Bug#1112841: dials: FTBFS with CMake 4

roehling at debian.org roehling at debian.org
Sun Aug 31 23:52:23 BST 2025 

Source: dials
Version: 3.22.1+dfsg3-1
Severity: serious
User: cmake at packages.debian.org
Usertags: cmake-4
Tags: ftbfs, forky, sid

Dear maintainer,

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

Log Summary:
-------------------------------------------------------------------------------
[...]
Setting up libboost-thread-dev:arm64 (1.83.0.2+b2) ...
Setting up libpangocairo-1.0-0:arm64 (1.56.3-1) ...
Setting up python3-ptyprocess (0.7.0-6) ...
Setting up python3-mrcfile (1.5.4-2) ...
Setting up python3-prompt-toolkit (3.0.52-1) ...
Setting up dh-python (6.20250414) ...
Setting up libatk-bridge2.0-0t64:arm64 (2.57.1-1) ...
Setting up python3-more-itertools (10.7.0-1) ...
Setting up libfabric1:arm64 (2.1.0-1.1) ...
Setting up python3-iniconfig (1.1.1-2) ...
Setting up libinput10:arm64 (1.28.1-1) ...
Setting up python3-sympy (1.14.0-2) ...
Setting up python3-attr (25.3.0-1) ...
Setting up python3-tornado (6.4.2-3) ...
Setting up python3-gemmi (0.7.1+ds-1) ...
Setting up python3-pure-eval (0.2.3-1) ...
Setting up tk8.6-blt2.5 (2.5.3+dfsg-8) ...
Setting up libqt5dbus5t64:arm64 (5.15.15+dfsg-6) ...
Setting up libglx-mesa0:arm64 (25.2.1-2) ...
Setting up python3-scipy (1.15.3-1) ...
Setting up libpython3-dev:arm64 (3.13.7-1) ...
Setting up python3-cairo (1.27.0-2) ...
Setting up python3-jaraco.functools (4.1.0-1) ...
Setting up libglx0:arm64 (1.7.0-1+b2) ...
Setting up python3-jaraco.context (6.0.1-1) ...
Setting up libcurl4t64:arm64 (8.16.0~rc2-1) ...
Setting up python3-joblib (1.4.2-5) ...
Setting up python3-parso (0.8.4-1) ...
Setting up python3-lz4 (4.4.4+dfsg-1) ...
Setting up libpocl2t64:arm64 (6.0-6) ...
Setting up python3-asttokens (3.0.0-2) ...
Setting up python3-charset-normalizer (3.4.3-1) ...
Setting up python3.13-dev (3.13.7-1) ...
Setting up python3-pytest (8.4.1-1) ...
Setting up blt (2.5.3+dfsg-8) ...
Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-9) ...
Setting up python3-tqdm (4.67.1-5) ...
Setting up python3-typeguard (4.4.4-1) ...
Setting up libqt5network5t64:arm64 (5.15.15+dfsg-6) ...
Setting up python3-threadpoolctl (3.1.0-1) ...
Setting up libcurl3t64-gnutls:arm64 (8.16.0~rc2-1) ...
Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-8) ...
Setting up python3-tabulate (0.9.0-1) ...
Setting up libqt5xml5t64:arm64 (5.15.15+dfsg-6) ...
Setting up python3-all (3.13.7-1) ...
Setting up python3-coverage (7.8.2+dfsg1-1) ...
Setting up python3-ordered-set (4.1.0-1) ...
Setting up python3-yaml (6.0.2-2) ...
Setting up python3-tk:arm64 (3.13.5-1) ...
Setting up debhelper (13.26) ...
Setting up python3-pytz (2025.2-3) ...
Setting up dconf-service (0.40.0-5) ...
Setting up fonts-urw-base35 (20200910-8) ...
Setting up libqt5test5t64:arm64 (5.15.15+dfsg-6) ...
Setting up python3-wheel (0.46.1-2) ...
Setting up python3-matplotlib-inline (0.1.7-1) ...
Setting up python3-comm (0.2.1-1) ...
