Diff of the two buildlogs: -- --- b1/build.log 2024-07-16 20:12:10.459813292 +0000 +++ b2/build.log 2024-07-16 20:14:50.892985784 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Aug 18 14:33:53 -12 2025 -I: pbuilder-time-stamp: 1755570833 +I: Current time: Wed Jul 17 10:12:13 +14 2024 +I: pbuilder-time-stamp: 1721160733 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./survivor_1.0.7-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.VgSTrs45/trustedkeys.kbx': General error -gpgv: Signature made Sat Nov 28 01:20:07 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.mxUxeHG9/trustedkeys.kbx': General error +gpgv: Signature made Sun Nov 29 03:20:07 2020 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key @@ -30,135 +30,166 @@ dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2405720/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3167748/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 17 10:12 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3167748/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3167748/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=42 ' - DISTRIBUTION='bullseye' - 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/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=20 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='0284eb5d904f457aaebc57cf296c842f' - 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='2405720' - PS1='# ' - PS2='> ' + INVOCATION_ID=1cee0174aa0f43b489aea1c76198ff4d + 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=3167748 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.mDA5Iywc/pbuilderrc_qq2r --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mDA5Iywc/b1 --logfile b1/build.log survivor_1.0.7-2.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://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.mDA5Iywc/pbuilderrc_5La3 --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mDA5Iywc/b2 --logfile b2/build.log survivor_1.0.7-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-22-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.94-1 (2024-06-21) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 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 Mar 27 2024 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 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Mar 27 2024 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 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 Mar 27 2024 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 Mar 27 2024 more - -rwsr-xr-x 1 root root 55528 Mar 27 2024 mount - -rwxr-xr-x 1 root root 18664 Mar 27 2024 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 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 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 Aug 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 Mar 27 2024 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Jan 19 2024 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 Mar 27 2024 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Mar 27 2024 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/2405720/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 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 Mar 29 00:09 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 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 69032 Mar 29 00:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 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 Mar 29 00:09 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 Mar 29 00:09 more + -rwsr-xr-x 1 root root 55528 Mar 29 00:09 mount + -rwxr-xr-x 1 root root 18664 Mar 29 00:09 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 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 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 9 Jul 17 10:12 sh -> /bin/bash + -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 Mar 29 00:09 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Jan 20 23:59 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 Mar 29 00:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Mar 29 00:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/3167748/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -228,7 +259,7 @@ Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] -Fetched 18.5 MB in 0s (49.8 MB/s) +Fetched 18.5 MB in 5s (3822 kB/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 ... 