Wed Dec 29 16:58:06 UTC 2021 I: starting to build minimac4/bullseye/amd64 on jenkins on '2021-12-29 16:57'
Wed Dec 29 16:58:06 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_12/98856/console.log
Wed Dec 29 16:58:06 UTC 2021 I: Downloading source for bullseye/minimac4=1.0.2-2
--2021-12-29 16:58:07-- http://cdn-fastly.deb.debian.org/debian/pool/main/m/minimac4/minimac4_1.0.2-2.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2008 (2.0K)
Saving to: ‘minimac4_1.0.2-2.dsc’
0K . 100% 178M=0s
2021-12-29 16:58:07 (178 MB/s) - ‘minimac4_1.0.2-2.dsc’ saved [2008/2008]
Wed Dec 29 16:58:07 UTC 2021 I: minimac4_1.0.2-2.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: minimac4
Binary: minimac4
Architecture: any
Version: 1.0.2-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Dylan Aïssi <daissi@debian.org>
Homepage: https://genome.sph.umich.edu/wiki/Minimac4
Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/minimac4
Vcs-Git: https://salsa.debian.org/med-team/minimac4.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 12), cmake, zlib1g-dev, libstatgen-dev
Package-List:
minimac4 deb science optional arch=any
Checksums-Sha1:
7ab0bf412d7c828adf95b88b8f4039a502504fd4 87759 minimac4_1.0.2.orig.tar.gz
44bfdb0de23b7da5f0ec8c8e3df8d593c9d2640d 1220608 minimac4_1.0.2-2.debian.tar.xz
Checksums-Sha256:
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d515cdbc1a48a504f8cc33d2520e15fde6fc519e202352192d4ae538e25fdf3e 1220608 minimac4_1.0.2-2.debian.tar.xz
Files:
ed40a971d4c32ea1e048a3283f8d4b10 87759 minimac4_1.0.2.orig.tar.gz
5e721b4113b28b1150356cd1c778e5d8 1220608 minimac4_1.0.2-2.debian.tar.xz
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Wed Dec 29 16:58:07 UTC 2021 I: Checking whether the package is not for us
Wed Dec 29 16:58:07 UTC 2021 I: Starting 1st build on remote node ionos15-amd64.debian.net.
Wed Dec 29 16:58:07 UTC 2021 I: Preparing to do remote build '1' on ionos15-amd64.debian.net.
Wed Dec 29 17:02:54 UTC 2021 I: Deleting $TMPDIR on ionos15-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Tue Jan 31 11:21:09 -12 2023
I: pbuilder-time-stamp: 1675207269
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz]
I: copying local configuration
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 [minimac4_1.0.2-2.dsc]
I: copying [./minimac4_1.0.2.orig.tar.gz]
I: copying [./minimac4_1.0.2-2.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.HjSjPj0j/trustedkeys.kbx': General error
gpgv: Signature made Tue Nov 5 08:36:50 2019 -12
gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54
gpgv: issuer "daissi@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./minimac4_1.0.2-2.dsc
dpkg-source: info: extracting minimac4 in minimac4-1.0.2
dpkg-source: info: unpacking minimac4_1.0.2.orig.tar.gz
dpkg-source: info: unpacking minimac4_1.0.2-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying Fix_spelling_error.patch
dpkg-source: info: applying Fix_reproducible_builds.patch
dpkg-source: info: applying Use_shared_zlib.patch
I: using fakeroot in build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/3210435/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,-fixfilepath parallel=16'
DISTRIBUTION=''
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='ee86235330784199aeb07aa2364a2788'
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='3210435'
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/tmp.uofEvoM9mE/pbuilderrc_HsnK --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.uofEvoM9mE/b1 --logfile b1/build.log minimac4_1.0.2-2.dsc'
SUDO_GID='111'
SUDO_UID='106'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://85.184.249.68:3128'
I: uname -a
Linux ionos15-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux
I: ls -l /bin
total 5476
-rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash
-rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2
-rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep
-rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2
-rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore
-rwxr-xr-x 1 root root 43936 Sep 23 2020 cat
-rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp
-rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod
-rwxr-xr-x 1 root root 72672 Sep 23 2020 chown
