Tue Jan 21 20:43:04 UTC 2025 I: starting to build libbioparser-dev/unstable/i386 on jenkins on '2025-01-21 20:42'
Tue Jan 21 20:43:04 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_6/53080/console.log
Tue Jan 21 20:43:04 UTC 2025 I: Downloading source for unstable/libbioparser-dev=3.1.0-1
--2025-01-21 20:43:04-- http://deb.debian.org/debian/pool/main/libb/libbioparser-dev/libbioparser-dev_3.1.0-1.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2066 (2.0K) [text/prs.lines.tag]
Saving to: ‘libbioparser-dev_3.1.0-1.dsc’
0K .. 100% 298M=0s
2025-01-21 20:43:04 (298 MB/s) - ‘libbioparser-dev_3.1.0-1.dsc’ saved [2066/2066]
Tue Jan 21 20:43:04 UTC 2025 I: libbioparser-dev_3.1.0-1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: libbioparser-dev
Binary: libbioparser-dev
Architecture: all
Version: 3.1.0-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://github.com/rvaser/bioparser/
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/libbioparser-dev
Vcs-Git: https://salsa.debian.org/med-team/libbioparser-dev.git
Build-Depends: debhelper-compat (= 13), cmake, zlib1g-dev, libgtest-dev, libbiosoup-dev (>> 0.11.0)
Package-List:
libbioparser-dev deb libdevel optional arch=all
Checksums-Sha1:
061efd61294089b4b82dc90d72c2fb015e794e7d 1016738 libbioparser-dev_3.1.0.orig.tar.gz
8b7f3ee45bcc4eebe8e730c4db20ad2974fb0ba4 3108 libbioparser-dev_3.1.0-1.debian.tar.xz
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5e6d9f2d831d768ae84b05b6b5ffff7efd9ea2b73a756de5db36a6f822a68490 3108 libbioparser-dev_3.1.0-1.debian.tar.xz
Files:
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2177dd518762ea9f95543ba47f933396 3108 libbioparser-dev_3.1.0-1.debian.tar.xz
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Tue Jan 21 20:43:04 UTC 2025 I: Checking whether the package is not for us
Tue Jan 21 20:43:04 UTC 2025 I: Starting 1st build on remote node ionos6-i386.debian.net.
Tue Jan 21 20:43:04 UTC 2025 I: Preparing to do remote build '1' on ionos6-i386.debian.net.
Tue Jan 21 20:43:27 UTC 2025 I: Deleting $TMPDIR on ionos6-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Mon Feb 23 15:06:05 -12 2026
I: pbuilder-time-stamp: 1771902365
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [libbioparser-dev_3.1.0-1.dsc]
I: copying [./libbioparser-dev_3.1.0.orig.tar.gz]
I: copying [./libbioparser-dev_3.1.0-1.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./libbioparser-dev_3.1.0-1.dsc: unsupported subcommand
dpkg-source: info: extracting libbioparser-dev in libbioparser-dev-3.1.0
dpkg-source: info: unpacking libbioparser-dev_3.1.0.orig.tar.gz
dpkg-source: info: unpacking libbioparser-dev_3.1.0-1.debian.tar.xz
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/91259/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='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='f824839b4a4e418288c0971ab8db2379'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
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='91259'
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.XgRuQ1CU/pbuilderrc_DyOV --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.XgRuQ1CU/b1 --logfile b1/build.log libbioparser-dev_3.1.0-1.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos6-i386 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) 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/91259/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), cmake, zlib1g-dev, libgtest-dev, libbiosoup-dev (>> 0.11.0)
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19837 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 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 libgtest-dev; however:
Package libgtest-dev is not installed.
pbuilder-satisfydepends-dummy depends on libbiosoup-dev (>> 0.11.0); however:
Package libbiosoup-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} googletest{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbiosoup-dev{a} libbrotli1{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} libgtest-dev{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} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{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:
ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget
0 packages upgraded, 63 newly installed, 0 to remove and 0 not upgraded.
Need to get 43.9 MB of archives. After unpacking 158 MB will be used.
Writing extended state information...
