Diff of the two buildlogs:
--
--- b1/build.log 2021-06-18 08:36:43.408072918 +0000
+++ b2/build.log 2021-06-18 08:41:10.510059934 +0000
@@ -1,6 +1,8 @@
-I: pbuilder: network access will be disabled during build
-I: Current time: Thu Jul 21 02:59:10 -12 2022
-I: pbuilder-time-stamp: 1658415550
+unshare: unshare failed: Cannot allocate memory
+W: pbuilder: unshare CLONE_NEWNET not available
+I: pbuilder: network access is available during build!
+I: Current time: Fri Jun 18 22:36:47 +14 2021
+I: pbuilder-time-stamp: 1624005407
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz]
I: copying local configuration
@@ -17,8 +19,8 @@
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.uf1rarcN/trustedkeys.kbx': General error
-gpgv: Signature made Sat Nov 28 01:20:07 2020 -12
+gpgv: keyblock resource '/tmp/dpkg-verify-sig.RxUYQPrh/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
@@ -30,137 +32,171 @@
dpkg-source: info: applying cross.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/8284/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/797/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos12-i386.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+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/797/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/797/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='i386'
- DEBIAN_FRONTEND='noninteractive'
- DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18'
- DISTRIBUTION=''
- HOME='/root'
- HOST_ARCH='i386'
+ 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]="i686-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=i386
+ DEBIAN_FRONTEND=noninteractive
+ DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10'
+ DIRSTACK=()
+ DISTRIBUTION=
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=i686
+ HOST_ARCH=i386
IFS='
'
- INVOCATION_ID='1bbe4300c42d4300b98e4289cd22f705'
- LANG='C'
- LANGUAGE='en_US:en'
- LC_ALL='C'
- LD_LIBRARY_PATH='/usr/lib/libeatmydata'
- LD_PRELOAD='libeatmydata.so'
- MAIL='/var/mail/root'
- OPTIND='1'
- PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
- PBCURRENTCOMMANDLINEOPERATION='build'
- PBUILDER_OPERATION='build'
- PBUILDER_PKGDATADIR='/usr/share/pbuilder'
- PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
- PBUILDER_SYSCONFDIR='/etc'
- PPID='8284'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=34dd4a9666a04d3f851eb743bd40992f
+ LANG=C
+ LANGUAGE=de_CH:de
+ LC_ALL=C
+ LD_LIBRARY_PATH=/usr/lib/libeatmydata
+ LD_PRELOAD=libeatmydata.so
+ MACHTYPE=i686-pc-linux-gnu
+ MAIL=/var/mail/root
+ OPTERR=1
+ OPTIND=1
+ OSTYPE=linux-gnu
+ PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+ PBCURRENTCOMMANDLINEOPERATION=build
+ PBUILDER_OPERATION=build
+ PBUILDER_PKGDATADIR=/usr/share/pbuilder
+ PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+ PBUILDER_SYSCONFDIR=/etc
+ PIPESTATUS=([0]="0")
+ POSIXLY_CORRECT=y
+ PPID=797
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.cLLjfDxxp6/pbuilderrc_Jsiz --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.cLLjfDxxp6/b1 --logfile b1/build.log survivor_1.0.7-2.dsc'
- SUDO_GID='112'
- SUDO_UID='107'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://85.184.249.68:3128'
+ PWD=/
+ SHELL=/bin/bash
+ SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+ SHLVL=3
+ SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.cLLjfDxxp6/pbuilderrc_1Oof --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.cLLjfDxxp6/b2 --logfile b2/build.log --extrapackages usrmerge survivor_1.0.7-2.dsc'
+ SUDO_GID=112
+ SUDO_UID=107
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
+ http_proxy=http://78.137.99.97:3128
I: uname -a
- Linux ionos16-i386 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux
+ Linux i-capture-the-hostname 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux
I: ls -l /bin
- total 5776
- -rwxr-xr-x 1 root root 1367848 Feb 24 2021 bash
- -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2
- -rwxr-xr-x 3 root root 38280 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 38280 Jul 20 2020 bzip2
- -rwxr-xr-x 1 root root 17768 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 38824 Sep 22 2020 cat
- -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp
- -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod
- -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown
- -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp
- -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash
- -rwxr-xr-x 1 root root 124904 Sep 22 2020 date
- -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd
- -rwxr-xr-x 1 root root 100752 Sep 22 2020 df
- -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir
- -rwxr-xr-x 1 root root 83644 Feb 7 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 34664 Sep 22 2020 echo
- -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep
- -rwxr-xr-x 1 root root 34664 Sep 22 2020 false
- -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep
- -rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt
- -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount
- -rwxr-xr-x 1 root root 210488 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 100952 Mar 2 2021 gzip
- -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname
- -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln
- -rwxr-xr-x 1 root root 55572 Feb 7 2020 login
- -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls
- -rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk
- -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir
- -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod
- -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp
- -rwxr-xr-x 1 root root 58920 Feb 7 2021 more
- -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount
- -rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint
- -rwxr-xr-x 1 root root 157996 Sep 22 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 38824 Sep 22 2020 pwd
