I: pbuilder: network access will be disabled during build
I: Current time: Thu Jun 13 00:34:32 +14 2024
I: pbuilder-time-stamp: 1718188472
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-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 [lumpy-sv_0.3.1+dfsg-7.dsc]
I: copying [./lumpy-sv_0.3.1+dfsg.orig.tar.xz]
I: copying [./lumpy-sv_0.3.1+dfsg-7.debian.tar.xz]
I: Extracting source
gpgv: Signature made Thu Oct 6 23:42:28 2022 +14
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 ./lumpy-sv_0.3.1+dfsg-7.dsc: no acceptable signature found
dpkg-source: info: extracting lumpy-sv in lumpy-sv-0.3.1+dfsg
dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_debian_packaged_libs.patch
dpkg-source: info: applying lumpyexpress.config.patch
dpkg-source: info: applying fix_shebang.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/125774/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 Jun 13 00:34 /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/125774/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/125774/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]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
BASH_VERSION='5.2.15(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 parallel=15'
DIRSTACK=()
DISTRIBUTION=bookworm
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=i686
HOST_ARCH=i386
IFS='
'
INVOCATION_ID=0a1255127313416b8055d6d93a49d117
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=125774
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.xxgLnENH/pbuilderrc_Ad0t --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xxgLnENH/b2 --logfile b2/build.log --extrapackages usrmerge lumpy-sv_0.3.1+dfsg-7.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://85.184.249.68:3128
I: uname -a
Linux i-capture-the-hostname 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux
I: ls -l /bin
total 6036
-rwxr-xr-x 1 root root 1408088 Apr 24 2023 bash
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2
-rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore
-rwxr-xr-x 1 root root 42920 Sep 21 2022 cat
-rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp
-rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod
-rwxr-xr-x 1 root root 79816 Sep 21 2022 chown
-rwxr-xr-x 1 root root 162024 Sep 21 2022 cp
-rwxr-xr-x 1 root root 136916 Jan 6 2023 dash
-rwxr-xr-x 1 root root 137160 Sep 21 2022 date
-rwxr-xr-x 1 root root 100364 Sep 21 2022 dd
-rwxr-xr-x 1 root root 108940 Sep 21 2022 df
-rwxr-xr-x 1 root root 162152 Sep 21 2022 dir
-rwxr-xr-x 1 root root 87760 Mar 24 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname
-rwxr-xr-x 1 root root 38760 Sep 21 2022 echo
-rwxr-xr-x 1 root root 41 Jan 25 2023 egrep
-rwxr-xr-x 1 root root 34664 Sep 21 2022 false
-rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep
-rwxr-xr-x 1 root root 84272 Mar 24 2023 findmnt
-rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount
-rwxr-xr-x 1 root root 218680 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 100952 Apr 10 2022 gzip
-rwxr-xr-x 1 root root 21916 Dec 20 2022 hostname
-rwxr-xr-x 1 root root 75756 Sep 21 2022 ln
-rwxr-xr-x 1 root root 55600 Mar 24 2023 login
-rwxr-xr-x 1 root root 162152 Sep 21 2022 ls
-rwxr-xr-x 1 root root 214568 Mar 24 2023 lsblk
-rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir
-rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod
-rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp
-rwxr-xr-x 1 root root 63016 Mar 24 2023 more
-rwsr-xr-x 1 root root 58912 Mar 24 2023 mount
-rwxr-xr-x 1 root root 13856 Mar 24 2023 mountpoint
-rwxr-xr-x 1 root root 157932 Sep 21 2022 mv
lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash
-rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 21 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir
-rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts
-rwxr-xr-x 1 root root 133224 Jan 6 2023 sed
lrwxrwxrwx 1 root root 9 Jun 13 00:34 sh -> /bin/bash
-rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 21 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 24 2023 su
-rwxr-xr-x 1 root root 38792 Sep 21 2022 sync
-rwxr-xr-x 1 root root 598456 Apr 7 2023 tar
-rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile
-rwxr-xr-x 1 root root 120776 Sep 21 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 21 2022 true
-rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Mar 24 2023 umount
-rwxr-xr-x 1 root root 38760 Sep 21 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress
-rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir
-rwxr-xr-x 1 root root 71216 Mar 24 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 20 2022 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 6460 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 8103 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/125774/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), dh-python, python3, libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools, python3-pysam
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19604 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 dh-python; however:
Package dh-python is not installed.
pbuilder-satisfydepends-dummy depends on python3; however:
Package python3 is not installed.
