Sat Apr 15 11:50:36 UTC 2023 I: starting to build snpomatic/bookworm/amd64 on jenkins on '2023-04-15 11:50'
Sat Apr 15 11:50:36 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_11/14653/console.log
Sat Apr 15 11:50:36 UTC 2023 I: Downloading source for bookworm/snpomatic=1.0-6
--2023-04-15 11:50:36-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/snpomatic/snpomatic_1.0-6.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2015 (2.0K) [text/prs.lines.tag]
Saving to: ‘snpomatic_1.0-6.dsc’
0K . 100% 102M=0s
2023-04-15 11:50:36 (102 MB/s) - ‘snpomatic_1.0-6.dsc’ saved [2015/2015]
Sat Apr 15 11:50:36 UTC 2023 I: snpomatic_1.0-6.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: snpomatic
Binary: snpomatic
Architecture: any
Version: 1.0-6
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Sascha Steinbiss <satta@debian.org>
Homepage: https://github.com/magnusmanske/snpomatic
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/snpomatic
Vcs-Git: https://salsa.debian.org/med-team/snpomatic.git
Testsuite: autopkgtest
Testsuite-Triggers: samtools
Build-Depends: debhelper-compat (= 13), asciidoctor, antiword
Package-List:
snpomatic deb science optional arch=any
Checksums-Sha1:
ce873229b63a44cf210a7c41ef866642bed72d1f 66546 snpomatic_1.0.orig.tar.gz
35a87bdedcc5a94805cdcaf39b6a80e5ba5226be 9816 snpomatic_1.0-6.debian.tar.xz
Checksums-Sha256:
b90123226e24edfa5c2ca296f9414b5aa005d3da77ad80b5c576adddbb38a094 66546 snpomatic_1.0.orig.tar.gz
934642fedc197dba7319f02870143d9a35e36bcbacad602d3198d8ee848463af 9816 snpomatic_1.0-6.debian.tar.xz
Files:
bac27c60847ad8036faafd7c9a335b5c 66546 snpomatic_1.0.orig.tar.gz
735ef54361edd4e8fbd41f8ef908c2ed 9816 snpomatic_1.0-6.debian.tar.xz
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Sat Apr 15 11:50:36 UTC 2023 I: Checking whether the package is not for us
Sat Apr 15 11:50:36 UTC 2023 I: Starting 1st build on remote node ionos1-amd64.debian.net.
Sat Apr 15 11:50:36 UTC 2023 I: Preparing to do remote build '1' on ionos1-amd64.debian.net.
Sat Apr 15 11:55:08 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Fri Apr 14 23:50:39 -12 2023
I: pbuilder-time-stamp: 1681559439
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: Copying source file
I: copying [snpomatic_1.0-6.dsc]
I: copying [./snpomatic_1.0.orig.tar.gz]
I: copying [./snpomatic_1.0-6.debian.tar.xz]
I: Extracting source
gpgv: Signature made Tue Feb 28 19:06:14 2023 -12
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 ./snpomatic_1.0-6.dsc: no acceptable signature found
dpkg-source: info: extracting snpomatic in snpomatic-1.0
dpkg-source: info: unpacking snpomatic_1.0.orig.tar.gz
dpkg-source: info: unpacking snpomatic_1.0-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_ungap
dpkg-source: info: applying hardening
dpkg-source: info: applying build_all_binaries
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1637784/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='e782ba0762dd4243a0eebac88f7c55ed'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='1637784'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.sDdImie3/pbuilderrc_QBks --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sDdImie3/b1 --logfile b1/build.log snpomatic_1.0-6.dsc'
SUDO_GID='110'
SUDO_UID='105'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://78.137.99.97:3128'
I: uname -a
Linux ionos1-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux
I: ls -l /bin
total 5632
-rwxr-xr-x 1 root root 1265648 Feb 12 08:05 bash
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 44016 Sep 20 2022 cat
-rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 72752 Sep 20 2022 chown
-rwxr-xr-x 1 root root 151152 Sep 20 2022 cp
-rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash
-rwxr-xr-x 1 root root 121904 Sep 20 2022 date
-rwxr-xr-x 1 root root 89240 Sep 20 2022 dd
-rwxr-xr-x 1 root root 102200 Sep 20 2022 df
-rwxr-xr-x 1 root root 151344 Sep 20 2022 dir
-rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname
-rwxr-xr-x 1 root root 43856 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep
-rwxr-xr-x 1 root root 35664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep
-rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt
-rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount
-rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname
-rwxr-xr-x 1 root root 72824 Sep 20 2022 ln
-rwxr-xr-x 1 root root 53024 Mar 23 00:40 login
-rwxr-xr-x 1 root root 151344 Sep 20 2022 ls
-rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk
-rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 59712 Mar 22 22:02 more
-rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount
-rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint
-rwxr-xr-x 1 root root 142968 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Feb 12 08:05 rbash -> bash
-rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 72752 Sep 20 2022 rm
-rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts
-rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed
lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash
-rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 85008 Sep 20 2022 stty
-rwsr-xr-x 1 root root 72000 Mar 22 22:02 su
-rwxr-xr-x 1 root root 39824 Sep 20 2022 sync
-rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar
-rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile
-rwxr-xr-x 1 root root 109616 Sep 20 2022 touch
-rwxr-xr-x 1 root root 35664 Sep 20 2022 true
-rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server
-rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount
-rwxr-xr-x 1 root root 43888 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/1637784/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: amd64
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), asciidoctor, antiword
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19596 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 asciidoctor; however:
Package asciidoctor is not installed.
pbuilder-satisfydepends-dummy depends on antiword; however:
Package antiword 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:
antiword{a} asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{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} libbsd0{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libruby{a} libruby3.1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} openssl{a} po-debconf{a} rake{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl fonts-lato libarchive-cpio-perl libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl lynx wget zip
0 packages upgraded, 50 newly installed, 0 to remove and 0 not upgraded.
Need to get 27.6 MB of archives. After unpacking 106 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.8-1 [1407 kB]
Get: 3 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB]
Get: 4 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get: 5 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get: 6 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get: 7 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get: 8 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 9 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get: 10 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get: 11 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get: 12 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get: 13 http://deb.debian.org/debian bookworm/main amd64 antiword amd64 0.37-16 [123 kB]
Get: 14 http://deb.debian.org/debian bookworm/main amd64 rubygems-integration all 1.18 [6704 B]
Get: 15 http://deb.debian.org/debian bookworm/main amd64 rake all 13.0.6-3 [83.9 kB]
Get: 16 http://deb.debian.org/debian bookworm/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB]
Get: 17 http://deb.debian.org/debian bookworm/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB]
Get: 18 http://deb.debian.org/debian bookworm/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB]
Get: 19 http://deb.debian.org/debian bookworm/main amd64 libruby amd64 1:3.1 [4972 B]
Get: 20 http://deb.debian.org/debian bookworm/main amd64 ruby-sdbm amd64 1.0.0-5+b1 [15.4 kB]
Get: 21 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB]
Get: 22 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB]
Get: 23 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-2 [103 kB]
Get: 24 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB]
Get: 25 http://deb.debian.org/debian bookworm/main amd64 libruby3.1 amd64 3.1.2-7 [5401 kB]
Get: 26 http://deb.debian.org/debian bookworm/main amd64 ruby3.1 amd64 3.1.2-7 [663 kB]
Get: 27 http://deb.debian.org/debian bookworm/main amd64 ruby-rubygems all 3.3.15-2 [293 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 ruby amd64 1:3.1 [5868 B]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 ruby-asciidoctor all 2.0.18-2 [211 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 asciidoctor all 2.0.18-2 [86.6 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 35 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 36 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 37 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 38 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 39 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 40 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 41 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 42 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 43 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 44 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 45 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 46 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB]
Get: 47 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 48 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 49 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 50 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Fetched 27.6 MB in 2s (17.9 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
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(Reading database ... 100%
(Reading database ... 19596 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package openssl.