19711 files and directories currently installed.) @@ -372,7 +403,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/survivor-1.0.7/ && 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 > ../survivor_1.0.7-2_source.changes +I: user script /srv/workspace/pbuilder/3167748/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/3167748/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/survivor-1.0.7/ && 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 > ../survivor_1.0.7-2_source.changes dpkg-buildpackage: info: source package survivor dpkg-buildpackage: info: source version 1.0.7-2 dpkg-buildpackage: info: source distribution unstable @@ -382,7 +417,7 @@ debian/rules clean dh clean --sourcedirectory=Debug dh_auto_clean -O--sourcedirectory=Debug - cd Debug && make -j42 clean + cd Debug && make -j20 clean make[1]: Entering directory '/build/reproducible-path/survivor-1.0.7/Debug' rm -rf ./src/vcfs/Annotate_vcf.o ./src/vcfs/Combine_3_VCF.o ./src/vcfs/Compoverlap_VCF.o ./src/vcfs/Detect_nested.o ./src/vcfs/Filter_vcf.o ./src/vcfs/Generate_distMat.o ./src/vcfs/Merge_VCF.o ./src/snp_overlap/Overlap_snps.o ./src/simulator/Error_scanner.o ./src/simulator/Eval_vcf.o ./src/simulator/Pac_Simulator.o ./src/simulator/SV_Simulator.o ./src/simulator/Sim_reads.o ./src/simulator/test_cov.o ./src/scrup_vcf/scrup_svs.o ./src/phasing/Phasing_vcf.o ./src/merge_vcf/IntervallTree.o ./src/merge_vcf/combine_svs.o ./src/convert/ConvertMQ0Bed.o ./src/convert/Convert_Assemblytics.o ./src/convert/Convert_Bionano.o ./src/convert/Convert_Honey_tails.o ./src/convert/Convert_MUMmer.o ./src/convert/Convert_Pindel.o ./src/convert/Convert_VCF_to_BED.o ./src/convert/Convert_hapcut2.o ./src/convert/Process_Coverage.o ./src/convert/Process_Lumpy.o ./src/convert/Update_bam_pacbio.o ./src/analysis_sv/GIAB_summary.o ./src/analysis_sv/MT_identifier.o ./src/analysis_sv/MUMmer_overlap.o ./src/analysis_sv/Select_samples.o ./src/analysis_sv/Simplify_SVs.o ./src/analysis_sv/Summ_mat.o ./src/CorrectAllele.o ./src/DetectDif.o ./src/Extract_Seq.o ./src/SURVIVOR.o ./src/Summarize_SV.o ./src/vcfs/Annotate_vcf.d ./src/vcfs/Combine_3_VCF.d ./src/vcfs/Compoverlap_VCF.d ./src/vcfs/Detect_nested.d ./src/vcfs/Filter_vcf.d ./src/vcfs/Generate_distMat.d ./src/vcfs/Merge_VCF.d ./src/snp_overlap/Overlap_snps.d ./src/simulator/Error_scanner.d ./src/simulator/Eval_vcf.d ./src/simulator/Pac_Simulator.d ./src/simulator/SV_Simulator.d ./src/simulator/Sim_reads.d ./src/simulator/test_cov.d ./src/scrup_vcf/scrup_svs.d ./src/phasing/Phasing_vcf.d ./src/merge_vcf/IntervallTree.d ./src/merge_vcf/combine_svs.d ./src/convert/ConvertMQ0Bed.d ./src/convert/Convert_Assemblytics.d ./src/convert/Convert_Bionano.d ./src/convert/Convert_Honey_tails.d ./src/convert/Convert_MUMmer.d ./src/convert/Convert_Pindel.d ./src/convert/Convert_VCF_to_BED.d ./src/convert/Convert_hapcut2.d ./src/convert/Process_Coverage.d ./src/convert/Process_Lumpy.d ./src/convert/Update_bam_pacbio.d ./src/analysis_sv/GIAB_summary.d ./src/analysis_sv/MT_identifier.d ./src/analysis_sv/MUMmer_overlap.d ./src/analysis_sv/Select_samples.d ./src/analysis_sv/Simplify_SVs.d ./src/analysis_sv/Summ_mat.d ./src/CorrectAllele.d ./src/DetectDif.d ./src/Extract_Seq.d ./src/SURVIVOR.d ./src/Summarize_SV.d SURVIVOR @@ -395,213 +430,249 @@ dh_autoreconf -O--sourcedirectory=Debug dh_auto_configure -O--sourcedirectory=Debug dh_auto_build -O--sourcedirectory=Debug - cd Debug && make -j42 "INSTALL=install --strip-program=true" + cd Debug && make -j20 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/survivor-1.0.7/Debug' Building file: ../src/vcfs/Annotate_vcf.cpp Building file: ../src/vcfs/Combine_3_VCF.cpp Building file: ../src/vcfs/Compoverlap_VCF.cpp Building file: ../src/vcfs/Detect_nested.cpp Invoking: Cross G++ Compiler +Invoking: Cross G++ Compiler +Building file: ../src/vcfs/Filter_vcf.cpp g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Annotate_vcf.d" -MT"src/vcfs/Annotate_vcf.o" -o "src/vcfs/Annotate_vcf.o" "../src/vcfs/Annotate_vcf.cpp" Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Combine_3_VCF.d" -MT"src/vcfs/Combine_3_VCF.o" -o "src/vcfs/Combine_3_VCF.o" "../src/vcfs/Combine_3_VCF.cpp" +Building file: ../src/vcfs/Generate_distMat.