pbuilder-satisfydepends-dummy depends on libbamtools-dev; however:
Package libbamtools-dev is not installed.
pbuilder-satisfydepends-dummy depends on libfastahack-dev; however:
Package libfastahack-dev is not installed.
pbuilder-satisfydepends-dummy depends on libgzstream-dev; however:
Package libgzstream-dev is not installed.
pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however:
Package libsqlite3-dev is not installed.
pbuilder-satisfydepends-dummy depends on libhts-dev; however:
Package libhts-dev is not installed.
pbuilder-satisfydepends-dummy depends on libssl-dev; however:
Package libssl-dev is not installed.
pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev; however:
Package libcurl4-gnutls-dev is not installed.
pbuilder-satisfydepends-dummy depends on samtools; however:
Package samtools is not installed.
pbuilder-satisfydepends-dummy depends on python3-pysam; however:
Package python3-pysam 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-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.2{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libfastahack-dev{a} libfastahack0{a} libfile-stripnondeterminism-perl{a} libgzstream-dev{a} libgzstream0{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsqlite3-dev{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pysam{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget
0 packages upgraded, 72 newly installed, 0 to remove and 0 not upgraded.
Need to get 36.9 MB of archives. After unpacking 134 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB]
Get: 2 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB]
Get: 3 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B]
Get: 11 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 13 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 15 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 21 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 22 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 23 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 24 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 26 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 31 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 32 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 33 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 34 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 35 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 36 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 37 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB]
Get: 38 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 39 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 40 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 41 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Get: 42 http://deb.debian.org/debian bookworm/main i386 python3-lib2to3 all 3.11.2-3 [76.3 kB]
Get: 43 http://deb.debian.org/debian bookworm/main i386 python3-distutils all 3.11.2-3 [131 kB]
Get: 44 http://deb.debian.org/debian bookworm/main i386 dh-python all 5.20230130 [104 kB]
Get: 45 http://deb.debian.org/debian bookworm/main i386 libbamtools2.5.2 i386 2.5.2+dfsg-4 [165 kB]
Get: 46 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB]
Get: 47 http://deb.debian.org/debian bookworm/main i386 libbamtools-dev i386 2.5.2+dfsg-4 [233 kB]
Get: 48 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB]
Get: 49 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB]
Get: 50 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB]
Get: 51 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB]
Get: 52 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1 [79.8 kB]
Get: 53 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB]
Get: 54 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB]
Get: 55 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB]
Get: 56 http://deb.debian.org/debian bookworm/main i386 libcurl3-gnutls i386 7.88.1-9 [412 kB]
Get: 57 http://deb.debian.org/debian bookworm/main i386 libcurl4-gnutls-dev i386 7.88.1-9 [527 kB]
Get: 58 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB]
Get: 59 http://deb.debian.org/debian bookworm/main i386 libdeflate-dev i386 1.14-1 [53.5 kB]
Get: 60 http://deb.debian.org/debian bookworm/main i386 libfastahack0 i386 1.0.0+dfsg-10 [28.4 kB]
Get: 61 http://deb.debian.org/debian bookworm/main i386 libfastahack-dev i386 1.0.0+dfsg-10 [30.0 kB]
Get: 62 http://deb.debian.org/debian bookworm/main i386 libgzstream0 i386 1.5+git20171107.9a20658-1+b2 [7444 B]
Get: 63 http://deb.debian.org/debian bookworm/main i386 libgzstream-dev i386 1.5+git20171107.9a20658-1+b2 [7688 B]
Get: 64 http://deb.debian.org/debian bookworm/main i386 libhtscodecs2 i386 1.3.0-4 [67.4 kB]
Get: 65 http://deb.debian.org/debian bookworm/main i386 libhts3 i386 1.16+ds-3 [469 kB]
Get: 66 http://deb.debian.org/debian bookworm/main i386 liblzma-dev i386 5.4.1-0.2 [272 kB]
Get: 67 http://deb.debian.org/debian bookworm/main i386 libhts-dev i386 1.16+ds-3 [1585 kB]
Get: 68 http://deb.debian.org/debian bookworm/main i386 libncurses6 i386 6.4-2 [111 kB]
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I: Building the package
I: user script /srv/workspace/pbuilder/125774/tmp/hooks/A99_set_merged_usr starting
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removed '/etc/unsupported-skip-usrmerge-conversion'
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hostname: Name or service not known
I: Running cd /build/lumpy-sv-0.3.1+dfsg/ && 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 > ../lumpy-sv_0.3.1+dfsg-7_source.changes
dpkg-buildpackage: info: source package lumpy-sv
dpkg-buildpackage: info: source version 0.3.1+dfsg-7
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 --with python3
dh_auto_clean
make -j15 clean
make[1]: Verzeichnis „/build/lumpy-sv-0.3.1+dfsg“ wird betreten
Cleaning up.