Preparing to unpack .../01-openssl_3.0.8-1_amd64.deb ...
Unpacking openssl (3.0.8-1) ...
Selecting previously unselected package ca-certificates.
Preparing to unpack .../02-ca-certificates_20230311_all.deb ...
Unpacking ca-certificates (20230311) ...
Selecting previously unselected package libmagic-mgc.
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/snpomatic-1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../snpomatic_1.0-6_source.changes
dpkg-buildpackage: info: source package snpomatic
dpkg-buildpackage: info: source version 1.0-6
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 amd64
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/snpomatic-1.0'
/usr/bin/make clean
make[2]: Entering directory '/build/snpomatic-1.0'
rm -f *.o
rm -f src/*.o
rm -f findknownsnps
rm -f variety
make[2]: Leaving directory '/build/snpomatic-1.0'
rm -rf debian/findknownsnps.1
rm -rf debian/findknownsnps.1.html
rm -f mapcontigs reassemble ungap
dh_auto_clean --
make -j15 clean
make[2]: Entering directory '/build/snpomatic-1.0'
rm -f *.o
rm -f src/*.o
rm -f findknownsnps
rm -f variety
make[2]: Leaving directory '/build/snpomatic-1.0'
make[1]: Leaving directory '/build/snpomatic-1.0'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/snpomatic.substvars debian/files
rm -fr -- debian/snpomatic/ debian/tmp/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
dh_auto_build
make -j15 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/snpomatic-1.0'
g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/findknownsnps.cpp -o src/findknownsnps.o
g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/global_functions.cpp -o src/global_functions.o
g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosome.cpp -o src/TChromosome.o
g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomalIndices.cpp -o src/TChromosomalIndices.o
g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TAlignmentOutput.cpp -o src/TAlignmentOutput.o
g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomeAlign.cpp -o src/TChromosomeAlign.o
g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/reassemble.cpp -o src/reassemble.o
g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/variety.cpp -o src/variety.o
g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/mapcontigs.cpp -o src/mapcontigs.o
g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/ungap.cpp -o src/ungap.o
src/TChromosome.cpp: In member function 'void TChromosome::read_chromosome(std::string, std::string)':
src/TChromosome.cpp:41:54: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wformat=]
41 | if ( DEBUGGING ) { fprintf ( stdout , "read %d nucleotides.\n" , sequence.length() ) ; fflush(stdout); }
| ~^ ~~~~~~~~~~~~~~~~~
| | |
| int std::__cxx11::basic_string<char>::size_type {aka long unsigned int}
| %ld
src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run(chrvec*)':
src/TChromosomalIndices.cpp:262:87: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector<TChromosome>::size_type' {aka 'long unsigned int'} [-Wformat=]
262 | if ( index_from == 0 && index_to == 0 ) fprintf ( stdout , "Indexing %d chromosomes ... " , chrs->size() ) ;
| ~^ ~~~~~~~~~~~~
| | |
| int std::vector<TChromosome>::size_type {aka long unsigned int}
| %ld
src/TChromosomalIndices.cpp:263:52: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector<TChromosome>::size_type' {aka 'long unsigned int'} [-Wformat=]
263 | else fprintf ( stdout , "Indexing %d chromosomes (%d-%d) ... " , chrs->size() , index_from , index_to ) ;
| ~^ ~~~~~~~~~~~~
| | |
| int std::vector<TChromosome>::size_type {aka long unsigned int}
| %ld
src/TChromosome.cpp:13:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
13 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps_gff(std::string)':
src/TChromosome.cpp:54:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
54 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::init()':
src/TChromosomeAlign.cpp:83:58: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wformat=]
83 | fprintf ( sam , "@SQ\tSN:%s\tLN:%d\n" , (*chrs)[i].name.c_str() , (*chrs)[i].sequence.length() ) ;
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int std::__cxx11::basic_string<char>::size_type {aka long unsigned int}
| %ld
src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps(std::string)':
src/TChromosome.cpp:95:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