- lrwxrwxrwx 1 root root 4 Feb 24 2021 rbash -> bash
- -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink
- -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm
- -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir
- -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts
- -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed
- lrwxrwxrwx 1 root root 4 Jul 19 03:46 sh -> dash
- -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep
- -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty
- -rwsr-xr-x 1 root root 79396 Feb 7 2021 su
- -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync
- -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar
- -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile
- -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch
- -rwxr-xr-x 1 root root 34664 Sep 22 2020 true
- -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server
- -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount
- -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname
- -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress
- -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir
- -rwxr-xr-x 1 root root 63024 Feb 7 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/8284/tmp/hooks/D02_print_environment finished
+ total 5796
+ -rwxr-xr-x 1 root root 1367848 Feb 25 10:57 bash
+ -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2
+ -rwxr-xr-x 3 root root 38280 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 38280 Jul 21 2020 bzip2
+ -rwxr-xr-x 1 root root 17768 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 38824 Sep 23 2020 cat
+ -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp
+ -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod
+ -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown
+ -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp
+ -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash
+ -rwxr-xr-x 1 root root 124904 Sep 23 2020 date
+ -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd
+ -rwxr-xr-x 1 root root 100752 Sep 23 2020 df
+ -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir
+ -rwxr-xr-x 1 root root 83644 Feb 8 04:38 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 34664 Sep 23 2020 echo
+ -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep
+ -rwxr-xr-x 1 root root 34664 Sep 23 2020 false
+ -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep
+ -rwxr-xr-x 1 root root 71928 Feb 8 04:38 findmnt
+ -rwsr-xr-x 1 root root 30112 Feb 27 06:12 fusermount
+ -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep
+ -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip
+ -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe
+ -rwxr-xr-x 1 root root 100952 Mar 3 13:30 gzip
+ -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname
+ -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln
+ -rwxr-xr-x 1 root root 55572 Feb 8 2020 login
+ -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls
+ -rwxr-xr-x 1 root root 153124 Feb 8 04:38 lsblk
+ -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir
+ -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod
+ -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp
+ -rwxr-xr-x 1 root root 58920 Feb 8 04:38 more
+ -rwsr-xr-x 1 root root 50720 Feb 8 04:38 mount
+ -rwxr-xr-x 1 root root 13856 Feb 8 04:38 mountpoint
+ -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv
+ lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname
+ lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5
+ -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd
+ lrwxrwxrwx 1 root root 4 Feb 25 10:57 rbash -> bash
+ -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink
+ -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm
+ -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir
+ -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts
+ -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed
+ lrwxrwxrwx 1 root root 4 Jun 18 22:38 sh -> bash
+ lrwxrwxrwx 1 root root 4 Jun 16 23:27 sh.distrib -> dash
+ -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep
+ -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty
+ -rwsr-xr-x 1 root root 79396 Feb 8 04:38 su
+ -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync
+ -rwxr-xr-x 1 root root 602584 Feb 17 23:55 tar
+ -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile
+ -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch
+ -rwxr-xr-x 1 root root 34664 Sep 23 2020 true
+ -rwxr-xr-x 1 root root 17768 Feb 27 06:12 ulockmgr_server
+ -rwsr-xr-x 1 root root 30236 Feb 8 04:38 umount
+ -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname
+ -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress
+ -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir
+ -rwxr-xr-x 1 root root 63024 Feb 8 04:38 wdctl
+ lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname
+ -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat
+ -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp
+ -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff
+ -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep
+ -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep
+ -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce
+ -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep
+ -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless
+ -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore
+ -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew
+I: user script /srv/workspace/pbuilder/797/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -230,7 +266,7 @@
Get: 30 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB]
Get: 32 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB]
-Fetched 18.8 MB in 0s (89.4 MB/s)
+Fetched 18.8 MB in 2s (8357 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 ... 19675 files and directories currently installed.)
