I: pbuilder: network access will be disabled during build
I: Current time: Sat Jan 17 17:42:30 +14 2026
I: pbuilder-time-stamp: 1768621350
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [survivor_1.0.7-4.dsc]
I: copying [./survivor_1.0.7.orig.tar.gz]
I: copying [./survivor_1.0.7-4.debian.tar.xz]
I: Extracting source
gpgv: Signature made Tue Dec 6 15:00:39 2022
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./survivor_1.0.7-4.dsc: no acceptable signature found
dpkg-source: info: extracting survivor in survivor-1.0.7
dpkg-source: info: unpacking survivor_1.0.7.orig.tar.gz
dpkg-source: info: unpacking survivor_1.0.7-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying cross.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/45720/tmp/hooks/D01_modify_environment starting
debug: Running on ionos16-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
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Jan 17 03:42 /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/45720/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/45720/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
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 parallel=21 '
DIRSTACK=()
DISTRIBUTION=unstable
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=i686
HOST_ARCH=i386
IFS='
'
INVOCATION_ID=04a9863129344fa1aae15f9ac355023e
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=45720
PS4='+ '
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.hwRN2Y0n/pbuilderrc_tdRt --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hwRN2Y0n/b2 --logfile b2/build.log survivor_1.0.7-4.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://213.165.73.152:3128
I: uname -a
Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/45720/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), zlib1g-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19952 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded.
Need to get 21.0 MB of archives. After unpacking 77.1 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 4 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 5 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-2 [201 kB]
Get: 6 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 7 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-6 [1198 kB]
Get: 8 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-12 [95.9 kB]
Get: 9 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 10 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 11 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB]
Get: 12 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-2 [723 kB]
Get: 16 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.20 [89.7 kB]
Get: 17 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-8 [517 kB]
Get: 18 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 21 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 22 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 23 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 24 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5+b1 [9583 kB]
Get: 25 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 26 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-2 [1631 kB]
Get: 27 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 28 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 29 http://deb.debian.org/debian unstable/main i386 debhelper all 13.20 [915 kB]
Get: 30 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Fetched 21.0 MB in 0s (92.8 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
(Reading database ... 5%
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(Reading database ... 20%
(Reading database ... 25%
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(Reading database ... 100%
(Reading database ... 19952 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:i386.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic1t64:i386 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.45-3+b1_i386.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.22.5-2_i386.deb ...
Unpacking gettext-base (0.22.5-2) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_i386.deb ...
Unpacking libuchardet0:i386 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.23.0-6_i386.deb ...
Unpacking groff-base (1.23.0-6) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.40.2-12_i386.deb ...
Unpacking bsdextrautils (2.40.2-12) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../08-libpipeline1_1.5.8-1_i386.deb ...
Unpacking libpipeline1:i386 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.13.0-1_i386.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-4_i386.deb ...
Unpacking m4 (1.4.19-4) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ...
Unpacking autopoint (0.22.5-2) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ...
Unpacking libdebhelper-perl (13.20) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.4.7-8_all.deb ...
Unpacking libtool (2.4.7-8) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../17-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.0-1) ...
Selecting previously unselected package libelf1t64:i386.
Preparing to unpack .../21-libelf1t64_0.192-4_i386.deb ...
Unpacking libelf1t64:i386 (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../22-dwz_0.15-1+b1_i386.deb ...
Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package libicu72:i386.
Preparing to unpack .../23-libicu72_72.1-5+b1_i386.deb ...
Unpacking libicu72:i386 (72.1-5+b1) ...
Selecting previously unselected package libxml2:i386.
Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_i386.deb ...
Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../25-gettext_0.22.5-2_i386.deb ...
Unpacking gettext (0.22.5-2) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../28-debhelper_13.20_all.deb ...
Unpacking debhelper (13.20) ...
Selecting previously unselected package zlib1g-dev:i386.
Preparing to unpack .../29-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_i386.deb ...
Unpacking zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libpipeline1:i386 (1.5.8-1) ...
Setting up libicu72:i386 (72.1-5+b1) ...
Setting up bsdextrautils (2.40.2-12) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.20) ...
Setting up libmagic1t64:i386 (1:5.45-3+b1) ...
Setting up gettext-base (0.22.5-2) ...
Setting up m4 (1.4.19-4) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:i386 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up autopoint (0.22.5-2) ...
Setting up autoconf (2.72-3) ...
Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:i386 (0.0.8-1+b2) ...
Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up gettext (0.22.5-2) ...
Setting up libtool (2.4.7-8) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up groff-base (1.23.0-6) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.20) ...