95 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/global_functions.cpp: In function 'void load_all_chromosomes(std::string, std::vector<TChromosome>&, bool)':
src/global_functions.cpp:146:54: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector<TChromosome>::size_type' {aka 'long unsigned int'} [-Wformat=]
146 | if ( DEBUGGING ) { fprintf ( stdout , "read %d chromosomes.\n" , chrs.size() ) ; fflush(stdout); }
| ~^ ~~~~~~~~~~~
| | |
| int std::vector<TChromosome>::size_type {aka long unsigned int}
| %ld
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::finish_sqlite(int, int, int)':
src/TChromosomeAlign.cpp:956:98: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wformat=]
956 | fprintf ( sqlite , "INSERT INTO chromosomes ( name , size ) VALUES ( \"%s\" , \"%d\") ;\n" , (*chrs)[a].name.c_str() , (*chrs)[a].sequence.length() ) ;
| ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| int std::__cxx11::basic_string<char>::size_type {aka long unsigned int}
| %ld
src/global_functions.cpp:116:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
116 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/global_functions.cpp: In function 'void incorporate_all_gff(std::string, std::vector<TChromosome>&)':
src/global_functions.cpp:165:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
165 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/global_functions.cpp: In function 'void incorporate_simple_snps(std::string, std::vector<TChromosome>&)':
src/global_functions.cpp:220:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
220 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_reads(std::string)':
src/TChromosomalIndices.cpp:33:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
33 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:37:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
37 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::reassemble_reads(FILE*, uint, index2type, index2type)':
src/TChromosomalIndices.cpp:126:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
126 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:127:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
127 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_regions(chrvec*, std::string)':
src/TChromosomalIndices.cpp:167:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
167 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::load_index(std::string)':
src/TChromosomalIndices.cpp:409:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
409 | fread ( &temp , sizeof ( temp ) , 1 , file ) ; // Version
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:410:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
410 | fread ( &temp , sizeof ( temp ) , 1 , file ) ; // position size
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:415:23: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
415 | fread ( &temp , sizeof ( temp ) , 1 , file ) ; // Sub-index size
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:419:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
419 | fread ( &i.index2 , sizeof ( i.index2 ) , 1 , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:420:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
420 | fread ( &i.position , sizeof ( i.position ) , 1 , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:421:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
421 | fread ( &i.chromosome , sizeof ( i.chromosome ) , 1 , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomalIndices.cpp:422:31: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
422 | fread ( &i.reverse_complement , sizeof ( i.reverse_complement ) , 1 , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::add_cigar_sqlite(const std::string&, const std::string&, uint, uint, char)':
src/TChromosomeAlign.cpp:1583:43: warning: format '%d' expects argument of type 'int', but argument 5 has type 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wformat=]
1583 | fprintf ( cigar , "%s %d %d %c %s %d %d + %d %s\n" ,
| ~^
| |
| int
| %ld
......
1586 | sequence.length() , // Read end
| ~~~~~~~~~~~~~~~~~
| |
| std::__cxx11::basic_string<char>::size_type {aka long unsigned int}
src/TChromosomeAlign.cpp:1583:55: warning: format '%d' expects argument of type 'int', but argument 9 has type 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wformat=]
1583 | fprintf ( cigar , "%s %d %d %c %s %d %d + %d %s\n" ,
| ~^
| |
| int
| %ld
......
