakeFiles/sniffles.dir/tree/IntervallList.cpp.o [ 52%] Building CXX object src/CMakeFiles/sniffles.dir/realign/SWCPU.cpp.o -[ 56%] Building CXX object src/CMakeFiles/sniffles.dir/realign/Realign.cpp.o cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/tree/IntervallList.cpp.o -c /build/sniffles-1.0.12b+ds/src/tree/IntervallList.cpp -[ 60%] Building CXX object src/CMakeFiles/sniffles.dir/print/VCFPrinter.cpp.o -[ 65%] Building CXX object src/CMakeFiles/sniffles.dir/print/BedpePrinter.cpp.o cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/realign/SWCPU.cpp.o -c /build/sniffles-1.0.12b+ds/src/realign/SWCPU.cpp +[ 56%] Building CXX object src/CMakeFiles/sniffles.dir/realign/Realign.cpp.o +[ 60%] Building CXX object src/CMakeFiles/sniffles.dir/print/VCFPrinter.cpp.o cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/realign/Realign.cpp.o -c /build/sniffles-1.0.12b+ds/src/realign/Realign.cpp cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/print/VCFPrinter.cpp.o -c /build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp -[ 69%] Building CXX object src/CMakeFiles/sniffles.dir/print/IPrinter.cpp.o +[ 65%] Building CXX object src/CMakeFiles/sniffles.dir/print/BedpePrinter.cpp.o cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/print/BedpePrinter.cpp.o -c /build/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp -cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/print/IPrinter.cpp.o -c /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp /build/sniffles-1.0.12b+ds/src/realign/SWCPU.cpp: In constructor 'SWCPUCor::SWCPUCor(int)': /build/sniffles-1.0.12b+ds/src/realign/SWCPU.cpp:30:35: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 30 | fprintf(stderr, "Allocationg: %llu\n", maxLen * sizeof(MatrixElement)); @@ -626,8 +659,36 @@ | | long unsigned int | long long unsigned int | %lu +[ 69%] Building CXX object src/CMakeFiles/sniffles.dir/print/IPrinter.cpp.o +cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/print/IPrinter.cpp.o -c /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp [ 73%] Building CXX object src/CMakeFiles/sniffles.dir/tree/BinTree.cpp.o cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/tree/BinTree.cpp.o -c /build/sniffles-1.0.12b+ds/src/tree/BinTree.cpp +/build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp: In member function 'virtual void VCFPrinter::print_body(Breakpoint*&, BamTools::RefVector)': +/build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:369:22: warning: format '%i' expects argument of type 'int', but argument 3 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] + 369 | fprintf(file, "%i", SV->get_sequence().size()); + | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ + | | | + | int std::__cxx11::basic_string::size_type {aka long unsigned int} + | %li +/build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:376:21: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] + 376 | fprintf(file, "%i", SV->get_length() * -1); + | ~^ ~~~~~~~~~~~~~~~~~~~~~ + | | | + | int long int + | %li +/build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:378:21: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] + 378 | fprintf(file, "%i", SV->get_length()); + | ~^ ~~~~~~~~~~~~~~~~ + | | | + | int long int + | %li +/build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp: In member function 'virtual void VCFPrinter::print_body_recall(Breakpoint*&, BamTools::RefVector)': +/build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:510:19: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] + 510 | fprintf(file, "%i", SV->get_length()); + | ~^ ~~~~~~~~~~~~~~~~ + | | | + | int long int + | %li /build/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp: In member function 'virtual void BedpePrinter::print_body(Breakpoint*&, BamTools::RefVector)': /build/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp:99:21: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 99 | fprintf(file, "%i", SV->get_length()); @@ -654,6 +715,26 @@ | | | | int long int | %li +[ 78%] Building CXX object src/CMakeFiles/sniffles.dir/print/NGMPrinter.cpp.o +cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/print/NGMPrinter.cpp.o -c /build/sniffles-1.0.12b+ds/src/print/NGMPrinter.cpp +/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function 'void Genotyper::update_svs_output(std::map, std::vector >)': +/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:343:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 343 | system(move.c_str()); + | ~~~~~~^~~~~~~~~~~~~~ +/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function 'void Genotyper::update_SVs2()': +/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:382:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 382 | system(del.c_str()); + | ~~~~~~^~~~~~~~~~~~~ +/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function 'void Genotyper::update_file(Breakpoint_Tree&, breakpoint_node*&)': +/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:719:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 719 | system(move.c_str()); + | ~~~~~~^~~~~~~~~~~~~~ +/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function 