Your message dated Mon, 20 Oct 2025 19:49:41 +0000
with message-id <[email protected]>
and subject line Bug#1113499: fixed in sibelia 3.0.7+dfsg-5
has caused the Debian Bug report #1113499,
regarding sibelia: FTBFS with CMake 4
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1113499: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1113499
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: sibelia
Version: 3.0.7+dfsg-3
Severity: serious
User: [email protected]
Usertags: cmake-4
Tags: ftbfs, forky, sid
Dear maintainer,
During a test rebuild for CMake 4, sibelia failed to rebuild.
Log Summary:
-------------------------------------------------------------------------------
[...]
Uploaders: Andreas Tille <[email protected]>
Homepage: http://bioinf.spbau.ru/sibelia
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/sibelia
Vcs-Git: https://salsa.debian.org/med-team/sibelia.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 12), cmake, libdivsufsort-dev, libboost-dev,
libseqan2-dev, libtclap-dev, libhts-dev
Package-List:
sibelia deb science optional arch=any
sibelia-examples deb science optional arch=all
Checksums-Sha1:
fab5441d7decc4e9dedbf1169549d85241c132cc 4833128 sibelia_3.0.7+dfsg.orig.tar.xz
88412f8aeaccc9d9f011c5da4db3637f95d49922 10240
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Checksums-Sha256:
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sibelia_3.0.7+dfsg-3.debian.tar.xz
Files:
38311be6d2eee4d5e4d4a8ccf2d9c85e 4833128 sibelia_3.0.7+dfsg.orig.tar.xz
388e525dada128486669834bc22336ff 10240 sibelia_3.0.7+dfsg-3.debian.tar.xz
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dpkg-source: warning: cannot verify inline signature for
./sibelia_3.0.7+dfsg-3.dsc: no acceptable signature found
dpkg-source: info: extracting sibelia in
/build/reproducible-path/sibelia-3.0.7+dfsg
dpkg-source: info: unpacking sibelia_3.0.7+dfsg.orig.tar.xz
dpkg-source: info: unpacking sibelia_3.0.7+dfsg-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_debian_packaged_libdivsufsort.patch
dpkg-source: info: applying use_debian_packaged_lagan.patch
dpkg-source: info: applying snpeff_is_removed.patch
dpkg-source: info: applying 2to3.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
LOGNAME=sbuild
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SHELL=/bin/sh
USER=sbuild
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -b
dpkg-buildpackage: info: source package sibelia
dpkg-buildpackage: info: source version 3.0.7+dfsg-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <[email protected]>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean --sourcedirectory=src
dh_auto_clean -O--sourcedirectory=src
dh_autoreconf_clean -O--sourcedirectory=src
dh_clean -O--sourcedirectory=src
debian/rules binary
dh binary --sourcedirectory=src
dh_update_autotools_config -O--sourcedirectory=src
dh_autoreconf -O--sourcedirectory=src
dh_auto_configure -O--sourcedirectory=src
cd obj-aarch64-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 "-GUnix
Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON
-DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu ../src
CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 has been removed from 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.
Or, add -DCMAKE_POLICY_VERSION_MINIMUM=3.5 to try configuring anyway.
-- Configuring incomplete, errors occurred!
cd obj-aarch64-linux-gnu && tail -v -n \+0 CMakeCache.txt
==> CMakeCache.txt <==
# This is the CMakeCache file.
# For build in directory:
/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-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!.
# VALUE is the current value for the KEY.
########################
# EXTERNAL cache entries
########################
//No help, variable specified on the command line.
CMAKE_BUILD_TYPE:UNINITIALIZED=None
//No help, variable specified on the command line.
CMAKE_EXPORT_NO_PACKAGE_REGISTRY:UNINITIALIZED=ON
//No help, variable specified on the command line.
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY:UNINITIALIZED=ON
//Value Computed by CMake.
CMAKE_FIND_PACKAGE_REDIRECTS_DIR:STATIC=/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles/pkgRedirects
//No help, variable specified on the command line.
CMAKE_FIND_USE_PACKAGE_REGISTRY:UNINITIALIZED=OFF
//No help, variable specified on the command line.