1590 | position + sequence.length() , // End on chromosome
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| std::__cxx11::basic_string<char>::size_type {aka long unsigned int}
src/reassemble.cpp: In function 'void read_fastq(std::string, std::vector<TRead>&, int)':
src/reassemble.cpp:319:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
319 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::add_nono_list(std::string)':
src/TChromosomeAlign.cpp:93:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
93 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::finish_sqlite(int, int, int)':
src/TChromosomeAlign.cpp:972:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
972 | fgets ( dummy , READ_CHAR_BUFFER , sqlite_cache ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_paired(std::string, std::string, uint, uint, uint)':
src/TChromosomeAlign.cpp:1070:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1070 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp:1075:39: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1075 | fgets ( c1 , READ_CHAR_BUFFER , file2 ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_fastq(std::string)':
src/TChromosomeAlign.cpp:1296:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1296 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp:1306:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1306 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp:1316:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1316 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp:1325:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1325 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_fasta(std::string)':
src/TChromosomeAlign.cpp:1374:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1374 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_fastq_variety(std::string)':
src/TChromosomeAlign.cpp:1628:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1628 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp:1637:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1637 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp:1647:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1647 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/TChromosomeAlign.cpp:1655:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1655 | fgets ( dummy , READ_CHAR_BUFFER , file ) ;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/findknownsnps.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o findknownsnps
g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/reassemble.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o reassemble
g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/variety.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o variety
g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/mapcontigs.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o mapcontigs
g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/ungap.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o ungap
make[1]: Leaving directory '/build/snpomatic-1.0'
dh_auto_test
rm -fr -- /tmp/dh-xdg-rundir-SQPnPr7V
create-stamp debian/debhelper-build-stamp
dh_prep
rm -f -- debian/snpomatic.substvars
rm -fr -- debian/.debhelper/generated/snpomatic/ debian/snpomatic/ debian/tmp/
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/snpomatic-1.0'
mkdir -p /build/snpomatic-1.0/debian/snpomatic/usr/bin
install -p findknownsnps /build/snpomatic-1.0/debian/snpomatic/usr/bin
# -- we don't install the others as they seem unmaintained/undocumented
#cp reassemble /build/snpomatic-1.0/debian/snpomatic/usr/bin
#cp variety /build/snpomatic-1.0/debian/snpomatic/usr/bin
#cp mapcontigs /build/snpomatic-1.0/debian/snpomatic/usr/bin
#cp ungap /build/snpomatic-1.0/debian/snpomatic/usr/bin
make[1]: Leaving directory '/build/snpomatic-1.0'
debian/rules override_dh_installdocs
make[1]: Entering directory '/build/snpomatic-1.0'
antiword doc/Manual.doc > doc/Manual.txt
mkdir -p debian/snpomatic/usr/share/doc/snpomatic
cp doc/Manual.txt debian/snpomatic/usr/share/doc/snpomatic
dh_installdocs --
install -p -m0644 debian/copyright debian/snpomatic/usr/share/doc/snpomatic/copyright
install -m0755 -d debian/snpomatic/usr/share/doc-base/
install -p -m0644 debian/doc-base debian/snpomatic/usr/share/doc-base/snpomatic.snpomatic
make[1]: Leaving directory '/build/snpomatic-1.0'
dh_installchangelogs
install -m0755 -d debian/snpomatic/usr/share/doc/snpomatic
install -p -m0644 debian/.debhelper/generated/snpomatic/dh_installchangelogs.dch.trimmed debian/snpomatic/usr/share/doc/snpomatic/changelog.Debian