-rwxr-xr-x 1 root root 151168 Sep 23 2020 cp
-rwxr-xr-x 1 root root 125560 Dec 10 2020 dash
-rwxr-xr-x 1 root root 113664 Sep 23 2020 date
-rwxr-xr-x 1 root root 80968 Sep 23 2020 dd
-rwxr-xr-x 1 root root 93936 Sep 23 2020 df
-rwxr-xr-x 1 root root 147176 Sep 23 2020 dir
-rwxr-xr-x 1 root root 84440 Jul 28 2021 dmesg
lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname
-rwxr-xr-x 1 root root 39712 Sep 23 2020 echo
-rwxr-xr-x 1 root root 28 Nov 9 2020 egrep
-rwxr-xr-x 1 root root 39680 Sep 23 2020 false
-rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep
-rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt
-rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount
-rwxr-xr-x 1 root root 203072 Nov 9 2020 grep
-rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip
-rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe
-rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip
-rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname
-rwxr-xr-x 1 root root 72840 Sep 23 2020 ln
-rwxr-xr-x 1 root root 56952 Feb 7 2020 login
-rwxr-xr-x 1 root root 147176 Sep 23 2020 ls
-rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk
-rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir
-rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod
-rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp
-rwxr-xr-x 1 root root 59632 Jul 28 2021 more
-rwsr-xr-x 1 root root 55528 Jul 28 2021 mount
-rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint
-rwxr-xr-x 1 root root 147080 Sep 23 2020 mv
lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd
lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash
-rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink
-rwxr-xr-x 1 root root 72704 Sep 23 2020 rm
-rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir
-rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts
-rwxr-xr-x 1 root root 122224 Dec 22 2018 sed
lrwxrwxrwx 1 root root 4 Jan 23 03:47 sh -> dash
-rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep
-rwxr-xr-x 1 root root 84928 Sep 23 2020 stty
-rwsr-xr-x 1 root root 71912 Jul 28 2021 su
-rwxr-xr-x 1 root root 39744 Sep 23 2020 sync
-rwxr-xr-x 1 root root 531928 Feb 16 2021 tar
-rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile
-rwxr-xr-x 1 root root 101408 Sep 23 2020 touch
-rwxr-xr-x 1 root root 39680 Sep 23 2020 true
-rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server
-rwsr-xr-x 1 root root 35040 Jul 28 2021 umount
-rwxr-xr-x 1 root root 39744 Sep 23 2020 uname
-rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress
-rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir
-rwxr-xr-x 1 root root 63744 Jul 28 2021 wdctl
lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat
-rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp
-rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff
-rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep
-rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep
-rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce
-rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep
-rwxr-xr-x 1 root root 2206 Mar 2 2021 zless
-rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore
-rwxr-xr-x 1 root root 4553 Mar 2 2021 znew
I: user script /srv/workspace/pbuilder/3210435/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 (= 12), cmake, zlib1g-dev, libstatgen-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19655 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 (= 12); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on cmake; however:
Package cmake is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libstatgen-dev; however:
Package libstatgen-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{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} libarchive13{a} libbrotli1{a} libcurl4{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libjsoncpp24{a} libldap-2.4-2{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps8{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libstatgen-dev{a} libstatgen0{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{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 psmisc publicsuffix wget
0 packages upgraded, 53 newly installed, 0 to remove and 0 not upgraded.
