Mon Feb 24 10:04:34 UTC 2025 I: starting to build flexbar/trixie/amd64 on jenkins on '2025-02-24 10:04'
Mon Feb 24 10:04:34 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_38/48135/console.log
Mon Feb 24 10:04:35 UTC 2025 I: Downloading source for trixie/flexbar=1:3.5.0-5
--2025-02-24 10:04:35-- http://deb.debian.org/debian/pool/main/f/flexbar/flexbar_3.5.0-5.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2041 (2.0K) [text/prs.lines.tag]
Saving to: ‘flexbar_3.5.0-5.dsc’
0K . 100% 339M=0s
2025-02-24 10:04:35 (339 MB/s) - ‘flexbar_3.5.0-5.dsc’ saved [2041/2041]
Mon Feb 24 10:04:35 UTC 2025 I: flexbar_3.5.0-5.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: flexbar
Binary: flexbar
Architecture: any
Version: 1:3.5.0-5
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Tony Travis <ajt@minke.ukfsn.org>
Homepage: https://github.com/seqan/flexbar
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/flexbar
Vcs-Git: https://salsa.debian.org/med-team/flexbar.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), libtbb-dev, cmake, libseqan2-dev, zlib1g-dev, libbz2-dev
Package-List:
flexbar deb science optional arch=any
Checksums-Sha1:
0c43550b73a08effdd3a7965e916dc9c6b64f8b2 44021 flexbar_3.5.0.orig.tar.gz
045efb9ac3a789f7903dd592234959f5c8865508 11436 flexbar_3.5.0-5.debian.tar.xz
Checksums-Sha256:
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b718a9bf496bfead917292eee67d085beb2864b750374794f34ff28bcb6e9795 11436 flexbar_3.5.0-5.debian.tar.xz
Files:
0e07bf4afebfd731c4718b401383224a 44021 flexbar_3.5.0.orig.tar.gz
e818565eaed0b2c567aeb296816f803c 11436 flexbar_3.5.0-5.debian.tar.xz
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Mon Feb 24 10:04:35 UTC 2025 I: Checking whether the package is not for us
Mon Feb 24 10:04:35 UTC 2025 I: Starting 1st build on remote node infom02-amd64.debian.net.
Mon Feb 24 10:04:35 UTC 2025 I: Preparing to do remote build '1' on infom02-amd64.debian.net.
Mon Feb 24 10:07:04 UTC 2025 I: Deleting $TMPDIR on infom02-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun Mar 29 04:27:37 -12 2026
I: pbuilder-time-stamp: 1774801657
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-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 [flexbar_3.5.0-5.dsc]
I: copying [./flexbar_3.5.0.orig.tar.gz]
I: copying [./flexbar_3.5.0-5.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./flexbar_3.5.0-5.dsc: unsupported subcommand
dpkg-source: info: extracting flexbar in flexbar-3.5.0
dpkg-source: info: unpacking flexbar_3.5.0.orig.tar.gz
dpkg-source: info: unpacking flexbar_3.5.0-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying no_march_native.patch
dpkg-source: info: applying 195a1ab2c2715b07df5acff58dc2a0396d9cd52d.patch
dpkg-source: info: applying 1c872fa10d474f090633fc95d409aa60607a3f96.patch
dpkg-source: info: applying 19722f2743c96235ff57948eda82f963cf734131.patch
dpkg-source: info: applying a9b0eb87a391aeaf760f8116dca777749c8b4f96.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1631578/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
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=12 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='d1c8e95135cb4c3ba79e0d468d7e0a6d'
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='1631578'
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.wLwf3taA/pbuilderrc_u1N9 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wLwf3taA/b1 --logfile b1/build.log flexbar_3.5.0-5.dsc'
SUDO_GID='109'
SUDO_UID='104'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
I: uname -a
Linux infom02-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/1631578/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), libtbb-dev, cmake, libseqan2-dev, zlib1g-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 ... 19802 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 libtbb-dev; however:
Package libtbb-dev is not installed.
pbuilder-satisfydepends-dummy depends on cmake; however:
Package cmake is not installed.
pbuilder-satisfydepends-dummy depends on libseqan2-dev; however:
Package libseqan2-dev is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-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} 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} libarchive13t64{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhwloc15{a} libicu72{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libssh2-1t64{a} libtasn1-6{a} libtbb-dev{a} libtbb12{a} libtbbbind-2-5{a} libtbbmalloc2{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{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:
bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libhwloc-plugins libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget
0 packages upgraded, 68 newly installed, 0 to remove and 0 not upgraded.