'void Genotyper::update_SVs()': +/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:858:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 858 | system(del.c_str()); + | ~~~~~~^~~~~~~~~~~~~ +[ 82%] Building CXX object src/CMakeFiles/sniffles.dir/plane-sweep/PlaneSweep_slim.cpp.o +cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/plane-sweep/PlaneSweep_slim.cpp.o -c /build/sniffles-1.0.12b+ds/src/plane-sweep/PlaneSweep_slim.cpp /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp: In function 'void write_read(Alignment*, FILE*&)': /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:21:29: warning: unknown conversion type character 'r' in format [-Wformat=] 21 | fprintf(ref_allel_reads, "%ref_plus", '\t'); @@ -697,52 +778,6 @@ /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:31:27: warning: too many arguments for format [-Wformat-extra-args] 31 | fprintf(ref_allel_reads, "%ref_plus", '\n'); | ^~~~~~~~~~~ -/build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp: In member function 'virtual void VCFPrinter::print_body(Breakpoint*&, BamTools::RefVector)': -/build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:369:22: warning: format '%i' expects argument of type 'int', but argument 3 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] - 369 | fprintf(file, "%i", SV->get_sequence().size()); - | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ - | | | - | int std::__cxx11::basic_string::size_type {aka long unsigned int} - | %li -/build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:376:21: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] - 376 | fprintf(file, "%i", SV->get_length() * -1); - | ~^ ~~~~~~~~~~~~~~~~~~~~~ - | | | - | int long int - | %li -/build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:378:21: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] - 378 | fprintf(file, "%i", SV->get_length()); - | ~^ ~~~~~~~~~~~~~~~~ - | | | - | int long int - | %li -/build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp: In member function 'virtual void VCFPrinter::print_body_recall(Breakpoint*&, BamTools::RefVector)': -/build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:510:19: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] - 510 | fprintf(file, "%i", SV->get_length()); - | ~^ ~~~~~~~~~~~~~~~~ - | | | - | int long int - | %li -[ 78%] Building CXX object src/CMakeFiles/sniffles.dir/print/NGMPrinter.cpp.o -cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/print/NGMPrinter.cpp.o -c /build/sniffles-1.0.12b+ds/src/print/NGMPrinter.cpp -/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function 'void Genotyper::update_svs_output(std::map, std::vector >)': -/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:343:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 343 | system(move.c_str()); - | ~~~~~~^~~~~~~~~~~~~~ -/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function 'void Genotyper::update_SVs2()': -/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:382:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 382 | system(del.c_str()); - | ~~~~~~^~~~~~~~~~~~~ -/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function 'void Genotyper::update_file(Breakpoint_Tree&, breakpoint_node*&)': -/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:719:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 719 | system(move.c_str()); - | ~~~~~~^~~~~~~~~~~~~~ -/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function 'void Genotyper::update_SVs()': -/build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:858:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 858 | system(del.c_str()); - | ~~~~~~^~~~~~~~~~~~~ -[ 82%] Building CXX object src/CMakeFiles/sniffles.dir/plane-sweep/PlaneSweep_slim.cpp.o -cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/plane-sweep/PlaneSweep_slim.cpp.o -c /build/sniffles-1.0.12b+ds/src/plane-sweep/PlaneSweep_slim.cpp [ 86%] Building CXX object src/CMakeFiles/sniffles.dir/cluster/Cluster_SVs.cpp.o cd /build/sniffles-1.0.12b+ds/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/cluster/Cluster_SVs.cpp.o -c /build/sniffles-1.0.12b+ds/src/cluster/Cluster_SVs.cpp [ 91%] Building CXX object src/CMakeFiles/sniffles.dir/force_calling/Force_calling.cpp.o @@ -809,8 +844,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'sniffles-dbgsym' in '../sniffles-dbgsym_1.0.12b+ds-1_amd64.deb'. dpkg-deb: building package 'sniffles' in '../sniffles_1.0.12b+ds-1_amd64.deb'. +dpkg-deb: building package 'sniffles-dbgsym' in '../sniffles-dbgsym_1.0.12b+ds-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../sniffles_1.0.12b+ds-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -818,12 +853,14 @@ 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/2062006/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2062006/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/1777030 and its subdirectories -I: Current time: Sat Feb 11 19:37:47 -12 2023 -I: pbuilder-time-stamp: 1676187467 +I: removing directory /srv/workspace/pbuilder/2062006 and its subdirectories +I: Current time: Mon Jan 10 15:17:40 +14 2022 +I: pbuilder-time-stamp: 1641777460