#rm -Rf /lib
#rm -f /src/api/*.o
#rm -f /src/api/internal/*.o
#rm -Rf /include
make[1]: Verzeichnis „/build/lumpy-sv-0.3.1+dfsg“ wird verlassen
dh_clean
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dh_auto_configure
dh_auto_build
make -j15 "INSTALL=install --strip-program=true"
make[1]: Verzeichnis „/build/lumpy-sv-0.3.1+dfsg“ wird betreten
[ -d bin ] || mkdir -p bin
[ -d bin ] || mkdir -p bin
[ -d obj ] || mkdir -p obj
make --no-print-directory -C src/filter/
cp scripts/lumpyexpress bin/lumpyexpress
[ -d bin ] || mkdir -p bin
cc -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz
> bin/lumpyexpress.config
Building lumpy:
=========================================================
#make --no-print-directory --directory= api
for dir in src/utils/bedFile src/utils/version src/utils/fileType src/utils/bedFilePE src/utils/genomeFile src/utils/BamTools-Ancillary src/utils/sequenceUtilities ; do \
echo "- Building in $dir"; \
make --no-print-directory -C $dir; \
echo ""; \
done
- Building in src/utils/bedFile
* compiling bedFile.cpp
cp src/filter/lumpy_filter bin
In file included from bedFile.cpp:12:
bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
- Building in src/utils/version
* compiling version.cpp
- Building in src/utils/fileType
* compiling fileType.cpp
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
In file included from bedFilePE.h:12,
from bedFilePE.cpp:15:
../../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’:
genomeFile.cpp:61:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable]
61 | long c2;
| ^~
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
* compiling BamAncillary.cpp
In file included from BamAncillary.h:12,
from BamAncillary.cpp:12:
..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from BamAncillary.h:12,
from BamAncillary.cpp:12:
..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
- Building in src/lumpy
* compiling lumpy.cpp
* compiling SV_Pair.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack lumpy.cpp -o ../../obj//lumpy.o
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Pair.cpp -o ../../obj//SV_Pair.o
* compiling SV_Evidence.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Evidence.cpp -o ../../obj//SV_Evidence.o
* compiling SV_BreakPoint.cpp
* compiling SV_Bedpe.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BreakPoint.cpp -o ../../obj//SV_BreakPoint.o
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Bedpe.cpp -o ../../obj//SV_Bedpe.o
* compiling SV_SplitRead.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitRead.cpp -o ../../obj//SV_SplitRead.o
* compiling SV_SplitReadReader.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitReadReader.cpp -o ../../obj//SV_SplitReadReader.o
* compiling SV_PairReader.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_PairReader.cpp -o ../../obj//SV_PairReader.o
* compiling SV_BedpeReader.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BedpeReader.cpp -o ../../obj//SV_BedpeReader.o
* compiling SV_BamReader.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BamReader.cpp -o ../../obj//SV_BamReader.o
* compiling SV_InterChromBamReader.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_InterChromBamReader.cpp -o ../../obj//SV_InterChromBamReader.o
* compiling SV_EvidenceReader.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_EvidenceReader.cpp -o ../../obj//SV_EvidenceReader.o
* compiling SV_Tools.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Tools.cpp -o ../../obj//SV_Tools.o
* compiling SV_VcfVariant.cpp
* compiling log_space.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_VcfVariant.cpp -o ../../obj//SV_VcfVariant.o
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack log_space.cpp -o ../../obj//log_space.o
In file included from SV_BreakPoint.h:19,
from SV_Evidence.h:22,
from SV_Evidence.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from SV_BreakPoint.h:19,
from SV_BreakPoint.cpp:16:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from SV_EvidenceReader.h:20,
from SV_EvidenceReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from SV_BreakPoint.h:19,
from SV_SplitReadReader.h:22,
from SV_SplitReadReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from SV_BreakPoint.h:19,
from SV_Evidence.h:22,
from SV_Bedpe.h:18,
from SV_BedpeReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from SV_BreakPoint.h:19,
from SV_PairReader.h:22,
from SV_BamReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from SV_BreakPoint.h:19,
