Mon May 8 18:11:51 UTC 2023 I: starting to build fastqtl/bookworm/amd64 on jenkins on '2023-05-08 18:11'
Mon May 8 18:11:51 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_20/19058/console.log
Mon May 8 18:11:51 UTC 2023 I: Downloading source for bookworm/fastqtl=2.184+v7+dfsg-3
--2023-05-08 18:11:51-- http://cdn-fastly.deb.debian.org/debian/pool/main/f/fastqtl/fastqtl_2.184%2bv7%2bdfsg-3.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2366 (2.3K) [text/prs.lines.tag]
Saving to: ‘fastqtl_2.184+v7+dfsg-3.dsc’
0K .. 100% 162M=0s
2023-05-08 18:11:51 (162 MB/s) - ‘fastqtl_2.184+v7+dfsg-3.dsc’ saved [2366/2366]
Mon May 8 18:11:51 UTC 2023 I: fastqtl_2.184+v7+dfsg-3.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: fastqtl
Binary: fastqtl, fastqtl-doc
Architecture: any all
Version: 2.184+v7+dfsg-3
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Dylan Aïssi <daissi@debian.org>
Homepage: http://fastqtl.sourceforge.net/
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/fastqtl
Vcs-Git: https://salsa.debian.org/med-team/fastqtl.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), dh-python, python3, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libgsl-dev, r-mathlib, zlib1g-dev, libblas-dev, libeigen3-dev, libhts-dev, libbz2-dev
Package-List:
fastqtl deb science optional arch=any
fastqtl-doc deb doc optional arch=all
Checksums-Sha1:
afda0774d21c6c870b5bf319751f46a641d1dd12 17128664 fastqtl_2.184+v7+dfsg.orig.tar.xz
b4f04e334d20302ee310bce9402ec9500d257227 20796 fastqtl_2.184+v7+dfsg-3.debian.tar.xz
Checksums-Sha256:
a16310e5cc00873707decb7dad8acd9d5ae22bf4ade1fdbba3a99afc650a6232 17128664 fastqtl_2.184+v7+dfsg.orig.tar.xz
b364ceb5f6b352e8c908475f9ae671622e542be42bee2fdaee0bd96d1cb66582 20796 fastqtl_2.184+v7+dfsg-3.debian.tar.xz
Files:
0315c13229da6648d451f9025370a919 17128664 fastqtl_2.184+v7+dfsg.orig.tar.xz
eea9107515f36d9e41ff982111c1d472 20796 fastqtl_2.184+v7+dfsg-3.debian.tar.xz
Dgit: e21732ceefe8551bfe0bd942d37499009e81fc77 debian archive/debian/2.184+v7+dfsg-3 https://git.dgit.debian.org/fastqtl
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Mon May 8 18:11:51 UTC 2023 I: Checking whether the package is not for us
Mon May 8 18:11:51 UTC 2023 I: Starting 1st build on remote node ionos15-amd64.debian.net.
Mon May 8 18:11:51 UTC 2023 I: Preparing to do remote build '1' on ionos15-amd64.debian.net.