Need to get 29.1 MB of archives. After unpacking 110 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB]
Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB]
Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB]
Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB]
Get: 6 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB]
Get: 7 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB]
Get: 8 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB]
Get: 9 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB]
Get: 10 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB]
Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB]
Get: 12 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB]
Get: 13 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB]
Get: 14 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB]
Get: 15 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB]
Get: 16 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB]
Get: 17 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get: 18 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB]
Get: 19 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB]
Get: 20 http://deb.debian.org/debian bullseye/main amd64 cmake-data all 3.18.4-2+deb11u1 [1725 kB]
Get: 21 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB]
Get: 22 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB]
Get: 23 http://deb.debian.org/debian bullseye/main amd64 libarchive13 amd64 3.4.3-2+b1 [343 kB]
Get: 24 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB]
Get: 25 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB]
Get: 26 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB]
Get: 27 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB]
Get: 28 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB]
Get: 29 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB]
Get: 30 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB]
Get: 31 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB]
Get: 32 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u1 [341 kB]
Get: 33 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB]
Get: 34 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp24 amd64 1.9.4-4 [78.9 kB]
Get: 35 http://deb.debian.org/debian bullseye/main amd64 librhash0 amd64 1.4.1-2 [129 kB]
Get: 36 http://deb.debian.org/debian bullseye/main amd64 libuv1 amd64 1.40.0-2 [132 kB]
Get: 37 http://deb.debian.org/debian bullseye/main amd64 cmake amd64 3.18.4-2+deb11u1 [5593 kB]
Get: 38 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB]
Get: 39 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB]
Get: 40 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 41 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 42 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB]
Get: 43 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get: 44 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get: 45 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB]
Get: 46 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB]
Get: 47 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB]
Get: 48 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get: 49 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 50 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB]
Get: 51 http://deb.debian.org/debian bullseye/main amd64 libstatgen0 amd64 1.0.14-7 [315 kB]
Get: 52 http://deb.debian.org/debian bullseye/main amd64 libstatgen-dev amd64 1.0.14-7 [121 kB]
Get: 53 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB]
Fetched 29.1 MB in 1s (43.5 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package bsdextrautils.
(Reading database ...
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fakeroot is already the newest version (1.25.3-1.1).
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I: Building the package
I: Running cd /build/minimac4-1.0.2/ && 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 > ../minimac4_1.0.2-2_source.changes
dpkg-buildpackage: info: source package minimac4
dpkg-buildpackage: info: source version 1.0.2-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Dylan Aïssi <daissi@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
fakeroot debian/rules clean
dh clean
dh_clean
debian/rules build
dh build
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu ..
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
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-- Found OpenMP_C: -fopenmp (found version "4.5")
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-- Found OpenMP: TRUE (found version "4.5")
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11")
-- Configuring done
-- Generating done
CMake Warning:
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CMAKE_EXPORT_NO_PACKAGE_REGISTRY
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dh_auto_build
cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1
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/usr/bin/c++ -DDATE=\"2019-11-05\" -DUSER=\"Reproducible\" -DVERSION=\"1.0.2\" -g -O2 -fdebug-prefix-map=/build/minimac4-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -fopenmp -std=gnu++11 -o CMakeFiles/minimac4.dir/src/Main.cpp.o -c /build/minimac4-1.0.2/src/Main.cpp
/usr/bin/c++ -DDATE=\"2019-11-05\" -DUSER=\"Reproducible\" -DVERSION=\"1.0.2\" -g -O2 -fdebug-prefix-map=/build/minimac4-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -fopenmp -std=gnu++11 -o CMakeFiles/minimac4.dir/src/MarkovModel.cpp.o -c /build/minimac4-1.0.2/src/MarkovModel.cpp