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Get: 3 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 4 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 5 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 6 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 7 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.23.1-1 [245 kB]
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Get: 26 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
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Get: 29 http://deb.debian.org/debian unstable/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 30 http://deb.debian.org/debian unstable/main i386 libidn2-0 i386 2.3.7-2+b1 [130 kB]
Get: 31 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8+b1 [20.9 kB]
Get: 32 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-8+b1 [61.3 kB]
Get: 33 http://deb.debian.org/debian unstable/main i386 libldap2 i386 2.6.9+dfsg-1 [205 kB]
Get: 34 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB]
Get: 35 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB]
Get: 36 http://deb.debian.org/debian unstable/main i386 libffi8 i386 3.4.6-1 [21.2 kB]
Get: 37 http://deb.debian.org/debian unstable/main i386 libp11-kit0 i386 0.25.5-3 [423 kB]
Get: 38 http://deb.debian.org/debian unstable/main i386 libtasn1-6 i386 4.19.0-3+b3 [51.1 kB]
Get: 39 http://deb.debian.org/debian unstable/main i386 libgnutls30t64 i386 3.8.8-2 [1451 kB]
Get: 40 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB]
Get: 41 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB]
Get: 42 http://deb.debian.org/debian unstable/main i386 libcurl4t64 i386 8.11.1-1+b1 [393 kB]
Get: 43 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 44 http://deb.debian.org/debian unstable/main i386 libjsoncpp26 i386 1.9.6-3 [90.0 kB]
Get: 45 http://deb.debian.org/debian unstable/main i386 librhash1 i386 1.4.5-1 [144 kB]
Get: 46 http://deb.debian.org/debian unstable/main i386 libuv1t64 i386 1.48.0-7 [157 kB]
Get: 47 http://deb.debian.org/debian unstable/main i386 cmake i386 3.31.4-2 [13.1 MB]
Get: 48 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 49 http://deb.debian.org/debian unstable/main i386 libtool all 2.5.4-2 [539 kB]
Get: 50 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 51 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 52 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB]
Get: 53 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.1-1 [8584 B]
Get: 54 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 55 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 56 http://deb.debian.org/debian unstable/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 57 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 58 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 59 http://deb.debian.org/debian unstable/main i386 debhelper all 13.24.1 [920 kB]
Get: 60 http://deb.debian.org/debian unstable/main i386 googletest all 1.15.2-1 [514 kB]
Get: 61 http://deb.debian.org/debian unstable/main i386 libbiosoup-dev all 0.11.0-2 [8000 B]
Get: 62 http://deb.debian.org/debian unstable/main i386 libgtest-dev i386 1.15.2-1 [272 kB]
Get: 63 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Fetched 43.9 MB in 1s (67.1 MB/s)
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(Reading database ... 19837 files and directories currently installed.)
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/libbioparser-dev-3.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libbioparser-dev_3.1.0-1_source.changes
dpkg-buildpackage: info: source package libbioparser-dev
dpkg-buildpackage: info: source version 3.1.0-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/libbioparser-dev-3.1.0'
dh_auto_configure -- -Dbioparser_build_tests=ON
cd obj-i686-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/i386-linux-gnu -Dbioparser_build_tests=ON ..
-- The CXX compiler identification is GNU 14.2.0
-- 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
-- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found suitable version "1.3.1", minimum required is "1.2.8")
CMake Warning (dev) at /usr/share/cmake-3.31/Modules/FetchContent.cmake:1953 (message):
Calling FetchContent_Populate(biosoup) is deprecated, call
FetchContent_MakeAvailable(biosoup) instead. Policy CMP0169 can be set to
OLD to allow FetchContent_Populate(biosoup) to be called directly for now,
but the ability to call it with declared details will be removed completely
in a future version.
Call Stack (most recent call first):
CMakeLists.txt:38 (FetchContent_Populate)
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning at /usr/share/cmake-3.31/Modules/FetchContent.cmake:2111 (message):
FETCHCONTENT_FULLY_DISCONNECTED is set to true, which requires the source
directory for dependency biosoup to already be populated. This generally
means it must not be set to true the first time CMake is run in a build
directory. The following source directory should already be populated, but
it doesn't exist:
/build/reproducible-path/libbioparser-dev-3.1.0/obj-i686-linux-gnu/_deps/biosoup-src
Policy CMP0170 controls enforcement of this requirement.
Call Stack (most recent call first):
/usr/share/cmake-3.31/Modules/FetchContent.cmake:1978:EVAL:1 (__FetchContent_Populate)
/usr/share/cmake-3.31/Modules/FetchContent.cmake:1978 (cmake_language)
CMakeLists.txt:38 (FetchContent_Populate)
CMake Error at CMakeLists.txt:39 (add_subdirectory):
add_subdirectory given source
"/build/reproducible-path/libbioparser-dev-3.1.0/obj-i686-linux-gnu/_deps/biosoup-src"
which is not an existing directory.
-- Configuring incomplete, errors occurred!
cd obj-i686-linux-gnu && tail -v -n \+0 CMakeCache.txt
==> CMakeCache.txt <==
# This is the CMakeCache file.
# For build in directory: /build/reproducible-path/libbioparser-dev-3.1.0/obj-i686-linux-gnu
# It was generated by CMake: /usr/bin/cmake
# You can edit this file to change values found and used by cmake.
# If you do not want to change any of the values, simply exit the editor.
# If you do want to change a value, simply edit, save, and exit the editor.
# The syntax for the file is as follows:
# KEY:TYPE=VALUE
# KEY is the name of a variable in the cache.
# TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!.
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# EXTERNAL cache entries
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// MinSizeRel ...
CMAKE_BUILD_TYPE:STRING=None
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CMAKE_COLOR_MAKEFILE:BOOL=ON
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dh_auto_configure: error: cd obj-i686-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/i386-linux-gnu -Dbioparser_build_tests=ON .. returned exit code 1
make[1]: *** [debian/rules:11: override_dh_auto_configure] Error 2
make[1]: Leaving directory '/build/reproducible-path/libbioparser-dev-3.1.0'
make: *** [debian/rules:8: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
I: copying local configuration
E: Failed autobuilding of package
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/91259 and its subdirectories
Tue Jan 21 20:43:28 UTC 2025 W: No second build log, what happened?