Mon May 8 18:14:45 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun Jun 9 12:34:57 -12 2024
I: pbuilder-time-stamp: 1717979697
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 [fastqtl_2.184+v7+dfsg-3.dsc]
I: copying [./fastqtl_2.184+v7+dfsg.orig.tar.xz]
I: copying [./fastqtl_2.184+v7+dfsg-3.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sat Oct 22 00:02:48 2022 -12
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./fastqtl_2.184+v7+dfsg-3.dsc: no acceptable signature found
dpkg-source: info: extracting fastqtl in fastqtl-2.184+v7+dfsg
dpkg-source: info: unpacking fastqtl_2.184+v7+dfsg.orig.tar.xz
dpkg-source: info: unpacking fastqtl_2.184+v7+dfsg-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 01_Makefile_dynamic_hardenings.patch
dpkg-source: info: applying 02_Replace_libtabix_by_libhts.patch
dpkg-source: info: applying 03_Reproducible_builds.patch
dpkg-source: info: applying cross.patch
dpkg-source: info: applying set_path.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/2382072/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=16'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='6ebaea9b2d33447c874768e8971a67bb'
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='2382072'
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.c4GfwhJg/pbuilderrc_4rB0 --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.c4GfwhJg/b1 --logfile b1/build.log fastqtl_2.184+v7+dfsg-3.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 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux
I: ls -l /bin
total 5632
-rwxr-xr-x 1 root root 1265648 Apr 23 2023 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 2023 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 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname
-rwxr-xr-x 1 root root 43856 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 2023 egrep
-rwxr-xr-x 1 root root 35664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep
-rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt
-rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount
-rwxr-xr-x 1 root root 203152 Jan 24 2023 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 2022 hostname
-rwxr-xr-x 1 root root 72824 Sep 20 2022 ln
-rwxr-xr-x 1 root root 53024 Mar 23 2023 login
-rwxr-xr-x 1 root root 151344 Sep 20 2022 ls
-rwxr-xr-x 1 root root 207168 Mar 22 2023 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 2023 more
-rwsr-xr-x 1 root root 59704 Mar 22 2023 mount
-rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint
-rwxr-xr-x 1 root root 142968 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 2023 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 2022 run-parts
-rwxr-xr-x 1 root root 126424 Jan 5 2023 sed
lrwxrwxrwx 1 root root 4 Jan 5 2023 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 2023 su
-rwxr-xr-x 1 root root 39824 Sep 20 2022 sync
-rwxr-xr-x 1 root root 531984 Apr 6 2023 tar
-rwxr-xr-x 1 root root 14520 Nov 2 2022 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 2023 ulockmgr_server
-rwsr-xr-x 1 root root 35128 Mar 22 2023 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 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 2022 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/2382072/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), dh-python, python3, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libgsl-dev, r-mathlib, zlib1g-dev, libblas-dev, libeigen3-dev, libhts-dev, libbz2-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 ... 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 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 libboost-dev; however:
Package libboost-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however:
Package libboost-iostreams-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however:
Package libboost-program-options-dev is not installed.
pbuilder-satisfydepends-dummy depends on libgsl-dev; however:
Package libgsl-dev is not installed.
pbuilder-satisfydepends-dummy depends on r-mathlib; however:
Package r-mathlib is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libblas-dev; however:
Package libblas-dev is not installed.
pbuilder-satisfydepends-dummy depends on libeigen3-dev; however:
Package libeigen3-dev is not installed.
pbuilder-satisfydepends-dummy depends on libhts-dev; however:
Package libhts-dev is not installed.
pbuilder-satisfydepends-dummy depends on libbz2-dev; however:
Package libbz2-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libeigen3-dev{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{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} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} r-mathlib{a} readline-common{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
bzip2-doc ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix r-base-core r-base-dev wget
0 packages upgraded, 84 newly installed, 0 to remove and 0 not upgraded.
Need to get 57.9 MB of archives. After unpacking 344 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB]
Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB]
Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB]
Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB]
Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB]
Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB]
Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B]
Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB]
Get: 12 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 13 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get: 14 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get: 15 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get: 16 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get: 17 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 18 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get: 19 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get: 20 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get: 21 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get: 22 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 23 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 24 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 25 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 26 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 27 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 35 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 36 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 37 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB]