/usr/bin/c++ -DDATE=\"2019-11-05\" -DUSER=\"Reproducible\" -DVERSION=\"1.0.2\" -g -O2 -fdebug-prefix-map=/build/minimac4-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -fopenmp -std=gnu++11 -o CMakeFiles/minimac4.dir/src/MarkovParameters.cpp.o -c /build/minimac4-1.0.2/src/MarkovParameters.cpp
[ 83%] Building CXX object CMakeFiles/minimac4.dir/src/Unique.cpp.o
/usr/bin/c++ -DDATE=\"2019-11-05\" -DUSER=\"Reproducible\" -DVERSION=\"1.0.2\" -g -O2 -fdebug-prefix-map=/build/minimac4-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -fopenmp -std=gnu++11 -o CMakeFiles/minimac4.dir/src/Unique.cpp.o -c /build/minimac4-1.0.2/src/Unique.cpp
[ 91%] Building CXX object CMakeFiles/minimac4.dir/src/Estimation.cpp.o
/usr/bin/c++ -DDATE=\"2019-11-05\" -DUSER=\"Reproducible\" -DVERSION=\"1.0.2\" -g -O2 -fdebug-prefix-map=/build/minimac4-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -fopenmp -std=gnu++11 -o CMakeFiles/minimac4.dir/src/Estimation.cpp.o -c /build/minimac4-1.0.2/src/Estimation.cpp
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from /usr/include/libStatGen/InputFile.h:23,
from /usr/include/libStatGen/StringBasics.h:36,
from /build/minimac4-1.0.2/src/MyVariables.h:5,
from /build/minimac4-1.0.2/src/Main.cpp:6:
In function 'char* strcpy(char*, const char*)',
inlined from 'void OutputFormatVariable::CreateCommandLine(int, char**)' at /build/minimac4-1.0.2/src/MyVariables.h:190:11:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:90:33: warning: 'char* __builtin_strcpy(char*, const char*)' writing 1 or more bytes into a region of size 0 overflows the destination [-Wstringop-overflow=]
90 | return __builtin___strcpy_chk (__dest, __src, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[100%] Linking CXX executable minimac4
/usr/bin/cmake -E cmake_link_script CMakeFiles/minimac4.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/minimac4-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libStatGen -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/minimac4.dir/src/Analysis.cpp.o CMakeFiles/minimac4.dir/src/AnalysisChunks.cpp.o CMakeFiles/minimac4.dir/src/DosageData.cpp.o CMakeFiles/minimac4.dir/src/HaplotypeSet.cpp.o CMakeFiles/minimac4.dir/src/Imputation.cpp.o CMakeFiles/minimac4.dir/src/ImputationStatistics.cpp.o CMakeFiles/minimac4.dir/src/Main.cpp.o CMakeFiles/minimac4.dir/src/MarkovModel.cpp.o CMakeFiles/minimac4.dir/src/MarkovParameters.cpp.o CMakeFiles/minimac4.dir/src/Unique.cpp.o CMakeFiles/minimac4.dir/src/Estimation.cpp.o -o minimac4 -lStatGen -lz
make[3]: Leaving directory '/build/minimac4-1.0.2/obj-x86_64-linux-gnu'
[100%] Built target minimac4
make[2]: Leaving directory '/build/minimac4-1.0.2/obj-x86_64-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /build/minimac4-1.0.2/obj-x86_64-linux-gnu/CMakeFiles 0
make[1]: Leaving directory '/build/minimac4-1.0.2/obj-x86_64-linux-gnu'
dh_auto_test
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary
dh binary
dh_testroot
dh_prep
dh_auto_install
cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/minimac4-1.0.2/debian/minimac4 AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/minimac4-1.0.2/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/build/minimac4-1.0.2 -B/build/minimac4-1.0.2/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /build/minimac4-1.0.2/obj-x86_64-linux-gnu/CMakeFiles /build/minimac4-1.0.2/obj-x86_64-linux-gnu//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/build/minimac4-1.0.2/obj-x86_64-linux-gnu'
make -f CMakeFiles/minimac4.dir/build.make CMakeFiles/minimac4.dir/depend
make[3]: Entering directory '/build/minimac4-1.0.2/obj-x86_64-linux-gnu'
cd /build/minimac4-1.0.2/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/minimac4-1.0.2 /build/minimac4-1.0.2 /build/minimac4-1.0.2/obj-x86_64-linux-gnu /build/minimac4-1.0.2/obj-x86_64-linux-gnu /build/minimac4-1.0.2/obj-x86_64-linux-gnu/CMakeFiles/minimac4.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/build/minimac4-1.0.2/obj-x86_64-linux-gnu'
make -f CMakeFiles/minimac4.dir/build.make CMakeFiles/minimac4.dir/build
make[3]: Entering directory '/build/minimac4-1.0.2/obj-x86_64-linux-gnu'
make[3]: Nothing to be done for 'CMakeFiles/minimac4.dir/build'.
make[3]: Leaving directory '/build/minimac4-1.0.2/obj-x86_64-linux-gnu'
[100%] Built target minimac4
make[2]: Leaving directory '/build/minimac4-1.0.2/obj-x86_64-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /build/minimac4-1.0.2/obj-x86_64-linux-gnu/CMakeFiles 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/build/minimac4-1.0.2/obj-x86_64-linux-gnu'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/build/minimac4-1.0.2/obj-x86_64-linux-gnu'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /build/minimac4-1.0.2/debian/minimac4/usr/bin/minimac4
make[1]: Leaving directory '/build/minimac4-1.0.2/obj-x86_64-linux-gnu'
dh_installdocs
dh_installchangelogs
dh_installexamples
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz
dh_strip
dh_makeshlibs
dh_shlibdeps
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/minimac4/usr/bin/minimac4 was not linked against libz.so.1 (it uses none of the library's symbols)
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'minimac4' in '../minimac4_1.0.2-2_amd64.deb'.
dpkg-deb: building package 'minimac4-dbgsym' in '../minimac4-dbgsym_1.0.2-2_amd64.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../minimac4_1.0.2-2_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/3210435 and its subdirectories
I: Current time: Tue Jan 31 11:25:55 -12 2023
I: pbuilder-time-stamp: 1675207555
Wed Dec 29 17:02:55 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net.
