[Debian-med-packaging] Bug#1112754: beads: FTBFS with CMake 4

roehling at debian.org roehling at debian.org
Sun Aug 31 23:36:30 BST 2025 

Source: beads
Version: 1.1.22-1
Severity: serious
User: cmake at packages.debian.org
Usertags: cmake-4

Dear maintainer,

During a test rebuild for CMake 4, beads failed to rebuild.

Log Summary:
-------------------------------------------------------------------------------
[...]

+------------------------------------------------------------------------------+
| Build                                        Fri, 29 Aug 2025 14:26:59 +0000 |
+------------------------------------------------------------------------------+


Unpack source
-------------

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 3.0 (quilt)
Source: beads
Binary: beads
Architecture: any
Version: 1.1.22-1
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>, Filippo Rusconi <lopippo at debian.org>
Homepage: http://pappso.inrae.fr/bioinfo/beads
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/beads
Vcs-Git: https://salsa.debian.org/med-team/beads.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), cmake, qtbase5-dev, cimg-dev, libodsstream-dev (>= 0.9.1)
Package-List:
 beads deb science optional arch=any
Checksums-Sha1:
 67143a42c4fc870eed007e95d554a93dd3b67b12 39989619 beads_1.1.22.orig.tar.gz
 e1881dfec18e5e1bc431d702bd6186938406cf4d 12172 beads_1.1.22-1.debian.tar.xz
Checksums-Sha256:
 cd328046cc357dc234c813d2a4a394f8932720541438a34d28f3a1333a584be2 39989619 beads_1.1.22.orig.tar.gz
 b60dc8d7c8d500985ca00f0fb448c97650c49e6b08c2bbba9d5d696188a4922e 12172 beads_1.1.22-1.debian.tar.xz
Files:
 1cc70362c5ec22ab496ecaa0a222e739 39989619 beads_1.1.22.orig.tar.gz
 d66068ffc04879ecef0a94dadf7af12b 12172 beads_1.1.22-1.debian.tar.xz

-----BEGIN PGP SIGNATURE-----
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=o2LO
-----END PGP SIGNATURE-----

dpkg-source: warning: cannot verify inline signature for ./beads_1.1.22-1.dsc: no acceptable signature found
dpkg-source: info: extracting beads in /build/reproducible-path/beads-1.1.22
dpkg-source: info: unpacking beads_1.1.22.orig.tar.gz
dpkg-source: info: unpacking beads_1.1.22-1.debian.tar.xz

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 beads
dpkg-buildpackage: info: source version 1.1.22-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Filippo Rusconi <lopippo at debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 debian/rules clean
dh clean
   dh_clean
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   dh_auto_configure
	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 -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu ..
CMake Error at CMakeLists.txt:8 (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/beads-1.1.22/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/beads-1.1.22/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_SKIP_INSTALL_ALL_DEPENDENCY:UNINITIALIZED=ON

//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/beads-1.1.22/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/beads-1.1.22
//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 -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu .. returned exit code 1
make: *** [debian/rules:10: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-08-29T14:27:04Z

-------------------------------------------------------------------------------

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/2389279/

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/152431/

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

More information about the Debian-med-packaging mailing list