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Compoverlap_VCF.d" -MT"src/vcfs/Compoverlap_VCF.o" -o "src/vcfs/Compoverlap_VCF.o" "../src/vcfs/Compoverlap_VCF.cpp" -Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Detect_nested.d" -MT"src/vcfs/Detect_nested.o" -o "src/vcfs/Detect_nested.o" "../src/vcfs/Detect_nested.cpp" -Building file: ../src/vcfs/Filter_vcf.cpp -Building file: ../src/vcfs/Generate_distMat.cpp -Building file: ../src/vcfs/Merge_VCF.cpp -Building file: ../src/snp_overlap/Overlap_snps.cpp -Invoking: Cross G++ Compiler Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Filter_vcf.d" -MT"src/vcfs/Filter_vcf.o" -o "src/vcfs/Filter_vcf.o" "../src/vcfs/Filter_vcf.cpp" Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Generate_distMat.d" -MT"src/vcfs/Generate_distMat.o" -o "src/vcfs/Generate_distMat.o" "../src/vcfs/Generate_distMat.cpp" -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Merge_VCF.d" -MT"src/vcfs/Merge_VCF.o" -o "src/vcfs/Merge_VCF.o" "../src/vcfs/Merge_VCF.cpp" -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/snp_overlap/Overlap_snps.d" -MT"src/snp_overlap/Overlap_snps.o" -o "src/snp_overlap/Overlap_snps.o" "../src/snp_overlap/Overlap_snps.cpp" +Building file: ../src/vcfs/Merge_VCF.cpp +Building file: ../src/snp_overlap/Overlap_snps.cpp Building file: ../src/simulator/Error_scanner.cpp +Invoking: Cross G++ Compiler Building file: ../src/simulator/Eval_vcf.cpp -Building file: ../src/simulator/Pac_Simulator.cpp +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/vcfs/Merge_VCF.d" -MT"src/vcfs/Merge_VCF.o" -o "src/vcfs/Merge_VCF.o" "../src/vcfs/Merge_VCF.cpp" Invoking: Cross G++ Compiler Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/snp_overlap/Overlap_snps.d" -MT"src/snp_overlap/Overlap_snps.o" -o "src/snp_overlap/Overlap_snps.o" "../src/snp_overlap/Overlap_snps.cpp" +Building file: ../src/simulator/Pac_Simulator.cpp g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Error_scanner.d" -MT"src/simulator/Error_scanner.o" -o "src/simulator/Error_scanner.o" "../src/simulator/Error_scanner.cpp" -Building file: ../src/simulator/SV_Simulator.cpp +Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Eval_vcf.d" -MT"src/simulator/Eval_vcf.o" -o "src/simulator/Eval_vcf.o" "../src/simulator/Eval_vcf.cpp" Invoking: Cross G++ Compiler +Building file: ../src/simulator/SV_Simulator.cpp g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Pac_Simulator.d" -MT"src/simulator/Pac_Simulator.o" -o "src/simulator/Pac_Simulator.o" "../src/simulator/Pac_Simulator.cpp" -Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/SV_Simulator.d" -MT"src/simulator/SV_Simulator.o" -o "src/simulator/SV_Simulator.o" "../src/simulator/SV_Simulator.cpp" Building file: ../src/simulator/Sim_reads.cpp +Invoking: Cross G++ Compiler Building file: ../src/simulator/test_cov.cpp +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/SV_Simulator.d" -MT"src/simulator/SV_Simulator.o" -o "src/simulator/SV_Simulator.o" "../src/simulator/SV_Simulator.cpp" Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/Sim_reads.d" -MT"src/simulator/Sim_reads.o" -o "src/simulator/Sim_reads.o" "../src/simulator/Sim_reads.cpp" +Building file: ../src/scrup_vcf/scrup_svs.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/simulator/test_cov.d" -MT"src/simulator/test_cov.o" -o "src/simulator/test_cov.o" "../src/simulator/test_cov.cpp" -Building file: ../src/scrup_vcf/scrup_svs.cpp Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/scrup_vcf/scrup_svs.d" -MT"src/scrup_vcf/scrup_svs.o" -o "src/scrup_vcf/scrup_svs.o" "../src/scrup_vcf/scrup_svs.cpp" Building file: ../src/phasing/Phasing_vcf.cpp +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/scrup_vcf/scrup_svs.d" -MT"src/scrup_vcf/scrup_svs.o" -o "src/scrup_vcf/scrup_svs.o" "../src/scrup_vcf/scrup_svs.cpp" Building file: ../src/merge_vcf/IntervallTree.cpp +Building file: ../src/merge_vcf/combine_svs.cpp Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/phasing/Phasing_vcf.d" -MT"src/phasing/Phasing_vcf.o" -o "src/phasing/Phasing_vcf.o" "../src/phasing/Phasing_vcf.cpp" Invoking: Cross G++ Compiler -g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/merge_vcf/IntervallTree.d" -MT"src/merge_vcf/IntervallTree.o" -o "src/merge_vcf/IntervallTree.o" "../src/merge_vcf/IntervallTree.cpp" -Building file: ../src/merge_vcf/combine_svs.cpp +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/phasing/Phasing_vcf.d" -MT"src/phasing/Phasing_vcf.o" -o "src/phasing/Phasing_vcf.o" "../src/phasing/Phasing_vcf.cpp" Building file: ../src/convert/ConvertMQ0Bed.cpp Invoking: Cross G++ Compiler +g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/merge_vcf/IntervallTree.d" -MT"src/merge_vcf/IntervallTree.o" -o "src/merge_vcf/IntervallTree.o" "../src/merge_vcf/IntervallTree.cpp" +Building file: ../src/convert/Convert_Assemblytics.cpp g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/merge_vcf/combine_svs.d" -MT"src/merge_vcf/combine_svs.o" -o "src/merge_vcf/combine_svs.o" "../src/merge_vcf/combine_svs.cpp" Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/ConvertMQ0Bed.d" -MT"src/convert/ConvertMQ0Bed.o" -o "src/convert/ConvertMQ0Bed.o" "../src/convert/ConvertMQ0Bed.cpp" -Building file: ../src/convert/Convert_Assemblytics.cpp -Building file: ../src/convert/Convert_Bionano.cpp Invoking: Cross G++ Compiler -Building file: ../src/convert/Convert_Honey_tails.cpp g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Assemblytics.d" -MT"src/convert/Convert_Assemblytics.o" -o "src/convert/Convert_Assemblytics.o" "../src/convert/Convert_Assemblytics.cpp" +../src/vcfs/Filter_vcf.cpp: In function ‘void translate(const char*, int, float, int, strentry&)’: +../src/vcfs/Filter_vcf.cpp:18:6: warning: variable ‘lumpy’ set but not used [-Wunused-but-set-variable] + 18 | int lumpy = 0; + | ^~~~~ +../src/simulator/Eval_vcf.cpp: In function ‘void reprotvals(const char*)’: +../src/simulator/Eval_vcf.cpp:102:8: warning: variable ‘dv’ set but not used [-Wunused-but-set-variable] + 102 | float dv = 0; //"# high-quality variant pairs" + | ^~ +../src/simulator/Eval_vcf.cpp:103:8: warning: variable ‘dr’ set but not used [-Wunused-but-set-variable] + 103 | float dr = 0; //"# high-quality reference pairs" + | ^~ +../src/simulator/Eval_vcf.cpp:104:6: warning: variable ‘gq’ set but not used [-Wunused-but-set-variable] + 104 | int gq = 0; //"Genotype Quality" + | ^~ +../src/simulator/Eval_vcf.cpp:105:6: warning: variable ‘rr’ set but not used [-Wunused-but-set-variable] + 105 | int rr = 0; + | ^~ +../src/simulator/Eval_vcf.cpp:106:6: warning: variable ‘rv’ set but not used [-Wunused-but-set-variable] + 106 | int rv = 0; + | ^~ +../src/snp_overlap/Overlap_snps.cpp: In function ‘void overlap_snps(std::string, std::string, int, int, int, std::string)’: +../src/snp_overlap/Overlap_snps.cpp:192:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 192 | for (size_t i = start; i <= stop; i++) { + | ~~^~~~~~~ +../src/snp_overlap/Overlap_snps.cpp: In function ‘void overlap_snps_gwas(std::string, std::string, int, int, std::string)’: +../src/snp_overlap/Overlap_snps.cpp:447:64: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 447 | if (genome.find(chr) != genome.end() && genome[chr].size() > pos) { + | ~~~~~~~~~~~~~~~~~~~^~~~~ +../src/snp_overlap/Overlap_snps.cpp: In function ‘void overlap_snpsGWASDB(std::string, std::string, int, int, int, std::string)’: +../src/snp_overlap/Overlap_snps.cpp:663:80: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 663 | if (genome.find(snps[i].chr) != genome.end() && genome[snps[i].chr].size() > snps[i].position) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +../src/snp_overlap/Overlap_snps.cpp: In function ‘void generate_random_regions(std::string, std::string, int, std::string)’: +../src/snp_overlap/Overlap_snps.cpp:767:50: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 767 | for (size_t pos = entries[i].start.pos; pos < entries[i].stop.pos; pos++) { + | ~~~~^~~~~~~~~~~~~~~~~~~~~ +../src/snp_overlap/Overlap_snps.cpp:781:47: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 781 | for (size_t pos = entries[i].start.pos; pos < entries[i].stop.pos; pos++) { + | ~~~~^~~~~~~~~~~~~~~~~~~~~ +../src/simulator/Error_scanner.cpp: In function ‘void computeAlignment(std::vector, char*, std::string, std::vector > >&, std::string)’: +../src/simulator/Error_scanner.cpp:173:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 173 | while (pos + 1 > error_mat.size()) { + | ~~~~~~~~^~~~~~~~~~~~~~~~~~ +../src/merge_vcf/combine_svs.cpp: In function ‘void print_GTs(std::ostringstream&, SVS_Node*)’: +../src/merge_vcf/combine_svs.cpp:213:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 213 | for (size_t i = 0; i < Parameter::Instance()->max_caller; i++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../src/merge_vcf/combine_svs.cpp:215:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] + 215 | if (pos < entry->caller_info.size() && i == entry->caller_info[pos]->id) { + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +../src/merge_vcf/combine_svs.cpp:215:44: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] + 215 | if (pos < entry->caller_info.size() && i == entry->caller_info[pos]->id) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Finished building: ../src/scrup_vcf/scrup_svs.cpp +../src/merge_vcf/combine_svs.cpp: In function ‘void combine_calls_svs(std::string, double, int, int, int, int, int, std::string)’: +../src/merge_vcf/combine_svs.cpp:688:10: warning: variable ‘type’ set but not used [-Wunused-but-set-variable] + 688 | short type = (*i)->type; + | ^~~~ +Finished building: ../src/convert/ConvertMQ0Bed.cpp + + +Building file: ../src/convert/Convert_Bionano.cpp Invoking: Cross G++ Compiler -Building file: ../src/convert/Convert_MUMmer.cpp g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Bionano.d" -MT"src/convert/Convert_Bionano.o" -o "src/convert/Convert_Bionano.o" "../src/convert/Convert_Bionano.cpp" +Building file: ../src/convert/Convert_Honey_tails.