@@ -373,8 +409,44 @@
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following additional packages will be installed:
+ libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl
+The following NEW packages will be installed:
+ libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge
+0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
+Need to get 59.5 kB of archives.
+After this operation, 157 kB of additional disk space will be used.
+Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B]
+Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B]
+Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB]
+Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 59.5 kB in 0s (849 kB/s)
+Selecting previously unselected package libnumber-compare-perl.
+(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 ... 21579 files and directories currently installed.)
+Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ...
+Unpacking libnumber-compare-perl (0.03-1.1) ...
+Selecting previously unselected package libtext-glob-perl.
+Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ...
+Unpacking libtext-glob-perl (0.11-1) ...
+Selecting previously unselected package libfile-find-rule-perl.
+Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ...
+Unpacking libfile-find-rule-perl (0.34-1) ...
+Selecting previously unselected package usrmerge.
+Preparing to unpack .../archives/usrmerge_25_all.deb ...
+Unpacking usrmerge (25) ...
+Setting up libtext-glob-perl (0.11-1) ...
+Setting up libnumber-compare-perl (0.03-1.1) ...
+Setting up libfile-find-rule-perl (0.34-1) ...
+Setting up usrmerge (25) ...
+The system has been successfully converted.
+Processing triggers for man-db (2.9.4-2) ...
+Not building database; man-db/auto-update is not 'true'.
I: Building the package
-I: Running cd /build/survivor-1.0.7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b
+I: Running cd /build/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
dpkg-buildpackage: info: source package survivor
dpkg-buildpackage: info: source version 1.0.7-2
dpkg-buildpackage: info: source distribution unstable
@@ -384,11 +456,11 @@
debian/rules clean
dh clean --sourcedirectory=Debug
dh_auto_clean -O--sourcedirectory=Debug
- cd Debug && make -j18 clean
-make[1]: Entering directory '/build/survivor-1.0.7/Debug'
+ cd Debug && make -j10 clean
+make[1]: Verzeichnis „/build/survivor-1.0.7/Debug“ wird betreten
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
-make[1]: Leaving directory '/build/survivor-1.0.7/Debug'
+make[1]: Verzeichnis „/build/survivor-1.0.7/Debug“ wird verlassen
dh_autoreconf_clean -O--sourcedirectory=Debug
dh_clean -O--sourcedirectory=Debug
debian/rules binary
@@ -397,62 +469,38 @@
dh_autoreconf -O--sourcedirectory=Debug
dh_auto_configure -O--sourcedirectory=Debug
dh_auto_build -O--sourcedirectory=Debug
- cd Debug && make -j18 "INSTALL=install --strip-program=true"
-make[1]: Entering directory '/build/survivor-1.0.7/Debug'
+ cd Debug && make -j10 "INSTALL=install --strip-program=true"
+make[1]: Verzeichnis „/build/survivor-1.0.7/Debug“ wird betreten
Building file: ../src/vcfs/Annotate_vcf.cpp
-Building file: ../src/vcfs/Combine_3_VCF.cpp
-Building file: ../src/vcfs/Compoverlap_VCF.cpp
-Invoking: Cross G++ Compiler
Invoking: Cross G++ Compiler
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"
+Building file: ../src/vcfs/Combine_3_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/Detect_nested.cpp
+Building file: ../src/vcfs/Compoverlap_VCF.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"
+Building file: ../src/vcfs/Detect_nested.cpp
+Building file: ../src/vcfs/Filter_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
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"
+Building file: ../src/vcfs/Generate_distMat.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"
Building file: ../src/vcfs/Merge_VCF.cpp
-Building file: ../src/snp_overlap/Overlap_snps.cpp
Invoking: Cross G++ Compiler
-Building file: ../src/simulator/Error_scanner.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"
+Building file: ../src/snp_overlap/Overlap_snps.cpp