Need to get 43.4 MB of archives. After unpacking 166 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get: 2 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get: 3 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 6 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 7 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 9 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 10 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-4 [92.4 kB]
Get: 11 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 12 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB]
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Get: 14 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 18 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.5-2 [2267 kB]
Get: 19 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
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Get: 22 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB]
Get: 23 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
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Get: 27 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB]
Get: 28 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB]
Get: 29 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 30 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB]
Get: 31 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB]
Get: 32 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB]
Get: 33 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB]
Get: 34 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 35 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB]
Get: 36 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 37 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 38 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 39 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get: 40 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 41 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 42 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 43 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.1-2 [369 kB]
Get: 44 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 45 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB]
Get: 46 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB]
Get: 47 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB]
Get: 48 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.5-2 [12.0 MB]
Get: 49 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 50 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 51 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 52 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 53 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 54 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 55 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 56 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 57 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 58 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 59 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 60 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB]
Get: 61 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB]
Get: 62 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.12.0-1 [164 kB]
Get: 63 http://deb.debian.org/debian trixie/main amd64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB]
Get: 64 http://deb.debian.org/debian trixie/main amd64 libtbbmalloc2 amd64 2022.0.0-1 [49.1 kB]
Get: 65 http://deb.debian.org/debian trixie/main amd64 libtbbbind-2-5 amd64 2022.0.0-1 [14.4 kB]
Get: 66 http://deb.debian.org/debian trixie/main amd64 libtbb12 amd64 2022.0.0-1 [90.9 kB]
Get: 67 http://deb.debian.org/debian trixie/main amd64 libtbb-dev amd64 2022.0.0-1 [199 kB]
Get: 68 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Fetched 43.4 MB in 0s (91.3 MB/s)
Preconfiguring packages ...
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(Reading database ... 19802 files and directories currently installed.)
Preparing to unpack .../00-libproc2-0_2%3a4.0.4-7_amd64.deb ...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/flexbar-3.5.0/ && 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 > ../flexbar_3.5.0-5_source.changes
dpkg-buildpackage: info: source package flexbar
dpkg-buildpackage: info: source version 1:3.5.0-5
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/reproducible-path/flexbar-3.5.0'
dh_auto_clean
rm -f test/result_*fast[aq] test/result_*.log
make[1]: Leaving directory '/build/reproducible-path/flexbar-3.5.0'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu ..
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Deprecation Warning at src/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- Performing Test COMPILER_SUPPORTS_CXX14
-- Performing Test COMPILER_SUPPORTS_CXX14 - Success
-- Flexbar 64 bit architecture
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1")
-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Configuring done (1.2s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LIBDIR
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
FETCHCONTENT_FULLY_DISCONNECTED
-- Build files have been written to: /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu
dh_auto_build
cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/flexbar-3.5.0 -B/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu'
make -f src/CMakeFiles/flexbar.dir/build.make src/CMakeFiles/flexbar.dir/depend
make[3]: Entering directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu'
cd /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/flexbar-3.5.0 /build/reproducible-path/flexbar-3.5.0/src /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu/src /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu/src/CMakeFiles/flexbar.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu'
make -f src/CMakeFiles/flexbar.dir/build.make src/CMakeFiles/flexbar.dir/build
make[3]: Entering directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu'
[ 50%] Building CXX object src/CMakeFiles/flexbar.dir/Flexbar.cpp.o