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Honey_tails.d" -MT"src/convert/Convert_Honey_tails.o" -o "src/convert/Convert_Honey_tails.o" "../src/convert/Convert_Honey_tails.cpp" +Finished building: ../src/simulator/test_cov.cpp + +Building file: ../src/convert/Convert_MUMmer.cpp Invoking: Cross G++ Compiler -Building file: ../src/convert/Convert_Pindel.cpp g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_MUMmer.d" -MT"src/convert/Convert_MUMmer.o" -o "src/convert/Convert_MUMmer.o" "../src/convert/Convert_MUMmer.cpp" -Building file: ../src/convert/Convert_VCF_to_BED.cpp +Finished building: ../src/simulator/Pac_Simulator.cpp + +Building file: ../src/convert/Convert_Pindel.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_Pindel.d" -MT"src/convert/Convert_Pindel.o" -o "src/convert/Convert_Pindel.o" "../src/convert/Convert_Pindel.cpp" -Building file: ../src/convert/Convert_hapcut2.cpp +Finished building: ../src/vcfs/Detect_nested.cpp + +Building file: ../src/convert/Convert_VCF_to_BED.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_VCF_to_BED.d" -MT"src/convert/Convert_VCF_to_BED.o" -o "src/convert/Convert_VCF_to_BED.o" "../src/convert/Convert_VCF_to_BED.cpp" +../src/convert/Convert_Honey_tails.cpp: In function ‘void parse_honey_tails(std::string, int, std::vector&)’: +../src/convert/Convert_Honey_tails.cpp:45:7: warning: variable ‘dist’ set but not used [-Wunused-but-set-variable] + 45 | int dist=0; + | ^~~~ +../src/convert/Convert_VCF_to_BED.cpp: In function ‘std::string print_entry_bed(strvcfentry&)’: +../src/convert/Convert_VCF_to_BED.cpp:348:13: warning: unknown escape sequence: '\/' + 348 | convert << "\tGT\t.\/."; + | ^~~~~~~~~~~~ +Finished building: ../src/convert/Convert_MUMmer.cpp + +Building file: ../src/convert/Convert_hapcut2.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Convert_hapcut2.d" -MT"src/convert/Convert_hapcut2.o" -o "src/convert/Convert_hapcut2.o" "../src/convert/Convert_hapcut2.cpp" +Finished building: ../src/phasing/Phasing_vcf.cpp + Building file: ../src/convert/Process_Coverage.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Process_Coverage.d" -MT"src/convert/Process_Coverage.o" -o "src/convert/Process_Coverage.o" "../src/convert/Process_Coverage.cpp" +Finished building: ../src/vcfs/Generate_distMat.cpp + Building file: ../src/convert/Process_Lumpy.cpp -Building file: ../src/convert/Update_bam_pacbio.cpp -Building file: ../src/analysis_sv/GIAB_summary.cpp -Invoking: Cross G++ Compiler Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Process_Lumpy.d" -MT"src/convert/Process_Lumpy.o" -o "src/convert/Process_Lumpy.o" "../src/convert/Process_Lumpy.cpp" -Building file: ../src/analysis_sv/MT_identifier.cpp +Finished building: ../src/vcfs/Compoverlap_VCF.cpp + +Building file: ../src/convert/Update_bam_pacbio.cpp +Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/convert/Update_bam_pacbio.d" -MT"src/convert/Update_bam_pacbio.o" -o "src/convert/Update_bam_pacbio.o" "../src/convert/Update_bam_pacbio.cpp" +Finished building: ../src/simulator/Sim_reads.cpp + +Building file: ../src/analysis_sv/GIAB_summary.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/GIAB_summary.d" -MT"src/analysis_sv/GIAB_summary.o" -o "src/analysis_sv/GIAB_summary.o" "../src/analysis_sv/GIAB_summary.cpp" +Finished building: ../src/simulator/Error_scanner.cpp + +Building file: ../src/analysis_sv/MT_identifier.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/MT_identifier.d" -MT"src/analysis_sv/MT_identifier.o" -o "src/analysis_sv/MT_identifier.o" "../src/analysis_sv/MT_identifier.cpp" +Finished building: ../src/convert/Process_Coverage.cpp + Building file: ../src/analysis_sv/MUMmer_overlap.cpp -Building file: ../src/analysis_sv/Select_samples.cpp Invoking: Cross G++ Compiler -Building file: ../src/analysis_sv/Simplify_SVs.cpp g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/MUMmer_overlap.d" -MT"src/analysis_sv/MUMmer_overlap.o" -o "src/analysis_sv/MUMmer_overlap.o" "../src/analysis_sv/MUMmer_overlap.cpp" -Building file: ../src/analysis_sv/Summ_mat.cpp +Finished building: ../src/convert/Convert_Assemblytics.cpp + +Building file: ../src/analysis_sv/Select_samples.