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/Eval_vcf.cpp
+Building file: ../src/simulator/Error_scanner.cpp
Invoking: Cross G++ Compiler
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/Eval_vcf.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"
-Building file: ../src/simulator/Pac_Simulator.cpp
-Invoking: Cross G++ Compiler
-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"
-Building file: ../src/simulator/SV_Simulator.cpp
-Building file: ../src/simulator/Sim_reads.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"
-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/simulator/test_cov.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
-Building file: ../src/phasing/Phasing_vcf.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"
-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"
-Building file: ../src/merge_vcf/IntervallTree.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
-Invoking: Cross G++ Compiler
-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"
../src/simulator/Error_scanner.cpp: In function ‘void computeAlignment(std::vector<CigarOp>, char*, std::string, std::vector<std::vector<std::vector<int> > >&, std::string)’:
../src/simulator/Error_scanner.cpp:173:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::vector<int> > >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
173 | while (pos + 1 > error_mat.size()) {
@@ -461,6 +509,10 @@
../src/vcfs/Filter_vcf.cpp:18:6: warning: variable ‘lumpy’ set but not used [-Wunused-but-set-variable]
18 | int lumpy = 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 ‘unsigned int’} and ‘int’ [-Wsign-compare]
+ 192 | for (size_t i = start; i <= stop; i++) {
+ | ~~^~~~~~~
../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"
@@ -477,10 +529,6 @@
../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 ‘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<char>::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
447 | if (genome.find(chr) != genome.end() && genome[chr].size() > pos) {
@@ -496,11 +544,66 @@
../src/snp_overlap/Overlap_snps.cpp:781:47: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
781 | for (size_t pos = entries[i].start.pos; pos < entries[i].stop.pos; pos++) {
| ~~~~^~~~~~~~~~~~~~~~~~~~~
+Finished building: ../src/vcfs/Detect_nested.cpp
+
+Building file: ../src/simulator/Pac_Simulator.cpp
+Invoking: Cross G++ Compiler
+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"
+Finished building: ../src/vcfs/Generate_distMat.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/SV_Simulator.d" -MT"src/simulator/SV_Simulator.o" -o "src/simulator/SV_Simulator.o" "../src/simulator/SV_Simulator.cpp"
+Finished building: ../src/simulator/Error_scanner.cpp
+
+Building file: ../src/simulator/Sim_reads.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"
+Finished building: ../src/simulator/Pac_Simulator.cpp
+
+Building file: ../src/simulator/test_cov.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"
+Finished building: ../src/vcfs/Compoverlap_VCF.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"
+Finished building: ../src/simulator/test_cov.cpp
+
+Building file: ../src/phasing/Phasing_vcf.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"
Finished building: ../src/scrup_vcf/scrup_svs.cpp
+Building file: ../src/merge_vcf/IntervallTree.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"
+Finished building: ../src/simulator/Sim_reads.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/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"
+Finished building: ../src/vcfs/Merge_VCF.cpp
+
Building file: ../src/convert/ConvertMQ0Bed.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"
+Finished building: ../src/vcfs/Filter_vcf.cpp
+
+Building file: ../src/convert/Convert_Assemblytics.cpp
+Invoking: Cross G++ Compiler
+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"
+Finished building: ../src/simulator/Eval_vcf.cpp
+
+Building file: ../src/convert/Convert_Bionano.cpp
+Invoking: Cross G++ Compiler
+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"