Setting up python3-pil:arm64 (11.3.0-1) ...
Setting up python3-inflect (7.3.1-2) ...
Setting up libgl1:arm64 (1.7.0-1+b2) ...
Setting up python3-flexparser (0.4-1) ...
Setting up python3-pandas (2.2.3+dfsg-9) ...
Setting up pocl-opencl-icd:arm64 (6.0-6) ...
Setting up python3-pil.imagetk:arm64 (11.3.0-1) ...
Setting up python3-executing (2.2.0-0.3) ...
Setting up python3-rlpycairo (0.3.0-3) ...
Setting up libpython3-all-dev:arm64 (3.13.7-1) ...
Setting up python3-jaraco.text (4.0.0-1) ...
Setting up python3-pexpect (4.9-3) ...
Setting up libglut3.12:arm64 (3.4.0-4) ...
Setting up python3-zmq (26.4.0-1) ...
Setting up python3-dev (3.13.7-1) ...
Setting up python3-requests (2.32.4+dfsg-1) ...
Setting up libboost-python1.83-dev (1.83.0-4.2) ...
Setting up python3-sklearn (1.4.2+dfsg-8) ...
Setting up python3-numexpr (2.11.0-1) ...
Setting up python3-pytools (2025.1.2-1) ...
Setting up libglew2.2:arm64 (2.2.0-4+b2) ...
Setting up python3-reportlab (4.4.3-1) ...
Setting up libhdf5-310:arm64 (1.14.5+repack-3) ...
Setting up libhsa-runtime64-1:arm64 (6.1.2-3) ...
Setting up cmake (4.1.1-1) ...
Setting up python3-jupyter-client (8.6.3-2) ...
Setting up libwxbase3.2-1t64:arm64 (3.2.8+dfsg-2) ...
Setting up python3-dials-data (2.4.0-3) ...
Setting up python3-build (1.2.2-4) ...
Setting up python3-stack-data (0.6.3-1) ...
Setting up python3-pyopencl (2025.1-1) ...
Setting up python3-pkg-resources (78.1.1-0.1) ...
Setting up python3-all-dev (3.13.7-1) ...
Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ...
Setting up libdebuginfod1t64:arm64 (0.192-4) ...
Setting up libcbf1t64:arm64 (0.9.7+dfsg1-5+b1) ...
Setting up python3-setuptools (78.1.1-0.1) ...
Setting up dconf-gsettings-backend:arm64 (0.40.0-5) ...
Setting up python3-jedi (0.19.1+ds1-1) ...
Setting up pybuild-plugin-pyproject (6.20250414) ...
Setting up libnetcdf22:arm64 (1:4.9.3-1+b1) ...
Setting up python3-h5py-serial (3.14.0-2) ...
Setting up python3-opengl (3.1.10+dfsg-1) ...
Setting up libboost-python-dev (1.83.0.2+b2) ...
Setting up python3-pint (0.25-1) ...
Setting up libqt5gui5t64:arm64 (5.15.15+dfsg-6) ...
Setting up gdb (16.3-4) ...
Setting up libamdhip64-5:arm64 (5.7.1-6) ...
Setting up python3-pooch (1.8.2-1) ...
Setting up python3-ipython (8.35.0-1) ...
Setting up python3-pycbf (0.9.7+dfsg1-5+b1) ...
Setting up python3-h5py (3.14.0-2) ...
Setting up python3-hdf5plugin (5.1.0-1) ...
Setting up python3-nxmx (0.0.4-1) ...
Setting up libgtk-3-common (3.24.50-2) ...
Setting up libcctbx0 (2024.10+ds2+~3.22.1+ds1-5) ...
Setting up libucx0:arm64 (1.18.1+ds-2+b1) ...
Setting up libqt5widgets5t64:arm64 (5.15.15+dfsg-6) ...
Setting up libqt5svg5:arm64 (5.15.15-2) ...
Setting up python3-debugpy (1.8.12+ds-1) ...
Setting up libqt5help5:arm64 (5.15.15-6) ...
Setting up libgtk-3-0t64:arm64 (3.24.50-2) ...
Setting up python3-ipykernel (6.30.1-1) ...
Setting up libqt5opengl5t64:arm64 (5.15.15+dfsg-6) ...
Setting up libwxgtk3.2-1t64:arm64 (3.2.8+dfsg-2) ...