from SV_PairReader.h:22,
from SV_PairReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from SV_BreakPoint.h:19,
from SV_PairReader.h:22,
from SV_InterChromBamReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12,
from SV_Pair.cpp:15:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12,
from lumpy.cpp:20:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12,
from SV_SplitRead.cpp:15:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from SV_BreakPoint.h:19,
from SV_PairReader.h:22,
from SV_Pair.cpp:19:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
SV_BreakPoint.cpp: In member function ‘bool SV_BreakPoint::merge(SV_BreakPoint*)’:
SV_BreakPoint.cpp:266:33: warning: variable ‘a_overlap_intr’ set but not used [-Wunused-but-set-variable]
266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr;
| ^~~~~~~~~~~~~~
SV_BreakPoint.cpp:266:50: warning: variable ‘b_overlap_intr’ set but not used [-Wunused-but-set-variable]
266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr;
| ^~~~~~~~~~~~~~
In file included from SV_BreakPoint.h:19,
from SV_SplitReadReader.h:22,
from SV_SplitRead.cpp:19:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from SV_BreakPoint.h:19,
from SV_Evidence.h:22,
from lumpy.cpp:24:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
SV_Evidence.cpp: In member function ‘virtual void SV_Evidence::set_bp_interval_probability(breakpoint_interval*)’:
SV_Evidence.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
81 | for (j = 0; j < size; ++j) {
| ~~^~~~~~
In file included from SV_BreakPoint.h:19,
from SV_VcfVariant.h:18,
from SV_VcfVariant.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from ../utils//bedFilePE/bedFilePE.h:12,
from SV_SplitRead.h:27,
from SV_SplitReadReader.cpp:16:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from ../utils//bedFilePE/bedFilePE.h:12,
from SV_BedpeReader.h:23,
from SV_Bedpe.h:19:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from ../utils//bedFilePE/bedFilePE.h:12,
from SV_SplitRead.h:27,
from SV_BamReader.cpp:19:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from SV_Tools.h:19,
from SV_Tools.cpp:24:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12,
from SV_Bedpe.cpp:14:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from ../utils//bedFilePE/bedFilePE.h:12,
from SV_SplitRead.h:27,
from SV_InterChromBamReader.cpp:19:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from SV_BedpeReader.h:21,
from SV_Bedpe.cpp:17:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
SV_BamReader.cpp: In member function ‘virtual void SV_BamReader::process_input_chr_pos(std::string, CHR_POS, UCSCBins<SV_BreakPoint*>&)’:
SV_BamReader.cpp:208:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘CHR_POS’ {aka ‘long long unsigned int’} [-Wsign-compare]
208 | ( bam.Position < pos ) ) {
| ~~~~~~~~~~~~~^~~~~
../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS) [with T = SV_BreakPoint*; BIN = unsigned int; CHR_POS = long long unsigned int]’:
../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins<T>::add(std::string, CHR_POS, CHR_POS, char, T) [with T = SV_BreakPoint*; std::string = std::__cxx11::basic_string<char>; CHR_POS = long long unsigned int]’
SV_BreakPoint.cpp:1286:14: required from here
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
SV_SplitRead.cpp: In member function ‘bool SV_SplitRead::is_sane()’:
SV_SplitRead.cpp:538:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
538 | if ( min_mapping_quality < reader->min_mapping_threshold )
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from SV_Tools.cpp:27:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS) [with T = int; BIN = unsigned int; CHR_POS = long long unsigned int]’:
../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins<T>::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int; std::string = std::__cxx11::basic_string<char>; CHR_POS = long long unsigned int]’
SV_Tools.cpp:541:32: required from here
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
SV_BreakPoint.cpp: In static member function ‘static int SV_BreakPoint::get_product(std::vector<SV_BreakPoint*>&, CHR_POS*, CHR_POS*, CHR_POS*, CHR_POS*, log_space**, log_space**)’:
SV_BreakPoint.cpp:1662:41: warning: ‘r_max_i’ may be used uninitialized [-Wmaybe-uninitialized]
1662 | CHR_POS abs_max_r = m_start_r + r_max_i;
| ^~~~~~~
SV_BreakPoint.cpp:1643:34: note: ‘r_max_i’ was declared here
1643 | unsigned int i, l_max_i, r_max_i;
| ^~~~~~~