Get: 38 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 39 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 40 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 41 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 42 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB]
Get: 43 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB]
Get: 44 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB]
Get: 45 http://deb.debian.org/debian bookworm/main amd64 icu-devtools amd64 72.1-3 [206 kB]
Get: 46 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB]
Get: 47 http://deb.debian.org/debian bookworm/main amd64 libblas-dev amd64 3.11.0-2 [158 kB]
Get: 48 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-20 [9510 kB]
Get: 49 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B]
Get: 50 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74.0 amd64 1.74.0+ds1-20 [487 kB]
Get: 51 http://deb.debian.org/debian bookworm/main amd64 libicu-dev amd64 72.1-3 [10.3 MB]
Get: 52 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74-dev amd64 1.74.0+ds1-20 [558 kB]
Get: 53 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams1.74-dev amd64 1.74.0+ds1-20 [248 kB]
Get: 54 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams-dev amd64 1.74.0.3 [4316 B]
Get: 55 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74.0 amd64 1.74.0+ds1-20 [328 kB]
Get: 56 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74-dev amd64 1.74.0+ds1-20 [358 kB]
Get: 57 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options-dev amd64 1.74.0.3 [4340 B]
Get: 58 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB]
Get: 59 http://deb.debian.org/debian bookworm/main amd64 libbz2-dev amd64 1.0.8-5+b1 [30.9 kB]
Get: 60 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB]
Get: 61 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB]
Get: 62 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB]
Get: 63 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB]
Get: 64 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB]
Get: 65 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB]
Get: 66 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB]
Get: 67 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB]
Get: 68 http://deb.debian.org/debian bookworm/main amd64 libcurl4-gnutls-dev amd64 7.88.1-9 [481 kB]
Get: 69 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB]
Get: 70 http://deb.debian.org/debian bookworm/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB]
Get: 71 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB]
Get: 72 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB]
Get: 73 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB]
Get: 74 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB]
Get: 75 http://deb.debian.org/debian bookworm/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB]
Get: 76 http://deb.debian.org/debian bookworm/main amd64 libgslcblas0 amd64 2.7.1+dfsg-3+b1 [116 kB]
Get: 77 http://deb.debian.org/debian bookworm/main amd64 libgsl27 amd64 2.7.1+dfsg-3+b1 [948 kB]
Get: 78 http://deb.debian.org/debian bookworm/main amd64 libgsl-dev amd64 2.7.1+dfsg-3+b1 [1152 kB]
Get: 79 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB]
Get: 80 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB]
Get: 81 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB]
Get: 82 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB]
Get: 83 http://deb.debian.org/debian bookworm/main amd64 libhts-dev amd64 1.16+ds-3 [1601 kB]
Get: 84 http://deb.debian.org/debian bookworm/main amd64 r-mathlib amd64 4.2.2.20221110-2 [2291 kB]
Fetched 57.9 MB in 1s (74.0 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.11-minimal:amd64.
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Setting up libexpat1:amd64 (2.5.0-1) ...
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Unpacking gettext-base (0.21-12) ...
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Selecting previously unselected package libarchive-zip-perl.
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Unpacking libicu72:amd64 (72.1-3) ...
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Unpacking libblas3:amd64 (3.11.0-2) ...
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Unpacking libblas-dev:amd64 (3.11.0-2) ...
Selecting previously unselected package libboost1.74-dev:amd64.
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Unpacking libboost1.74-dev:amd64 (1.74.0+ds1-20) ...
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Unpacking libboost-dev:amd64 (1.74.0.3) ...
Selecting previously unselected package libboost-regex1.74.0:amd64.
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Unpacking libboost-regex1.74.0:amd64 (1.74.0+ds1-20) ...
Selecting previously unselected package libicu-dev:amd64.
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Unpacking libicu-dev:amd64 (72.1-3) ...
Selecting previously unselected package libboost-regex1.74-dev:amd64.
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Unpacking libboost-regex1.74-dev:amd64 (1.74.0+ds1-20) ...
Selecting previously unselected package libboost-iostreams1.74-dev:amd64.
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Unpacking libboost-iostreams1.74-dev:amd64 (1.74.0+ds1-20) ...
Selecting previously unselected package libboost-iostreams-dev:amd64.
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Unpacking libboost-iostreams-dev:amd64 (1.74.0.3) ...
Selecting previously unselected package libboost-program-options1.74.0:amd64.
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Selecting previously unselected package libboost-program-options-dev:amd64.
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Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ...
Selecting previously unselected package libldap-2.5-0:amd64.
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Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ...
Selecting previously unselected package libnghttp2-14:amd64.
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Unpacking libnghttp2-14:amd64 (1.52.0-1) ...
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Unpacking libpsl5:amd64 (0.21.2-1) ...
Selecting previously unselected package librtmp1:amd64.
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Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:amd64.
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Unpacking libssh2-1:amd64 (1.10.0-3+b1) ...
Selecting previously unselected package libcurl3-gnutls:amd64.
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Unpacking libcurl3-gnutls:amd64 (7.88.1-9) ...