cd /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -I/build/reproducible-path/flexbar-3.5.0/include -g -O2 -ffile-prefix-map=/build/reproducible-path/flexbar-3.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -MD -MT src/CMakeFiles/flexbar.dir/Flexbar.cpp.o -MF CMakeFiles/flexbar.dir/Flexbar.cpp.o.d -o CMakeFiles/flexbar.dir/Flexbar.cpp.o -c /build/reproducible-path/flexbar-3.5.0/src/Flexbar.cpp
In file included from /usr/include/c++/14/string:51,
from /build/reproducible-path/flexbar-3.5.0/src/Flexbar.h:10,
from /build/reproducible-path/flexbar-3.5.0/src/Flexbar.cpp:24:
In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const seqan::SimpleType<unsigned char, seqan::Dna5_>; _Up = seqan::SimpleType<unsigned char, seqan::Dna5_>; bool _IsMove = false]',
inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const seqan::SimpleType<unsigned char, seqan::Dna5_>*; _OI = seqan::SimpleType<unsigned char, seqan::Dna5_>*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30,
inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const seqan::SimpleType<unsigned char, seqan::Dna5_>*; _OI = seqan::SimpleType<unsigned char, seqan::Dna5_>*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42,
inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const seqan::SimpleType<unsigned char, seqan::Dna5_>*; _OI = seqan::SimpleType<unsigned char, seqan::Dna5_>*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31,
inlined from '_OI std::copy(_II, _II, _OI) [with _II = const seqan::SimpleType<unsigned char, seqan::Dna5_>*; _OI = seqan::SimpleType<unsigned char, seqan::Dna5_>*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7,
inlined from 'void seqan::_arrayCopyForwardDefault(TSource1, TSource2, TTarget) [with TTarget = SimpleType<unsigned char, Dna5_>*; TSource1 = const SimpleType<unsigned char, Dna5_>*; TSource2 = const SimpleType<unsigned char, Dna5_>*]' at /usr/include/seqan/basic/array_construct_destruct.h:635:14,
inlined from 'void seqan::arrayCopyForward(TSource1, TSource2, TTarget) [with TTarget = SimpleType<unsigned char, Dna5_>*; TSource1 = const SimpleType<unsigned char, Dna5_>*; TSource2 = const SimpleType<unsigned char, Dna5_>*]' at /usr/include/seqan/basic/array_construct_destruct.h:644:29,
inlined from 'void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, True) [with TValueSource = const SimpleType<unsigned char, Dna5_>; TValueTarget = SimpleType<unsigned char, Dna5_>]' at /usr/include/seqan/basic/array_construct_destruct.h:1003:21,
inlined from 'void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = const SimpleType<unsigned char, Dna5_>; TValueTarget = SimpleType<unsigned char, Dna5_>]' at /usr/include/seqan/basic/array_construct_destruct.h:1031:31,
inlined from 'static void seqan::AppendString_<TExpand>::append_(TTarget&, TSource&) [with TTarget = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >; TSource = const seqan::SimpleType<unsigned char, seqan::Dna5_>; TExpand = seqan::Tag<seqan::TagGenerous_>]' at /usr/include/seqan/sequence/string_base.h:1238:31,
inlined from 'void seqan::append(String<TValue, TSpec>&, const TSource&, Tag<TUsage>) [with TTargetValue = SimpleType<unsigned char, Dna5_>; TTargetSpec = Alloc<>; TSource = SimpleType<unsigned char, Dna5_>; TExpand = TagGenerous_]' at /usr/include/seqan/sequence/string_base.h:1287:42,
inlined from 'void seqan::append(TTarget&&, const TSource&) [with TTarget = String<SimpleType<unsigned char, Dna5_>, Alloc<> >&; TSource = SimpleType<unsigned char, Dna5_>]' at /usr/include/seqan/sequence/sequence_interface.h:903:11,
inlined from 'void SeqAlignAlgo<TSeqStr>::alignGlobal(TAlignResults&, flexbar::Alignments&, flexbar::ComputeCycle&, unsigned int, flexbar::TrimEnd) [with TSeqStr = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]' at /build/reproducible-path/flexbar-3.5.0/src/SeqAlignAlgo.h:132:85:
/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' reading between 2 and 9223372036854775807 bytes from a region of size 1 [-Wstringop-overread]
452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/flexbar-3.5.0/src/PairedAlign.h:8,
from /build/reproducible-path/flexbar-3.5.0/src/Flexbar.h:34:
/build/reproducible-path/flexbar-3.5.0/src/SeqAlignAlgo.h: In member function 'void SeqAlignAlgo<TSeqStr>::alignGlobal(TAlignResults&, flexbar::Alignments&, flexbar::ComputeCycle&, unsigned int, flexbar::TrimEnd) [with TSeqStr = seqan::String<seqan::SimpleType<unsigned char, seqan::Dna5_>, seqan::Alloc<> >]':
/build/reproducible-path/flexbar-3.5.0/src/SeqAlignAlgo.h:132:124: note: source object '<anonymous>' of size 1
132 | else if(m_umiTags && *it2 == 'N') append(a.umiTag, (TChar) *it1);
| ^~~~~~~~~~~~
[100%] Linking CXX executable ../flexbar
cd /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/flexbar.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/flexbar-3.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/flexbar.dir/link.d CMakeFiles/flexbar.dir/Flexbar.cpp.o -o ../flexbar -lpthread /usr/lib/x86_64-linux-gnu/libtbb.so.12.14 -lz -lbz2
make[3]: Leaving directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu'
[100%] Built target flexbar
make[2]: Leaving directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu/CMakeFiles 0
make[1]: Leaving directory '/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/flexbar-3.5.0'
cd test ; \
export PATH="/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu:$PATH" ; \
echo $PATH ; \
export HOME=/tmp ; \
which flexbar ; \
./flexbar_test.sh
/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
/build/reproducible-path/flexbar-3.5.0/obj-x86_64-linux-gnu/flexbar
Testing fasta:
Test 1 OK
Test 2 OK
Test 3 OK
Test 4 OK
Test 5 OK
Testing fastq:
Test 1 OK
Test 2 OK
Test 3 OK
Test 4 OK
Test 5 OK
Testing decompression:
Test gzip OK
Test bzip2 OK
rm -f test/result_*fast[aq] test/result_*.log
make[1]: Leaving directory '/build/reproducible-path/flexbar-3.5.0'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install --destdir=debian/flexbar/
dh_install
dh_installdocs
dh_installchangelogs
dh_installexamples
dh_installman
dh_lintian
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'flexbar' in '../flexbar_3.5.0-5_amd64.deb'.