CMAKE_INSTALL_LIBDIR:UNINITIALIZED=lib/aarch64-linux-gnu
//No help, variable specified on the command line.
CMAKE_INSTALL_LOCALSTATEDIR:UNINITIALIZED=/var
//No help, variable specified on the command line.
CMAKE_INSTALL_PREFIX:UNINITIALIZED=/usr
//No help, variable specified on the command line.
CMAKE_INSTALL_RUNSTATEDIR:UNINITIALIZED=/run
//No help, variable specified on the command line.
CMAKE_INSTALL_SYSCONFDIR:UNINITIALIZED=/etc
//No help, variable specified on the command line.
CMAKE_VERBOSE_MAKEFILE:UNINITIALIZED=ON
//No help, variable specified on the command line.
FETCHCONTENT_FULLY_DISCONNECTED:UNINITIALIZED=ON
########################
# INTERNAL cache entries
########################
//This is the directory where this CMakeCache.txt was created
CMAKE_CACHEFILE_DIR:INTERNAL=/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu
//Major version of cmake used to create the current loaded cache
CMAKE_CACHE_MAJOR_VERSION:INTERNAL=4
//Minor version of cmake used to create the current loaded cache
CMAKE_CACHE_MINOR_VERSION:INTERNAL=1
//Patch version of cmake used to create the current loaded cache
CMAKE_CACHE_PATCH_VERSION:INTERNAL=1
//Path to CMake executable.
CMAKE_COMMAND:INTERNAL=/usr/bin/cmake
//Path to cpack program executable.
CMAKE_CPACK_COMMAND:INTERNAL=/usr/bin/cpack
//Path to ctest program executable.
CMAKE_CTEST_COMMAND:INTERNAL=/usr/bin/ctest
//Name of external makefile project generator.
CMAKE_EXTRA_GENERATOR:INTERNAL=
//Name of generator.
CMAKE_GENERATOR:INTERNAL=Unix Makefiles
//Generator instance identifier.
CMAKE_GENERATOR_INSTANCE:INTERNAL=
//Name of generator platform.
CMAKE_GENERATOR_PLATFORM:INTERNAL=
//Name of generator toolset.
CMAKE_GENERATOR_TOOLSET:INTERNAL=
//Source directory with the top level CMakeLists.txt file for this
// project
CMAKE_HOME_DIRECTORY:INTERNAL=/build/reproducible-path/sibelia-3.0.7+dfsg/src
//Name of CMakeLists files to read
CMAKE_LIST_FILE_NAME:INTERNAL=CMakeLists.txt
//number of local generators
CMAKE_NUMBER_OF_MAKEFILES:INTERNAL=1
//Path to CMake installation.
CMAKE_ROOT:INTERNAL=/usr/share/cmake-4.1
dh_auto_configure: error: cd obj-aarch64-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 "-GUnix
Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON
-DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu ../src returned exit code 1
make: *** [debian/rules:11: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-08-30T19:57:55Z
-------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here (for the next 30 days):
https://debusine.debian.net/artifact/2411100/
The most likely cause of build failures is the removed backwards compatibility
for
CMake versions earlier than 3.5. You can find additional information in my
debian-devel announcement:
https://lists.debian.org/debian-devel/2025/04/msg00310.html
About the archive rebuild: The build was made on debusine.debian.net,
using sbuild.
You can find the build task here:
https://debusine.debian.net/work-request/154851/
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks,
Timo
--- End Message ---
--- Begin Message ---
Source: sibelia
Source-Version: 3.0.7+dfsg-5
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
sibelia, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated sibelia package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 20 Oct 2025 21:10:24 +0200
Source: sibelia
Architecture: source
Version: 3.0.7+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1113499
Changes:
sibelia (3.0.7+dfsg-5) unstable; urgency=medium
.
* Fix build with CMake 4
Closes: #1113499
* d/watch: version=5
* Standards-Version: 4.7.2 (routine-update)
* debhelper-compat 13 (routine-update)
* debputy lint --auto-fix (routine-update)
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