+Finished building: ../src/phasing/Phasing_vcf.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"
../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 ‘unsigned int’} and ‘int’ [-Wsign-compare]
213 | for (size_t i = 0; i < Parameter::Instance()->max_caller; i++) {
@@ -515,80 +618,65 @@
../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/simulator/test_cov.cpp
-
-Building file: ../src/convert/Convert_Assemblytics.cpp
-Invoking: Cross G++ Compiler
-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"
-Finished building: ../src/vcfs/Detect_nested.cpp
-
-Building file: ../src/convert/Convert_Bionano.cpp
-Invoking: Cross G++ Compiler
-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"
-Finished building: ../src/simulator/Pac_Simulator.cpp
Finished building: ../src/convert/ConvertMQ0Bed.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"
Building file: ../src/convert/Convert_MUMmer.cpp
Invoking: Cross G++ Compiler
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"
-Finished building: ../src/phasing/Phasing_vcf.cpp
+../src/convert/Convert_Honey_tails.cpp: In function ‘void parse_honey_tails(std::string, int, std::vector<strvcfentry>&)’:
+../src/convert/Convert_Honey_tails.cpp:45:7: warning: variable ‘dist’ set but not used [-Wunused-but-set-variable]
+ 45 | int dist=0;
+ | ^~~~
+Finished building: ../src/snp_overlap/Overlap_snps.cpp
+Finished building: ../src/vcfs/Combine_3_VCF.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"
-Finished building: ../src/vcfs/Generate_distMat.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<strvcfentry>&)’:
-../src/convert/Convert_Honey_tails.cpp:45:7: warning: variable ‘dist’ set but not used [-Wunused-but-set-variable]
- 45 | int dist=0;
- | ^~~~
-Finished building: ../src/simulator/Error_scanner.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"
../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/simulator/Sim_reads.cpp
+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/merge_vcf/IntervallTree.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/convert/Convert_MUMmer.cpp
+Finished building: ../src/convert/Convert_Assemblytics.cpp
Building file: ../src/convert/Process_Lumpy.cpp
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"
-Finished building: ../src/vcfs/Compoverlap_VCF.cpp
+Finished building: ../src/convert/Convert_Honey_tails.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/merge_vcf/IntervallTree.cpp
+Finished building: ../src/convert/Process_Coverage.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/convert/Process_Coverage.cpp
+Finished building: ../src/vcfs/Annotate_vcf.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/Convert_Assemblytics.cpp
+Finished building: ../src/convert/Convert_Bionano.cpp
Building file: ../src/analysis_sv/MUMmer_overlap.cpp
Invoking: Cross G++ Compiler
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"
-Finished building: ../src/convert/Convert_Honey_tails.cpp
+Finished building: ../src/convert/Convert_Pindel.cpp
Building file: ../src/analysis_sv/Select_samples.cpp
Invoking: Cross G++ Compiler
@@ -605,7 +693,7 @@
Building file: ../src/analysis_sv/Simplify_SVs.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"
-Finished building: ../src/convert/Convert_Pindel.cpp
+Finished building: ../src/analysis_sv/MT_identifier.cpp
Building file: ../src/analysis_sv/Summ_mat.cpp
Invoking: Cross G++ Compiler
@@ -614,39 +702,35 @@
Building file: ../src/CorrectAllele.cpp
Invoking: Cross G++ Compiler
+Finished building: ../src/convert/Convert_VCF_to_BED.cpp
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"
-Finished building: ../src/convert/Convert_Bionano.cpp
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"
-Finished building: ../src/simulator/Eval_vcf.cpp
+../src/analysis_sv/Simplify_SVs.cpp: In function ‘sv_simple_str parse_line_sv(char*, int, std::vector<std::__cxx11::basic_string<char> >, std::string&)’:
+../src/analysis_sv/Simplify_SVs.cpp:54:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
+ 54 | for (size_t i = 0; i < buffer_size && buffer[i] != '\0' && buffer[i] != '\n'; i++) {
+ | ~~^~~~~~~~~~~~~