SV_BreakPoint.cpp:1650:41: warning: ‘l_max_i’ may be used uninitialized [-Wmaybe-uninitialized]
1650 | CHR_POS abs_max_l = m_start_l + l_max_i;
| ^~~~~~~
SV_BreakPoint.cpp:1643:25: note: ‘l_max_i’ was declared here
1643 | unsigned int i, l_max_i, r_max_i;
| ^~~~~~~
SV_Tools.cpp: In function ‘int read_distro_file(std::string, double**, int*, int*)’:
SV_Tools.cpp:156:14: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized]
156 | *end = last;
| ~~~~~^~~~~~
SV_Tools.cpp:143:13: note: ‘last’ was declared here
143 | int last;
| ^~~~
SV_SplitRead.cpp: In static member function ‘static void SV_SplitRead::process_split(const BamTools::BamAlignment&, BamTools::RefVector, std::map<std::__cxx11::basic_string<char>, BamTools::BamAlignment>&, UCSCBins<SV_BreakPoint*>&, int, int, SV_SplitReadReader*)’:
SV_SplitRead.cpp:653:25: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
653 | free(new_split_read);
| ~~~~^~~~~~~~~~~~~~~~
SV_SplitRead.cpp:641:41: note: returned from ‘void* operator new(std::size_t)’
641 | _reader);
| ^
* linking lumpy
g++ -Wl,-z,relro -Wl,-z,now -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -o ../../bin//lumpy ../../obj//lumpy.o ../../obj//SV_Pair.o ../../obj//SV_Evidence.o ../../obj//SV_BreakPoint.o ../../obj//SV_Bedpe.o ../../obj//SV_SplitRead.o ../../obj//SV_SplitReadReader.o ../../obj//SV_PairReader.o ../../obj//SV_BedpeReader.o ../../obj//SV_BamReader.o ../../obj//SV_InterChromBamReader.o ../../obj//SV_EvidenceReader.o ../../obj//SV_Tools.o ../../obj//SV_VcfVariant.o ../../obj//log_space.o ../../obj//BamAncillary.o ../../obj//sequenceUtils.o ../../obj//bedFilePE.o ../../obj//bedFile.o ../../obj//genomeFile.o ../../obj//fileType.o \
-L../utils//BamTools/lib/ -lbamtools \
-lz -L /build/lumpy-sv-0.3.1+dfsg/debian/.debhelper/generated/_source/home/src/zlib-1.2.8 \
-lgzstream -lz -lm -ldl -lpthread
make[1]: Verzeichnis „/build/lumpy-sv-0.3.1+dfsg“ wird verlassen
dh_auto_test
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
debian/rules override_dh_install
make[1]: Verzeichnis „/build/lumpy-sv-0.3.1+dfsg“ wird betreten
cat debian/missing-sources/pe.pos_sorted.sam |samtools view -Sb - > data/pe.pos_sorted.bam
cat debian/missing-sources/sr.pos_sorted.sam |samtools view -Sb - > data/sr.pos_sorted.bam
dh_install
rm -f debian/lumpy-sv*/usr/share/lumpy-sv/scripts/lumpyexpress.config
make[1]: Verzeichnis „/build/lumpy-sv-0.3.1+dfsg“ wird verlassen
dh_installdocs
dh_installchangelogs
dh_installman
debian/rules override_dh_python3
make[1]: Verzeichnis „/build/lumpy-sv-0.3.1+dfsg“ wird betreten
dh_python3 --shebang=/usr/bin/python3
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/bedpe_sort.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/check_sorting.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/cnvanator_to_bedpes.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/extractSplitReads_BwaMem
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/get_coverages.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/get_exclude_regions.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/l_merge.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/l_sort.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/pairend_distro.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/prob_bedpe_to_bedgraph.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/vcfToBedpe
make[1]: Verzeichnis „/build/lumpy-sv-0.3.1+dfsg“ wird verlassen
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dwz: debian/lumpy-sv/usr/bin/lumpy: DWARF compression not beneficial - old size 4451152 new size 4463816
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dpkg-gencontrol: warning: package lumpy-sv: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package lumpy-sv: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums
dh_builddeb
dpkg-deb: Paket »lumpy-sv-examples« wird in »../lumpy-sv-examples_0.3.1+dfsg-7_all.deb« gebaut.
dpkg-deb: Paket »lumpy-sv« wird in »../lumpy-sv_0.3.1+dfsg-7_i386.deb« gebaut.
dpkg-deb: Paket »lumpy-sv-dbgsym« wird in »../lumpy-sv-dbgsym_0.3.1+dfsg-7_i386.deb« gebaut.
dpkg-genbuildinfo --build=binary -O../lumpy-sv_0.3.1+dfsg-7_i386.buildinfo
dpkg-genchanges --build=binary -O../lumpy-sv_0.3.1+dfsg-7_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/125774/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/125774/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/125774 and its subdirectories
I: Current time: Thu Jun 13 00:36:32 +14 2024
I: pbuilder-time-stamp: 1718188592