rm -f debian/snpomatic.debhelper.log
debian/rules override_dh_installman
make[1]: Entering directory '/build/snpomatic-1.0'
asciidoctor -a docdate='' -b manpage debian/findknownsnps.1.adoc
dh_installman --
install -m0755 -d debian/snpomatic/usr/share/man/man1/
install -p -m0644 ./debian/findknownsnps.1 debian/snpomatic/usr/share/man/man1/findknownsnps.1
man-recode --to-code UTF-8 --suffix .dh-new debian/snpomatic/usr/share/man/man1/findknownsnps.1
mv debian/snpomatic/usr/share/man/man1/findknownsnps.1.dh-new debian/snpomatic/usr/share/man/man1/findknownsnps.1
chmod 0644 -- debian/snpomatic/usr/share/man/man1/findknownsnps.1
make[1]: Leaving directory '/build/snpomatic-1.0'
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
cd debian/snpomatic
chmod a-x usr/share/doc/snpomatic/Manual.txt usr/share/doc/snpomatic/changelog.Debian usr/share/man/man1/findknownsnps.1
gzip -9nf usr/share/doc/snpomatic/Manual.txt usr/share/doc/snpomatic/changelog.Debian usr/share/man/man1/findknownsnps.1
cd '/build/snpomatic-1.0'
dh_fixperms
find debian/snpomatic ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/snpomatic/usr/share/doc -type f -a -true -a ! -regex 'debian/snpomatic/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/snpomatic/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/snpomatic/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/snpomatic -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/snpomatic/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
dh_missing
dh_dwz -a
dwz -- debian/snpomatic/usr/bin/findknownsnps
dh_strip -a
install -m0755 -d debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/3b
objcopy --only-keep-debug --compress-debug-sections debian/snpomatic/usr/bin/findknownsnps debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/3b/810963cbbd5564cdeb1502b187405d8f3448f0.debug
chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/3b/810963cbbd5564cdeb1502b187405d8f3448f0.debug
strip --remove-section=.comment --remove-section=.note debian/snpomatic/usr/bin/findknownsnps
objcopy --add-gnu-debuglink debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/3b/810963cbbd5564cdeb1502b187405d8f3448f0.debug debian/snpomatic/usr/bin/findknownsnps
install -m0755 -d debian/.debhelper/snpomatic/dbgsym-root/usr/share/doc
ln -s snpomatic debian/.debhelper/snpomatic/dbgsym-root/usr/share/doc/snpomatic-dbgsym
install -m0755 -d debian/.debhelper/snpomatic
dh_makeshlibs -a
rm -f debian/snpomatic/DEBIAN/shlibs
dh_shlibdeps -a
install -m0755 -d debian/snpomatic/DEBIAN
dpkg-shlibdeps -Tdebian/snpomatic.substvars debian/snpomatic/usr/bin/findknownsnps
dh_installdeb
install -m0755 -d debian/snpomatic/DEBIAN
dh_gencontrol
install -m0755 -d debian/snpomatic/DEBIAN
echo misc:Depends= >> debian/snpomatic.substvars
echo misc:Pre-Depends= >> debian/snpomatic.substvars
install -m0755 -d debian/.debhelper/snpomatic/dbgsym-root/DEBIAN
dpkg-gencontrol -psnpomatic -ldebian/changelog -Tdebian/snpomatic.substvars -Pdebian/.debhelper/snpomatic/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=snpomatic-dbgsym "-DDepends=snpomatic (= \${binary:Version})" "-DDescription=debug symbols for snpomatic" -DBuild-Ids=3b810963cbbd5564cdeb1502b187405d8f3448f0 -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/DEBIAN/control
dpkg-gencontrol -psnpomatic -ldebian/changelog -Tdebian/snpomatic.substvars -Pdebian/snpomatic
chmod 0644 -- debian/snpomatic/DEBIAN/control
dh_md5sums
install -m0755 -d debian/snpomatic/DEBIAN
cd debian/snpomatic >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/snpomatic/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/snpomatic/dbgsym-root/DEBIAN
cd debian/.debhelper/snpomatic/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/DEBIAN/md5sums
dh_builddeb
dpkg-deb --root-owner-group --build debian/snpomatic ..
dpkg-deb --root-owner-group --build debian/.debhelper/snpomatic/dbgsym-root ..
dpkg-deb: building package 'snpomatic-dbgsym' in '../snpomatic-dbgsym_1.0-6_amd64.deb'.
dpkg-deb: building package 'snpomatic' in '../snpomatic_1.0-6_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../snpomatic_1.0-6_amd64.buildinfo
dpkg-genchanges --build=binary -O../snpomatic_1.0-6_amd64.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: 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/1637784 and its subdirectories
I: Current time: Fri Apr 14 23:55:06 -12 2023
I: pbuilder-time-stamp: 1681559706
Sat Apr 15 11:55:08 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net.