Selecting previously unselected package libcurl4-gnutls-dev:amd64.
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Unpacking libcurl4-gnutls-dev:amd64 (7.88.1-9) ...
Selecting previously unselected package libdeflate0:amd64.
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Unpacking libdeflate0:amd64 (1.14-1) ...
Selecting previously unselected package libdeflate-dev:amd64.
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Unpacking libdeflate-dev:amd64 (1.14-1) ...
Selecting previously unselected package libpkgconf3:amd64.
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Unpacking libpkgconf3:amd64 (1.8.1-1) ...
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Unpacking pkgconf-bin (1.8.1-1) ...
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Unpacking pkgconf:amd64 (1.8.1-1) ...
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Unpacking pkg-config:amd64 (1.8.1-1) ...
Selecting previously unselected package libeigen3-dev.
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Unpacking libeigen3-dev (3.4.0-4) ...
Selecting previously unselected package libgslcblas0:amd64.
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I: Building the package
I: Running cd /build/fastqtl-2.184+v7+dfsg/ && 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 > ../fastqtl_2.184+v7+dfsg-3_source.changes
dpkg-buildpackage: info: source package fastqtl
dpkg-buildpackage: info: source version 2.184+v7+dfsg-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean --with python3
dh_auto_clean
make -j16 clean
make[1]: Entering directory '/build/fastqtl-2.184+v7+dfsg'
rm -f obj/*.o bin/fastQTL
make[1]: Leaving directory '/build/fastqtl-2.184+v7+dfsg'
dh_clean
debian/rules binary
dh binary --with python3
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/fastqtl-2.184+v7+dfsg'
mkdir -p /build/fastqtl-2.184+v7+dfsg/obj/
mkdir -p /build/fastqtl-2.184+v7+dfsg/bin/
dh_auto_build -- CXXFLAGS='-g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14'
make -j16 "INSTALL=install --strip-program=true" "CXXFLAGS=-g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14"
make[2]: Entering directory '/build/fastqtl-2.184+v7+dfsg'
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisMapping.o -c src/analysisMapping.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisNominal.o -c src/analysisNominal.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisNominalBest.o -c src/analysisNominalBest.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutation.o -c src/analysisPermutation.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutationInteraction.o -c src/analysisPermutationInteraction.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutationPerGroup.o -c src/analysisPermutationPerGroup.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/analysisPermutationSequence.o -c src/analysisPermutationSequence.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/commands.o -c src/commands.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/df.o -c src/df.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/fastQTL.o -c src/fastQTL.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/management.o -c src/management.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/mle.o -c src/mle.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readCovariates.o -c src/readCovariates.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readGenotypes.o -c src/readGenotypes.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readGroups.o -c src/readGroups.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readInclusionsExclusions.o -c src/readInclusionsExclusions.cpp -Isrc
In file included from src/management.cpp:20:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from src/analysisMapping.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readInteractions.o -c src/readInteractions.cpp -Isrc
In file included from src/analysisNominal.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readPhenotypes.o -c src/readPhenotypes.cpp -Isrc
In file included from src/analysisPermutationSequence.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/readThresholds.o -c src/readThresholds.cpp -Isrc
In file included from src/analysisPermutationPerGroup.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/residualizer.o -c src/residualizer.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/tabix.o -c src/utils/tabix.cpp -Isrc
g++ -std=c++11 -O3 -D_FAST_CORRELATION -Wall -Wextra -Wno-sign-compare -g -ffile-prefix-map=/build/fastqtl-2.184+v7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -o obj/utils.o -c src/utils/utils.cpp -Isrc