Processing triggers for libc-bin (2.40-4) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/45720/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/45720/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_1.0.7-4_source.changes
dpkg-buildpackage: info: source package survivor
dpkg-buildpackage: info: source version 1.0.7-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean --sourcedirectory=Debug
dh_auto_clean -O--sourcedirectory=Debug
cd Debug && make -j21 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
make[1]: Leaving directory '/build/reproducible-path/survivor-1.0.7/Debug'
dh_autoreconf_clean -O--sourcedirectory=Debug
dh_clean -O--sourcedirectory=Debug
debian/rules binary
dh binary --sourcedirectory=Debug
dh_update_autotools_config -O--sourcedirectory=Debug
dh_autoreconf -O--sourcedirectory=Debug
dh_auto_configure -O--sourcedirectory=Debug
dh_auto_build -O--sourcedirectory=Debug
cd Debug && make -j21 "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
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"
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/Filter_vcf.cpp
Invoking: Cross G++ Compiler
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"
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
Building file: ../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/vcfs/Generate_distMat.d" -MT"src/vcfs/Generate_distMat.o" -o "src/vcfs/Generate_distMat.o" "../src/vcfs/Generate_distMat.cpp"
Building file: ../src/simulator/Error_scanner.cpp
Invoking: Cross G++ Compiler
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/simulator/Eval_vcf.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"
Invoking: Cross G++ Compiler
Building file: ../src/simulator/Pac_Simulator.cpp
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/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/Pac_Simulator.d" -MT"src/simulator/Pac_Simulator.o" -o "src/simulator/Pac_Simulator.o" "../src/simulator/Pac_Simulator.cpp"
Building file: ../src/simulator/test_cov.cpp
Invoking: Cross G++ Compiler
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/scrup_vcf/scrup_svs.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"
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"
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
Building file: ../src/merge_vcf/IntervallTree.cpp
Building file: ../src/merge_vcf/combine_svs.cpp
Building file: ../src/convert/ConvertMQ0Bed.cpp
Invoking: Cross G++ Compiler
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/convert/Convert_Assemblytics.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"
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"
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"
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"
../src/vcfs/Filter_vcf.cpp: In function ‘void translate(const char*, int, float, int, strentry&)’:
../src/vcfs/Filter_vcf.cpp:18:13: warning: variable ‘lumpy’ set but not used [-Wunused-but-set-variable]
18 | int lumpy = 0;
| ^~~~~
../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:173:32: 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()) {
| ~~~~~~~~^~~~~~~~~~~~~~~~~~
../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:192:58: 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:447:92: 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) {
| ~~~~~~~~~~~~~~~~~~~^~~~~
../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:663:108: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘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:767:85: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘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:781:61: 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++) {
| ~~~~^~~~~~~~~~~~~~~~~~~~~
../src/merge_vcf/combine_svs.cpp: In function ‘void print_GTs(std::ostringstream&, SVS_Node*)’:
../src/merge_vcf/combine_svs.cpp:213:30: 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++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../src/merge_vcf/combine_svs.cpp:215:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Support_Node*>::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
215 | if (pos < entry->caller_info.size() && i == entry->caller_info[pos]->id) {
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../src/merge_vcf/combine_svs.cpp:215:58: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
215 | if (pos < entry->caller_info.size() && i == entry->caller_info[pos]->id) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../src/simulator/Eval_vcf.cpp: In function ‘void reprotvals(const char*)’:
../src/simulator/Eval_vcf.cpp:102:15: warning: variable ‘dv’ set but not used [-Wunused-but-set-variable]
102 | float dv = 0; //"# high-quality variant pairs"
| ^~
../src/simulator/Eval_vcf.cpp:103:15: warning: variable ‘dr’ set but not used [-Wunused-but-set-variable]
103 | float dr = 0; //"# high-quality reference pairs"
| ^~
../src/simulator/Eval_vcf.cpp:104:13: warning: variable ‘gq’ set but not used [-Wunused-but-set-variable]
104 | int gq = 0; //"Genotype Quality"
| ^~
../src/simulator/Eval_vcf.cpp:105:13: warning: variable ‘rr’ set but not used [-Wunused-but-set-variable]
105 | int rr = 0;
| ^~
../src/simulator/Eval_vcf.cpp:106:13: warning: variable ‘rv’ set but not used [-Wunused-but-set-variable]
106 | int rv = 0;
| ^~
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"
../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:688:31: 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_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/scrup_vcf/scrup_svs.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/simulator/Pac_Simulator.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"