Wed Dec 29 17:02:55 UTC 2021 I: Preparing to do remote build '2' on ionos1-amd64.debian.net.
Wed Dec 29 17:03:47 UTC 2021 I: Deleting $TMPDIR on ionos1-amd64.debian.net.
Wed Dec 29 17:03:47 UTC 2021 I: minimac4_1.0.2-2_amd64.changes:
Format: 1.8
Date: Tue, 05 Nov 2019 21:31:52 +0100
Source: minimac4
Binary: minimac4 minimac4-dbgsym
Architecture: amd64
Version: 1.0.2-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Dylan Aïssi <daissi@debian.org>
Description:
minimac4 - Fast Imputation Based on State Space Reduction HMM
Closes: 943897
Changes:
minimac4 (1.0.2-2) unstable; urgency=medium
.
* Fix autopkgtest. (Closes: #943897)
Checksums-Sha1:
f6ab15709a612adb3412f11164e585980710d523 2236972 minimac4-dbgsym_1.0.2-2_amd64.deb
ca3eab43ff64a8b0cd38012315982946fff9226a 5902 minimac4_1.0.2-2_amd64.buildinfo
2629f20fb311632042dfa6f6311b25984cbbd9d0 1359400 minimac4_1.0.2-2_amd64.deb
Checksums-Sha256:
332654de06baf7b461532e3445e4acefa39318919062370db5d372ed548cc419 2236972 minimac4-dbgsym_1.0.2-2_amd64.deb
8081d22ad26295551d00d3526a3fe444c7e65483569f27e21ef6734ddddb4cbf 5902 minimac4_1.0.2-2_amd64.buildinfo
46786a6ef17fa0f2f86682b5ff6a8b6ab0f05d8ee884d412b777de613ca095e4 1359400 minimac4_1.0.2-2_amd64.deb
Files:
24f1045a735be28f1120003c588515ab 2236972 debug optional minimac4-dbgsym_1.0.2-2_amd64.deb
82319ddbc6f92a217db58443b2aabd42 5902 science optional minimac4_1.0.2-2_amd64.buildinfo
ee63ba734f7e866415feac8b8f66d188 1359400 science optional minimac4_1.0.2-2_amd64.deb
Wed Dec 29 17:03:48 UTC 2021 I: will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.uofEvoM9mE/minimac4_1.0.2-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.uofEvoM9mE/minimac4_1.0.2-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.uofEvoM9mE/minimac4_1.0.2-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.uofEvoM9mE/b1/minimac4_1.0.2-2_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.uofEvoM9mE/b2/minimac4_1.0.2-2_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: 0.362s)
0.362s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.064s)
0.064s 10 calls diffoscope.comparators.binary.FilesystemFile
0.000s 8 calls abc.DotChangesFile
Wed Dec 29 17:03:51 UTC 2021 I: found no differences in the changes files, and a .buildinfo file also exists.
Wed Dec 29 17:03:51 UTC 2021 I: minimac4 from bullseye built successfully and reproducibly on amd64.
Wed Dec 29 17:03:53 UTC 2021 I: Submitting .buildinfo files to external archives:
Wed Dec 29 17:03:53 UTC 2021 I: Submitting 8.0K b1/minimac4_1.0.2-2_amd64.buildinfo.asc
Wed Dec 29 17:03:54 UTC 2021 I: Submitting 8.0K b2/minimac4_1.0.2-2_amd64.buildinfo.asc
Wed Dec 29 17:03:55 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Wed Dec 29 17:03:55 UTC 2021 I: Done submitting .buildinfo files.
Wed Dec 29 17:03:55 UTC 2021 I: Removing signed minimac4_1.0.2-2_amd64.buildinfo.asc files:
removed './b1/minimac4_1.0.2-2_amd64.buildinfo.asc'
removed './b2/minimac4_1.0.2-2_amd64.buildinfo.asc'