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/Select_samples.d" -MT"src/analysis_sv/Select_samples.o" -o "src/analysis_sv/Select_samples.o" "../src/analysis_sv/Select_samples.cpp" -Invoking: Cross G++ Compiler +Finished building: ../src/convert/Update_bam_pacbio.cpp +Finished building: ../src/convert/Convert_Bionano.cpp + + +Building file: ../src/analysis_sv/Simplify_SVs.cpp +Building file: ../src/analysis_sv/Summ_mat.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/Simplify_SVs.d" -MT"src/analysis_sv/Simplify_SVs.o" -o "src/analysis_sv/Simplify_SVs.o" "../src/analysis_sv/Simplify_SVs.cpp" +Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/analysis_sv/Summ_mat.d" -MT"src/analysis_sv/Summ_mat.o" -o "src/analysis_sv/Summ_mat.o" "../src/analysis_sv/Summ_mat.cpp" +Finished building: ../src/convert/Convert_Pindel.cpp + +Finished building: ../src/convert/Convert_Honey_tails.cpp Building file: ../src/CorrectAllele.cpp -Building file: ../src/DetectDif.cpp -Building file: ../src/Extract_Seq.cpp + Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/CorrectAllele.d" -MT"src/CorrectAllele.o" -o "src/CorrectAllele.o" "../src/CorrectAllele.cpp" -Invoking: Cross G++ Compiler +Building file: ../src/DetectDif.cpp Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/DetectDif.d" -MT"src/DetectDif.o" -o "src/DetectDif.o" "../src/DetectDif.cpp" +../src/analysis_sv/MUMmer_overlap.cpp: In function ‘void comp_entries_mummer(std::vector&, std::string, int)’: +../src/analysis_sv/MUMmer_overlap.cpp:60:7: warning: variable ‘stop’ set but not used [-Wunused-but-set-variable] + 60 | int stop = 0; + | ^~~~ +../src/analysis_sv/MUMmer_overlap.cpp:61:7: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] + 61 | int len = 0; + | ^~~ +Finished building: ../src/merge_vcf/IntervallTree.cpp +Finished building: ../src/convert/Convert_hapcut2.cpp + + +Building file: ../src/Extract_Seq.cpp +Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Extract_Seq.d" -MT"src/Extract_Seq.o" -o "src/Extract_Seq.o" "../src/Extract_Seq.cpp" Building file: ../src/SURVIVOR.cpp -Building file: ../src/Summarize_SV.cpp -Invoking: Cross G++ Compiler Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/SURVIVOR.d" -MT"src/SURVIVOR.o" -o "src/SURVIVOR.o" "../src/SURVIVOR.cpp" +Finished building: ../src/analysis_sv/MT_identifier.cpp + +Building file: ../src/Summarize_SV.cpp +Invoking: Cross G++ Compiler g++ -O3 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Summarize_SV.d" -MT"src/Summarize_SV.o" -o "src/Summarize_SV.o" "../src/Summarize_SV.cpp" -../src/simulator/Error_scanner.cpp: In function ‘void computeAlignment(std::vector, char*, std::string, std::vector > >&, std::string)’: -../src/simulator/Error_scanner.cpp:173:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 173 | while (pos + 1 > error_mat.size()) { - | ~~~~~~~~^~~~~~~~~~~~~~~~~~ -../src/vcfs/Filter_vcf.cpp: In function ‘void translate(const char*, int, float, int, strentry&)’: -../src/vcfs/Filter_vcf.cpp:18:6: warning: variable ‘lumpy’ set but not used [-Wunused-but-set-variable] - 18 | int lumpy = 0; - | ^~~~~ -../src/convert/Convert_Honey_tails.cpp: In function ‘void parse_honey_tails(std::string, int, std::vector&)’: -../src/convert/Convert_Honey_tails.cpp:45:7: warning: variable ‘dist’ set but not used [-Wunused-but-set-variable] - 45 | int dist=0; - | ^~~~ ../src/analysis_sv/Simplify_SVs.cpp: In function ‘sv_simple_str parse_line_sv(char*, int, std::vector >, std::string&)’: ../src/analysis_sv/Simplify_SVs.cpp:54:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 54 | for (size_t i = 0; i < buffer_size && buffer[i] != '\0' && buffer[i] != '\n'; i++) { | ~~^~~~~~~~~~~~~ -Finished building: ../src/convert/ConvertMQ0Bed.cpp - ../src/analysis_sv/Simplify_SVs.cpp: In function ‘void print_gene_sv(std::string, sv_simple_str, FILE*&, int, std::map, std::vector > >)’: ../src/analysis_sv/Simplify_SVs.cpp:118:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map, bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 118 | if (count + 1 < entry.accessions.size()) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -../src/merge_vcf/combine_svs.cpp: In function ‘void print_GTs(std::ostringstream&, SVS_Node*)’: -../src/merge_vcf/combine_svs.cpp:213:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 