Finished building: ../src/vcfs/Detect_nested.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_Honey_tails.cpp: In function ‘void parse_honey_tails(std::string, int, std::vector<strvcfentry>&)’:
../src/convert/Convert_Honey_tails.cpp:45:21: warning: variable ‘dist’ set but not used [-Wunused-but-set-variable]
45 | int dist=0;
| ^~~~
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"
../src/convert/Convert_VCF_to_BED.cpp: In function ‘std::string print_entry_bed(strvcfentry&)’:
../src/convert/Convert_VCF_to_BED.cpp:348:20: warning: unknown escape sequence: '\/'
348 | convert << "\tGT\t.\/.";
| ^~~~~~~~~~~~
Finished building: ../src/vcfs/Generate_distMat.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/convert/Convert_MUMmer.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/Error_scanner.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/Convert_Assemblytics.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/simulator/Sim_reads.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/vcfs/Compoverlap_VCF.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"
Finished building: ../src/convert/Convert_Bionano.cpp
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/Process_Coverage.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/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/vcfs/Filter_vcf.cpp
Building file: ../src/CorrectAllele.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"
Finished building: ../src/convert/Convert_Honey_tails.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/analysis_sv/MT_identifier.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/convert/Convert_Pindel.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"
../src/analysis_sv/MUMmer_overlap.cpp: In function ‘void comp_entries_mummer(std::vector<strvcfentry>&, std::string, int)’:
../src/analysis_sv/MUMmer_overlap.cpp:60:21: warning: variable ‘stop’ set but not used [-Wunused-but-set-variable]
60 | int stop = 0;
| ^~~~
../src/analysis_sv/MUMmer_overlap.cpp:61:21: warning: variable ‘len’ set but not used [-Wunused-but-set-variable]
61 | int len = 0;
| ^~~
../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:54:30: 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:118:31: 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_hapcut2.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"
Finished building: ../src/merge_vcf/IntervallTree.cpp
Finished building: ../src/convert/Update_bam_pacbio.cpp
Finished building: ../src/DetectDif.cpp
Finished building: ../src/analysis_sv/Select_samples.cpp
../src/Summarize_SV.cpp: In function ‘void summary_venn(std::string, bool, std::string)’:
../src/Summarize_SV.cpp:608:65: warning: format ‘%e’ expects argument of type ‘double’, but argument 3 has type ‘int’ [-Wformat=]
608 | fprintf(file, "%e", 0);
| ~^ ~
| | |
| | int
| double
| %d
Finished building: ../src/simulator/Eval_vcf.cpp
Finished building: ../src/convert/Process_Lumpy.cpp
Finished building: ../src/convert/Convert_VCF_to_BED.cpp
Finished building: ../src/analysis_sv/MUMmer_overlap.cpp
Finished building: ../src/SURVIVOR.cpp
Finished building: ../src/vcfs/Merge_VCF.cpp
Finished building: ../src/CorrectAllele.cpp
Finished building: ../src/analysis_sv/Summ_mat.cpp
Finished building: ../src/vcfs/Combine_3_VCF.cpp
Finished building: ../src/merge_vcf/combine_svs.cpp
Finished building: ../src/snp_overlap/Overlap_snps.cpp
Finished building: ../src/analysis_sv/Simplify_SVs.cpp
../src/Summarize_SV.cpp: In function ‘void summary_SV_stream(int, int, std::string)’:
../src/Summarize_SV.cpp:302:70: warning: ‘type’ may be used uninitialized [-Wmaybe-uninitialized]
302 | if (max_size < 0 || (leng < max_size || type == 3)) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
../src/Summarize_SV.cpp:281:39: note: ‘type’ was declared here
281 | short type;
| ^~~~
Finished building: ../src/analysis_sv/GIAB_summary.cpp
Finished building: ../src/simulator/SV_Simulator.cpp
Finished building: ../src/Extract_Seq.cpp
Finished building: ../src/vcfs/Annotate_vcf.cpp
Finished building: ../src/Summarize_SV.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
Finished building target: SURVIVOR
make[1]: Leaving directory '/build/reproducible-path/survivor-1.0.7/Debug'
dh_auto_test -O--sourcedirectory=Debug
create-stamp debian/debhelper-build-stamp
dh_testroot -O--sourcedirectory=Debug
dh_prep -O--sourcedirectory=Debug
dh_auto_install --destdir=debian/survivor/ -O--sourcedirectory=Debug
dh_install -O--sourcedirectory=Debug
dh_installdocs -O--sourcedirectory=Debug
dh_installchangelogs -O--sourcedirectory=Debug
dh_installman -O--sourcedirectory=Debug
dh_installsystemduser -O--sourcedirectory=Debug
dh_perl -O--sourcedirectory=Debug
dh_link -O--sourcedirectory=Debug
dh_strip_nondeterminism -O--sourcedirectory=Debug
dh_compress -O--sourcedirectory=Debug
dh_fixperms -O--sourcedirectory=Debug
dh_missing -O--sourcedirectory=Debug
dh_dwz -a -O--sourcedirectory=Debug
dh_strip -a -O--sourcedirectory=Debug
dh_makeshlibs -a -O--sourcedirectory=Debug
dh_shlibdeps -a -O--sourcedirectory=Debug
dh_installdeb -O--sourcedirectory=Debug
dh_gencontrol -O--sourcedirectory=Debug
dh_md5sums -O--sourcedirectory=Debug
dh_builddeb -O--sourcedirectory=Debug
dpkg-deb: building package 'survivor-dbgsym' in '../survivor-dbgsym_1.0.7-4_i386.deb'.
dpkg-deb: building package 'survivor' in '../survivor_1.0.7-4_i386.deb'.
dpkg-genbuildinfo --build=binary -O../survivor_1.0.7-4_i386.buildinfo
dpkg-genchanges --build=binary -O../survivor_1.0.7-4_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)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/45720/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/45720/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/45720 and its subdirectories
I: Current time: Sat Jan 17 17:43:09 +14 2026
I: pbuilder-time-stamp: 1768621389