In file included from src/analysisNominalBest.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
src/utils/tabix.cpp: In constructor 'Tabix::Tabix(std::string&)':
src/utils/tabix.cpp:17:22: warning: 'int bgzf_is_bgzf(const char*)' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
17 | if ( bgzf_is_bgzf(cfilename)!=1 )
| ~~~~~~~~~~~~^~~~~~~~~~~
In file included from src/utils/tabix.hpp:12,
from src/utils/tabix.cpp:6:
/usr/include/htslib/bgzf.h:270:9: note: declared here
270 | int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
| ^~~~~~~~~~~~
In file included from src/analysisPermutation.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from src/analysisPermutationInteraction.cpp:17:
src/data.h: In member function 'double data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/data.h:180:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
180 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/data.h:181:9: note: here
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/data.h:181:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
181 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/data.h:182:9: note: here
182 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
g++ -std=c++11 -O3 -Wl,-z,relro -Wl,-z,now obj/analysisMapping.o obj/analysisNominal.o obj/analysisNominalBest.o obj/analysisPermutation.o obj/analysisPermutationInteraction.o obj/analysisPermutationPerGroup.o obj/analysisPermutationSequence.o obj/commands.o obj/df.o obj/fastQTL.o obj/management.o obj/mle.o obj/readCovariates.o obj/readGenotypes.o obj/readGroups.o obj/readInclusionsExclusions.o obj/readInteractions.o obj/readPhenotypes.o obj/readThresholds.o obj/residualizer.o obj/tabix.o obj/utils.o -lRmath -lhts -lm -lz -lbz2 -lboost_iostreams -lboost_program_options -lgslcblas -lgsl -lblas -o bin/fastQTL
make[2]: Leaving directory '/build/fastqtl-2.184+v7+dfsg'
cd /build/fastqtl-2.184+v7+dfsg/example/ && \
tar Jcvf examples.tar.xz * --sort=name --mode=go=rX,u+rw,a-s --owner=root --group=root --numeric-owner
covariates.txt.gz
genotypes.vcf.gz
genotypes.vcf.gz.tbi
interaction.txt
phenotypes.bed.gz
phenotypes.bed.gz.tbi
make[1]: Leaving directory '/build/fastqtl-2.184+v7+dfsg'
dh_auto_test
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
dh_install
dh_installdocs
dh_installchangelogs
dh_installman
dh_python3
I: dh_python3 tools:114: replacing shebang in debian/fastqtl/usr/bin/sort_index_pairs.py
I: dh_python3 tools:114: replacing shebang in debian/fastqtl/usr/bin/run_chunk.py
I: dh_python3 tools:114: replacing shebang in debian/fastqtl/usr/bin/run_FastQTL_threaded.py
I: dh_python3 tools:114: replacing shebang in debian/fastqtl/usr/bin/merge_chunks.py
I: dh_python3 tools:114: replacing shebang in debian/fastqtl/usr/bin/annotate_outputs.py
dh_lintian
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
debian/rules execute_after_dh_fixperms-arch
make[1]: Entering directory '/build/fastqtl-2.184+v7+dfsg'
chmod -x debian/*/usr/share/fastqtl/*.R
make[1]: Leaving directory '/build/fastqtl-2.184+v7+dfsg'
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/fastqtl/usr/bin/fastQTL was not linked against libblas.so.3 (it uses none of the library's symbols)
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'fastqtl-doc' in '../fastqtl-doc_2.184+v7+dfsg-3_all.deb'.
dpkg-deb: building package 'fastqtl' in '../fastqtl_2.184+v7+dfsg-3_amd64.deb'.
dpkg-deb: building package 'fastqtl-dbgsym' in '../fastqtl-dbgsym_2.184+v7+dfsg-3_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../fastqtl_2.184+v7+dfsg-3_amd64.buildinfo
dpkg-genchanges --build=binary -O../fastqtl_2.184+v7+dfsg-3_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/2382072 and its subdirectories
I: Current time: Sun Jun 9 12:37:47 -12 2024
I: pbuilder-time-stamp: 1717979867
Mon May 8 18:14:46 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net.
Mon May 8 18:14:46 UTC 2023 I: Preparing to do remote build '2' on ionos1-amd64.debian.net.
Mon May 8 18:17:30 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net.
Mon May 8 18:17:30 UTC 2023 I: fastqtl_2.184+v7+dfsg-3_amd64.changes:
Format: 1.8
Date: Sat, 22 Oct 2022 13:50:04 +0200
Source: fastqtl
Binary: fastqtl fastqtl-dbgsym fastqtl-doc
Architecture: amd64 all
Version: 2.184+v7+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
fastqtl - Quantitative Trait Loci (QTL) mapper in cis for molecular phenoty
fastqtl-doc - QTL mapper in cis for molecular phenotypes - documentation
Closes: 1021994 1021995
Changes:
fastqtl (2.184+v7+dfsg-3) unstable; urgency=medium
.