213 | for (size_t i = 0; i < Parameter::Instance()->max_caller; i++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../src/merge_vcf/combine_svs.cpp:215:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] - 215 | if (pos < entry->caller_info.size() && i == entry->caller_info[pos]->id) { - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -../src/merge_vcf/combine_svs.cpp:215:44: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 215 | if (pos < entry->caller_info.size() && i == entry->caller_info[pos]->id) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../src/convert/Convert_VCF_to_BED.cpp: In function ‘std::string print_entry_bed(strvcfentry&)’: -../src/convert/Convert_VCF_to_BED.cpp:348:13: warning: unknown escape sequence: '\/' - 348 | convert << "\tGT\t.\/."; - | ^~~~~~~~~~~~ -../src/merge_vcf/combine_svs.cpp: In function ‘void combine_calls_svs(std::string, double, int, int, int, int, int, std::string)’: -../src/merge_vcf/combine_svs.cpp:688:10: warning: variable ‘type’ set but not used [-Wunused-but-set-variable] - 688 | short type = (*i)->type; - | ^~~~ -../src/simulator/Eval_vcf.cpp: In function ‘void reprotvals(const char*)’: -../src/simulator/Eval_vcf.cpp:102:8: warning: variable ‘dv’ set but not used [-Wunused-but-set-variable] - 102 | float dv = 0; //"# high-quality variant pairs" - | ^~ -../src/simulator/Eval_vcf.cpp:103:8: warning: variable ‘dr’ set but not used [-Wunused-but-set-variable] - 103 | float dr = 0; //"# high-quality reference pairs" - | ^~ -../src/simulator/Eval_vcf.cpp:104:6: warning: variable ‘gq’ set but not used [-Wunused-but-set-variable] - 104 | int gq = 0; //"Genotype Quality" - | ^~ -../src/simulator/Eval_vcf.cpp:105:6: warning: variable ‘rr’ set but not used [-Wunused-but-set-variable] - 105 | int rr = 0; - | ^~ -../src/simulator/Eval_vcf.cpp:106:6: warning: variable ‘rv’ set but not used [-Wunused-but-set-variable] - 106 | int rv = 0; - | ^~ -../src/analysis_sv/MUMmer_overlap.cpp: In function ‘void comp_entries_mummer(std::vector&, std::string, int)’: -../src/analysis_sv/MUMmer_overlap.cpp:60:7: warning: variable ‘stop’ set but not used [-Wunused-but-set-variable] - 60 | int stop = 0; - | ^~~~ -../src/analysis_sv/MUMmer_overlap.cpp:61:7: warning: variable ‘len’ set but not used [-Wunused-but-set-variable] - 61 | int len = 0; - | ^~~ -../src/snp_overlap/Overlap_snps.cpp: In function ‘void overlap_snps(std::string, std::string, int, int, int, std::string)’: -../src/snp_overlap/Overlap_snps.cpp:192:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 192 | for (size_t i = start; i <= stop; i++) { - | ~~^~~~~~~ -../src/snp_overlap/Overlap_snps.cpp: In function ‘void overlap_snps_gwas(std::string, std::string, int, int, std::string)’: -../src/snp_overlap/Overlap_snps.cpp:447:64: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 447 | if (genome.find(chr) != genome.end() && genome[chr].size() > pos) { - | ~~~~~~~~~~~~~~~~~~~^~~~~ -../src/snp_overlap/Overlap_snps.cpp: In function ‘void overlap_snpsGWASDB(std::string, std::string, int, int, int, std::string)’: -../src/snp_overlap/Overlap_snps.cpp:663:80: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 663 | if (genome.find(snps[i].chr) != genome.end() && genome[snps[i].chr].size() > snps[i].position) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -../src/snp_overlap/Overlap_snps.cpp: In function ‘void generate_random_regions(std::string, std::string, int, std::string)’: -../src/snp_overlap/Overlap_snps.cpp:767:50: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 767 | for (size_t pos = entries[i].start.pos; pos < entries[i].stop.pos; pos++) { - | ~~~~^~~~~~~~~~~~~~~~~~~~~ -../src/snp_overlap/Overlap_snps.cpp:781:47: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] - 781 | for (size_t pos = entries[i].start.pos; pos < entries[i].stop.pos; pos++) { - | ~~~~^~~~~~~~~~~~~~~~~~~~~ -Finished building: ../src/simulator/test_cov.cpp - -Finished building: ../src/scrup_vcf/scrup_svs.cpp +Finished building: ../src/analysis_sv/MUMmer_overlap.cpp ../src/Summarize_SV.cpp: In function ‘void summary_venn(std::string, bool, std::string)’: ../src/Summarize_SV.cpp:608:23: warning: format ‘%e’ expects argument of type ‘double’, but argument 3 has type ‘int’ [-Wformat=] @@ -611,84 +682,48 @@ | | int | double | %d -Finished building: ../src/convert/Process_Coverage.cpp - -Finished building: ../src/convert/Convert_MUMmer.cpp +Finished building: ../src/vcfs/Merge_VCF.cpp -Finished building: ../src/simulator/Pac_Simulator.cpp +Finished building: ../src/convert/Convert_VCF_to_BED.cpp -Finished building: ../src/vcfs/Detect_nested.cpp +Finished building: ../src/simulator/Eval_vcf.cpp Finished building: ../src/DetectDif.cpp -Finished building: ../src/analysis_sv/MT_identifier.cpp - -Finished building: ../src/SURVIVOR.cpp - -Finished building: ../src/convert/Update_bam_pacbio.cpp - -Finished building: ../src/analysis_sv/Select_samples.cpp - -Finished building: ../src/phasing/Phasing_vcf.cpp - -Finished building: ../src/vcfs/Generate_distMat.cpp - -Finished building: ../src/analysis_sv/MUMmer_overlap.cpp - -Finished building: ../src/analysis_sv/Summ_mat.cpp -Finished building: ../src/simulator/Error_scanner.cpp +Finished building: ../src/vcfs/Filter_vcf.cpp +Finished building: ../src/snp_overlap/Overlap_snps.cpp +Finished building: ../src/SURVIVOR.cpp Finished building: ../src/CorrectAllele.cpp -Finished building: ../src/convert/Convert_hapcut2.cpp - -Finished building: ../src/convert/Convert_Honey_tails.cpp -Finished building: ../src/simulator/Sim_reads.cpp - -Finished building: ../src/convert/Convert_Assemblytics.cpp - -Finished building: ../src/convert/Convert_Pindel.cpp +Finished building: ../src/analysis_sv/Select_samples.cpp -Finished building: ../src/vcfs/Compoverlap_VCF.cpp +Finished building: ../src/convert/Process_Lumpy.cpp ../src/Summarize_SV.cpp: In function ‘void summary_SV_stream(int, int, std::string)’: ../src/Summarize_SV.cpp:302:42: warning: ‘type’ may be used uninitialized in this function [-Wmaybe-uninitialized] 302 | if (max_size < 0 || (leng < max_size || type == 3)) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -Finished building: ../src/analysis_sv/Simplify_SVs.cpp -Finished building: ../src/convert/Convert_Bionano.cpp -Finished building: ../src/convert/Process_Lumpy.cpp - +Finished building: ../src/analysis_sv/Summ_mat.cpp +Finished building: ../src/vcfs/Combine_3_VCF.cpp +Finished building: ../src/simulator/SV_Simulator.cpp -Finished building: ../src/merge_vcf/IntervallTree.cpp -Finished building: ../src/convert/Convert_VCF_to_BED.cpp +Finished building: ../src/merge_vcf/combine_svs.cpp -Finished building: ../src/vcfs/Merge_VCF.cpp +Finished building: ../src/analysis_sv/Simplify_SVs.cpp -Finished building: ../src/Extract_Seq.cpp Finished building: ../src/analysis_sv/GIAB_summary.cpp +Finished building: ../src/vcfs/Annotate_vcf.cpp -Finished building: ../src/simulator/Eval_vcf.cpp - -Finished building: ../src/vcfs/Filter_vcf.cpp +Finished building: ../src/Extract_Seq.cpp Finished building: ../src/Summarize_SV.cpp -Finished building: ../src/snp_overlap/Overlap_snps.cpp - -Finished building: ../src/vcfs/Combine_3_VCF.cpp - -Finished building: ../src/merge_vcf/combine_svs.cpp - -Finished building: ../src/simulator/SV_Simulator.cpp - -Finished building: ../src/vcfs/Annotate_vcf.cpp - Building target: SURVIVOR Invoking: Cross G++ Linker g++ -o SURVIVOR ./src/vcfs/Annotate_vcf.o ./src/vcfs/Combine_3_VCF.o ./src/vcfs/Compoverlap_VCF.o ./src/vcfs/Detect_nested.o ./src/vcfs/Filter_vcf.o ./src/vcfs/Generate_distMat.o ./src/vcfs/Merge_VCF.o ./src/snp_overlap/Overlap_snps.o ./src/simulator/Error_scanner.o ./src/simulator/Eval_vcf.o ./src/simulator/Pac_Simulator.o ./src/simulator/SV_Simulator.o ./src/simulator/Sim_reads.o ./src/simulator/test_cov.o ./src/scrup_vcf/scrup_svs.o ./src/phasing/Phasing_vcf.o ./src/merge_vcf/IntervallTree.o ./src/merge_vcf/combine_svs.o ./src/convert/ConvertMQ0Bed.o ./src/convert/Convert_Assemblytics.o ./src/convert/Convert_Bionano.o ./src/convert/Convert_Honey_tails.o ./src/convert/Convert_MUMmer.o ./src/convert/Convert_Pindel.o ./src/convert/Convert_VCF_to_BED.o ./src/convert/Convert_hapcut2.o ./src/convert/Process_Coverage.o ./src/convert/Process_Lumpy.o ./src/convert/Update_bam_pacbio.o ./src/analysis_sv/GIAB_summary.o ./src/analysis_sv/MT_identifier.o ./src/analysis_sv/MUMmer_overlap.o ./src/analysis_sv/Select_samples.o ./src/analysis_sv/Simplify_SVs.o ./src/analysis_sv/Summ_mat.o ./src/CorrectAllele.o ./src/DetectDif.o ./src/Extract_Seq.o ./src/SURVIVOR.o ./src/Summarize_SV.o -lz @@ -728,12 +763,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3167748/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3167748/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/2405720 and its subdirectories -I: Current time: Mon Aug 18 14:35:06 -12 2025 -I: pbuilder-time-stamp: 1755570906 +I: removing directory /srv/workspace/pbuilder/3167748 and its subdirectories +I: Current time: Wed Jul 17 10:14:50 +14 2024 +I: pbuilder-time-stamp: 1721160890