dpkg-deb: building package 'flexbar-dbgsym' in '../flexbar-dbgsym_3.5.0-5_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../flexbar_3.5.0-5_amd64.buildinfo
dpkg-genchanges --build=binary -O../flexbar_3.5.0-5_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/1631578 and its subdirectories
I: Current time: Sun Mar 29 04:30:03 -12 2026
I: pbuilder-time-stamp: 1774801803
Mon Feb 24 10:07:04 UTC 2025 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net.
Mon Feb 24 10:07:04 UTC 2025 I: Preparing to do remote build '2' on infom01-amd64.debian.net.
Mon Feb 24 10:09:22 UTC 2025 I: Deleting $TMPDIR on infom01-amd64.debian.net.
Mon Feb 24 10:09:22 UTC 2025 I: flexbar_3.5.0-5_amd64.changes:
Format: 1.8
Date: Fri, 10 Feb 2023 11:37:36 +0100
Source: flexbar
Binary: flexbar flexbar-dbgsym
Architecture: amd64
Version: 1:3.5.0-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
flexbar - flexible barcode and adapter removal for sequencing platforms
Closes: 1008220 1011656
Changes:
flexbar (1:3.5.0-5) unstable; urgency=medium
.
[ Andreas Tille ]
* Set upstream metadata fields: Archive.
* Port to onetbb (thanks to Liam Keegan - see
https://github.com/seqan/flexbar/pull/41/)
Closes: #1008220, #1011656
* Fix watch file
.
[ Étienne Mollier ]
* onetbb.patch: port Paired* classes.
.
[ Andreas Tille ]
* Standards-Version: 4.6.2 (routine-update)
Checksums-Sha1:
f84e970b83f174a91f6af0e38c7de5bb6f696a63 4342252 flexbar-dbgsym_3.5.0-5_amd64.deb
eee64a4b1c10775271daef61fd704f54b0385914 6117 flexbar_3.5.0-5_amd64.buildinfo
afc9ae94b49fa69da28c8262cc7c780a56e0c433 375836 flexbar_3.5.0-5_amd64.deb
Checksums-Sha256:
6c79de70894d801bfe8d529841a8680e11d8985e365283feb127df0f38635836 4342252 flexbar-dbgsym_3.5.0-5_amd64.deb
39c48d50c78a29b59fbcf4c72e9935f9298c1c5fc0a883ce3d9391d21b48cece 6117 flexbar_3.5.0-5_amd64.buildinfo
dc241675ef93f324107768f0a969820f2f14945d6cfb78f9a353ecc101c40411 375836 flexbar_3.5.0-5_amd64.deb
Files:
cb56202c0b6a82256c4e1d57088f44c9 4342252 debug optional flexbar-dbgsym_3.5.0-5_amd64.deb
d6fb2bcd9358c1843613d573769b8036 6117 science optional flexbar_3.5.0-5_amd64.buildinfo
9776e71ec3616f89df9533d6da7bcb5e 375836 science optional flexbar_3.5.0-5_amd64.deb
Mon Feb 24 10:09:24 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_38-48135.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.wLwf3taA/flexbar_3.5.0-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.wLwf3taA/flexbar_3.5.0-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.wLwf3taA/flexbar_3.5.0-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.wLwf3taA/b1/flexbar_3.5.0-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.wLwf3taA/b2/flexbar_3.5.0-5_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 diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.003s)
0.003s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 223ms
CPU time consumed: 225ms
Mon Feb 24 10:09:24 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Mon Feb 24 10:09:24 UTC 2025 I: flexbar from trixie built successfully and reproducibly on amd64.
Mon Feb 24 10:09:25 UTC 2025 I: Submitting .buildinfo files to external archives:
Mon Feb 24 10:09:25 UTC 2025 I: Submitting 8.0K b1/flexbar_3.5.0-5_amd64.buildinfo.asc
Mon Feb 24 10:09:26 UTC 2025 I: Submitting 8.0K b2/flexbar_3.5.0-5_amd64.buildinfo.asc
Mon Feb 24 10:09:27 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Mon Feb 24 10:09:27 UTC 2025 I: Done submitting .buildinfo files.
Mon Feb 24 10:09:27 UTC 2025 I: Removing signed flexbar_3.5.0-5_amd64.buildinfo.asc files:
removed './b1/flexbar_3.5.0-5_amd64.buildinfo.asc'
removed './b2/flexbar_3.5.0-5_amd64.buildinfo.asc'