* Team upload.
* d/rules: only fix permissions for arch-any builds. (Closes: #1021994)
* d/t/fastqtl_expected_output.txt: update to match behavior of v7.
(Closes: #1021995)
Checksums-Sha1:
e82351d712050455cfb1dbf245bbb6527537d13e 5756484 fastqtl-dbgsym_2.184+v7+dfsg-3_amd64.deb
5795f6c91025a1015eed9eddf12ac8b744713235 17104760 fastqtl-doc_2.184+v7+dfsg-3_all.deb
b88ce760c156906cb3f6f4227af71d8cedeb968b 7467 fastqtl_2.184+v7+dfsg-3_amd64.buildinfo
036718713e7be36d9a90fcb1c30b7a8b50e5fc1a 234268 fastqtl_2.184+v7+dfsg-3_amd64.deb
Checksums-Sha256:
30899255a694d2dc3beb9142766e7cf07ae5488365ab7b153c0aba7697540a64 5756484 fastqtl-dbgsym_2.184+v7+dfsg-3_amd64.deb
e5018e5a44816e3e282c7d6fdad79303b2807f21a4a3b52cfb54672bb7091ffa 17104760 fastqtl-doc_2.184+v7+dfsg-3_all.deb
8d72b1012842f9daa3186dbbc34d8b676f68e3c285eee0c98438ee98736e6051 7467 fastqtl_2.184+v7+dfsg-3_amd64.buildinfo
1f8f5b2e2a5f36a52e1837762fc9cad40cbb1b96845fff69d7ac54a09baae1a6 234268 fastqtl_2.184+v7+dfsg-3_amd64.deb
Files:
433132677f06d9a6a3569100a9da6c4f 5756484 debug optional fastqtl-dbgsym_2.184+v7+dfsg-3_amd64.deb
2886c8cf66641316a48787367452a718 17104760 doc optional fastqtl-doc_2.184+v7+dfsg-3_all.deb
3b910a0b0e5b61de26b7473aa59731e1 7467 science optional fastqtl_2.184+v7+dfsg-3_amd64.buildinfo
f52bd725e8b4ef74e7988eaeee45ce01 234268 science optional fastqtl_2.184+v7+dfsg-3_amd64.deb
Mon May 8 18:17:35 UTC 2023 I: diffoscope 242 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.c4GfwhJg/fastqtl_2.184+v7+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.c4GfwhJg/fastqtl_2.184+v7+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.c4GfwhJg/fastqtl_2.184+v7+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.c4GfwhJg/b1/fastqtl_2.184+v7+dfsg-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.c4GfwhJg/b2/fastqtl_2.184+v7+dfsg-3_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: 7.559s)
7.559s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 2.015s)
2.015s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.001s)
0.001s 1 call specialize
Mon May 8 18:17:52 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists.
Mon May 8 18:17:52 UTC 2023 I: fastqtl from bookworm built successfully and reproducibly on amd64.
Mon May 8 18:18:04 UTC 2023 I: Submitting .buildinfo files to external archives:
Mon May 8 18:18:04 UTC 2023 I: Submitting 12K b1/fastqtl_2.184+v7+dfsg-3_amd64.buildinfo.asc
Mon May 8 18:18:05 UTC 2023 I: Submitting 12K b2/fastqtl_2.184+v7+dfsg-3_amd64.buildinfo.asc
Mon May 8 18:18:06 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Mon May 8 18:18:06 UTC 2023 I: Done submitting .buildinfo files.
Mon May 8 18:18:06 UTC 2023 I: Removing signed fastqtl_2.184+v7+dfsg-3_amd64.buildinfo.asc files:
removed './b1/fastqtl_2.184+v7+dfsg-3_amd64.buildinfo.asc'
removed './b2/fastqtl_2.184+v7+dfsg-3_amd64.buildinfo.asc'