+../src/analysis_sv/Simplify_SVs.cpp: In function ‘void print_gene_sv(std::string, sv_simple_str, FILE*&, int, std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >)’:
+../src/analysis_sv/Simplify_SVs.cpp:118:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, bool>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
+ 118 | if (count + 1 < entry.accessions.size()) {
+ | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
+Finished building: ../src/analysis_sv/Select_samples.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"
-Finished building: ../src/analysis_sv/MT_identifier.cpp
+Finished building: ../src/simulator/SV_Simulator.cpp
Building file: ../src/SURVIVOR.cpp
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/vcfs/Merge_VCF.cpp
-Finished building: ../src/vcfs/Filter_vcf.cpp
-
+Finished building: ../src/merge_vcf/combine_svs.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/analysis_sv/Simplify_SVs.cpp: In function ‘sv_simple_str parse_line_sv(char*, int, std::vector<std::__cxx11::basic_string<char> >, std::string&)’:
-../src/analysis_sv/Simplify_SVs.cpp:54:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
- 54 | for (size_t i = 0; i < buffer_size && buffer[i] != '\0' && buffer[i] != '\n'; i++) {
- | ~~^~~~~~~~~~~~~
-../src/analysis_sv/Simplify_SVs.cpp: In function ‘void print_gene_sv(std::string, sv_simple_str, FILE*&, int, std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >)’:
-../src/analysis_sv/Simplify_SVs.cpp:118:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, bool>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
- 118 | if (count + 1 < entry.accessions.size()) {
- | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
-Finished building: ../src/convert/Convert_VCF_to_BED.cpp
-
Finished building: ../src/convert/Process_Lumpy.cpp
Finished building: ../src/analysis_sv/MUMmer_overlap.cpp
@@ -659,34 +743,22 @@
| | int
| double
| %d
-Finished building: ../src/analysis_sv/Select_samples.cpp
-
Finished building: ../src/DetectDif.cpp
-Finished building: ../src/vcfs/Combine_3_VCF.cpp
-
-Finished building: ../src/snp_overlap/Overlap_snps.cpp
+Finished building: ../src/analysis_sv/Summ_mat.cpp
Finished building: ../src/SURVIVOR.cpp
-Finished building: ../src/merge_vcf/combine_svs.cpp
-
-Finished building: ../src/analysis_sv/Summ_mat.cpp
-
Finished building: ../src/CorrectAllele.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/simulator/SV_Simulator.cpp
-
Finished building: ../src/analysis_sv/Simplify_SVs.cpp
Finished building: ../src/analysis_sv/GIAB_summary.cpp
-Finished building: ../src/vcfs/Annotate_vcf.cpp
-
Finished building: ../src/Extract_Seq.cpp
Finished building: ../src/Summarize_SV.cpp
@@ -696,7 +768,7 @@
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
Finished building target: SURVIVOR
-make[1]: Leaving directory '/build/survivor-1.0.7/Debug'
+make[1]: Verzeichnis „/build/survivor-1.0.7/Debug“ wird verlassen
dh_auto_test -O--sourcedirectory=Debug
create-stamp debian/debhelper-build-stamp
dh_testroot -O--sourcedirectory=Debug
@@ -721,20 +793,21 @@
dh_gencontrol -O--sourcedirectory=Debug
dh_md5sums -O--sourcedirectory=Debug
dh_builddeb -O--sourcedirectory=Debug
-dpkg-deb: building package 'survivor' in '../survivor_1.0.7-2_i386.deb'.
-dpkg-deb: building package 'survivor-dbgsym' in '../survivor-dbgsym_1.0.7-2_i386.deb'.
+dpkg-deb: Paket »survivor-dbgsym« wird in »../survivor-dbgsym_1.0.7-2_i386.deb« gebaut.
+dpkg-deb: Paket »survivor« wird in »../survivor_1.0.7-2_i386.deb« gebaut.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../survivor_1.0.7-2_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
-I: copying local configuration
+I: user script /srv/workspace/pbuilder/797/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/797/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/8284 and its subdirectories
-I: Current time: Thu Jul 21 02:59:42 -12 2022
-I: pbuilder-time-stamp: 1658415583
+I: removing directory /srv/workspace/pbuilder/797 and its subdirectories
+I: Current time: Fri Jun 18 22:41:09 +14 2021
+I: pbuilder-time-stamp: 1624005669