[Debian-med-packaging] Bug#1113466: relion: FTBFS with CMake 4

Mon Sep 1 00:03:54 BST 2025

Source: relion
Version: 3.1.3-4
Severity: serious
User: cmake at packages.debian.org
Usertags: cmake-4
Tags: ftbfs, forky, sid

Dear maintainer,

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

Log Summary:
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[...]

+------------------------------------------------------------------------------+
| Build                                        Sat, 30 Aug 2025 16:57:46 +0000 |
+------------------------------------------------------------------------------+

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

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: relion
Binary: relion, relion-gui
Architecture: any
Version: 3.1.3-4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Roland Fehrenbacher <rfehren at debian.org>, Andreas Tille <tille at debian.org>,
Homepage: https://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/relion
Vcs-Git: https://salsa.debian.org/med-team/relion.git
Testsuite: autopkgtest
Build-Depends: cmake, debhelper-compat (= 13), libfftw3-dev, libfltk1.3-dev, mpi-default-dev, libtiff-dev, fluid
Package-List:
 relion deb science optional arch=any
 relion-gui deb science optional arch=any
Checksums-Sha1:
 c6ca397db6c711f87305bd803f672345f7487bae 2345487 relion_3.1.3.orig.tar.gz
 cbd977bd73a6270bab2fc9aca5779296c528315b 12056 relion_3.1.3-4.debian.tar.xz
Checksums-Sha256:
 f10934058e0670807b7004899d7b5103c21ad77841219352c66a33f98586d42e 2345487 relion_3.1.3.orig.tar.gz
 5dfd505bf26bb03602300ad0b21ed1e6459f97491725abdb5dfa79427972a46a 12056 relion_3.1.3-4.debian.tar.xz
Files:
 5ddaf9afe51d743c5f58f625d9fd1cb7 2345487 relion_3.1.3.orig.tar.gz
 d7e1621d2cf43aa84fc9c84f31ece31b 12056 relion_3.1.3-4.debian.tar.xz

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dpkg-source: warning: cannot verify inline signature for ./relion_3.1.3-4.dsc: no acceptable signature found
dpkg-source: info: extracting relion in /build/reproducible-path/relion-3.1.3
dpkg-source: info: unpacking relion_3.1.3.orig.tar.gz
dpkg-source: info: unpacking relion_3.1.3-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 0001-Repair-wrong-comment-sign-pointed-out-by-Alexey-Roma.patch
dpkg-source: info: applying typos.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 relion
dpkg-buildpackage: info: source version 3.1.3-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier at debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 debian/rules clean
dh clean
   debian/rules override_dh_clean
make[1]: Entering directory '/build/reproducible-path/relion-3.1.3'
dh_clean
rm -rf build
make[1]: Leaving directory '/build/reproducible-path/relion-3.1.3'
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/relion-3.1.3'
mkdir /build/reproducible-path/relion-3.1.3/build
cd /build/reproducible-path/relion-3.1.3/build; \
CC=gcc CXX=g++ cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SKIP_RPATH=TRUE -DDoublePrec_GPU=ON -DGUI=ON -DCUDA=OFF /build/reproducible-path/relion-3.1.3
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!
make[1]: *** [debian/rules:37: override_dh_auto_configure] Error 1
make[1]: Leaving directory '/build/reproducible-path/relion-3.1.3'
make: *** [debian/rules:33: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-08-30T16:57:57Z

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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/2410094/

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/154727/

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