Sat Apr 15 11:55:08 UTC 2023 I: Preparing to do remote build '2' on ionos15-amd64.debian.net.
Sat Apr 15 11:55:47 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net.
Sat Apr 15 11:55:48 UTC 2023 I: snpomatic_1.0-6_amd64.changes:
Format: 1.8
Date: Wed, 01 Mar 2023 08:01:21 +0100
Source: snpomatic
Binary: snpomatic snpomatic-dbgsym
Architecture: amd64
Version: 1.0-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
snpomatic - fast, stringent short-read mapping software
Changes:
snpomatic (1.0-6) unstable; urgency=medium
.
* Team upload.
.
[ Anatoliy Gunya ]
* Do not create two identical doc-base files
.
[ Andreas Tille ]
* Standards-Version: 4.6.2 (routine-update)
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Update watch file format version to 4.
* Set upstream metadata fields: Repository, Repository-Browse.
Checksums-Sha1:
0ad4118e6960f4d3a28c274850cb0cdd392b93f3 1011336 snpomatic-dbgsym_1.0-6_amd64.deb
cab8145369f8370c65e4d04af31ce92a25fcfabb 5628 snpomatic_1.0-6_amd64.buildinfo
716e462ef5ea61de5460d339b1ecbee43f3407aa 85092 snpomatic_1.0-6_amd64.deb
Checksums-Sha256:
d98eb6375c697585d73ab266595f24e589eb9433a25a7c3a740794295a49eec6 1011336 snpomatic-dbgsym_1.0-6_amd64.deb
799ba2709b0d82bfadd0b2af7a0d4fd07dd08e6d6679914a097a575ee3e3d5f0 5628 snpomatic_1.0-6_amd64.buildinfo
2d72c8f92be32bd7eae555538613c4938d119517b6cdeab1b3c47e54b829a061 85092 snpomatic_1.0-6_amd64.deb
Files:
7e577af713b04854103ec0e89715f41a 1011336 debug optional snpomatic-dbgsym_1.0-6_amd64.deb
7c7448468dce0148736212aced369a83 5628 science optional snpomatic_1.0-6_amd64.buildinfo
e7e4158a9b7470fdcfaad5cae18150b5 85092 science optional snpomatic_1.0-6_amd64.deb
Sat Apr 15 11:55:49 UTC 2023 I: diffoscope 240 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.sDdImie3/snpomatic_1.0-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.sDdImie3/snpomatic_1.0-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.sDdImie3/snpomatic_1.0-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.sDdImie3/b1/snpomatic_1.0-6_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.sDdImie3/b2/snpomatic_1.0-6_amd64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.337s)
0.337s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.028s)
0.028s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Sat Apr 15 11:55:50 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists.
Sat Apr 15 11:55:50 UTC 2023 I: snpomatic from bookworm built successfully and reproducibly on amd64.
Sat Apr 15 11:55:52 UTC 2023 I: Submitting .buildinfo files to external archives:
Sat Apr 15 11:55:52 UTC 2023 I: Submitting 8.0K b1/snpomatic_1.0-6_amd64.buildinfo.asc
Sat Apr 15 11:55:53 UTC 2023 I: Submitting 8.0K b2/snpomatic_1.0-6_amd64.buildinfo.asc
Sat Apr 15 11:55:55 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sat Apr 15 11:55:55 UTC 2023 I: Done submitting .buildinfo files.
Sat Apr 15 11:55:55 UTC 2023 I: Removing signed snpomatic_1.0-6_amd64.buildinfo.asc files:
removed './b1/snpomatic_1.0-6_amd64.buildinfo.asc'
removed './b2/snpomatic_1.0-6_amd64.buildinfo.asc'