Setting up libcctbx-dev (2024.10+ds2+~3.22.1+ds1-5) ...
Setting up libqt5printsupport5t64:arm64 (5.15.15+dfsg-6) ...
Setting up libopenmpi40:arm64 (5.0.8-4) ...
Setting up libwxgtk-gl3.2-1t64:arm64 (3.2.8+dfsg-2) ...
Setting up libqt5designer5:arm64 (5.15.15-6) ...
Setting up python3-wxgtk4.0 (4.2.3+dfsg-2) ...
Setting up libhdf5-openmpi-310:arm64 (1.14.5+repack-3) ...
Setting up python3-qtconsole (5.6.1-4) ...
Setting up python3-pyqt5 (5.15.11+dfsg-2) ...
Setting up python3-pyqt5.qtsvg (5.15.11+dfsg-2) ...
Setting up bitshuffle (0.5.2-1+b3) ...
Setting up python3-pyqt5.qtopengl (5.15.11+dfsg-2) ...
Setting up python3-pymol (3.1.0+dfsg-1+b1) ...
Setting up python3-fonttools (4.57.0-1) ...
Setting up python3-ufolib2 (0.17.1+dfsg1-1) ...
Setting up python3-matplotlib (3.10.1+dfsg1-4) ...
Setting up python3-fabio (2024.9.0-8) ...
Setting up python3-silx (2.2.1+dfsg-3) ...
Setting up python3-cctbx (2024.10+ds2+~3.22.1+ds1-5) ...
/usr/lib/python3/dist-packages/iotbx/pdb/utils.py:18: SyntaxWarning: invalid escape sequence '\{'
  []_,.;:"&<>()/\{}'`~!@#$%*|+-
/usr/lib/python3/dist-packages/iotbx/pdb/utils.py:46: SyntaxWarning: invalid escape sequence '\/'
  special_characters = """[]_,.;:"&<>()\/\{}'`~!@#$%*|+-"""
/usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:724: SyntaxWarning: invalid escape sequence '\o'
  width=pairwise_differences_db, label='$\omega_{hkl}$'
/usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:739: SyntaxWarning: invalid escape sequence '\o'
  axes[0].set_ylabel('Distribution of $\omega_{hbk}$')
/usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:740: SyntaxWarning: invalid escape sequence '\o'
  axes[0].set_xlabel('Normalized PD ($\omega_{hbk}$)')
/usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:759: SyntaxWarning: invalid escape sequence '\o'
  axes[1].set_xlabel('Sorted Normalized PD ($\omega_{hbk}$)')
/usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:778: SyntaxWarning: invalid escape sequence '\s'
  axes[2].set_ylabel('Standard Deviation of $I_{hbk}/\sigma_{hbk}$')
/usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:807: SyntaxWarning: invalid escape sequence '\m'
  axes_sadd.set_ylabel('$s_{\mathrm{fac}}^2 \\times s_{\mathrm{add}}^2$')
Setting up python3-pyfai (2025.03-1) ...
Processing triggers for debianutils (5.23.2) ...
Processing triggers for libc-bin (2.41-12) ...
Processing triggers for systemd (258~rc3-1) ...
Processing triggers for sgml-base (1.31+nmu1) ...
Setting up w3c-sgml-lib (1.3-3) ...
Setting up python3-biopython (1.85+dfsg-4) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20250419) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.

+------------------------------------------------------------------------------+
| Check architectures                          Fri, 29 Aug 2025 16:51:34 +0000 |
+------------------------------------------------------------------------------+

E: dsc: arm64 not in arch list or does not match any arch wildcards: amd64 -- skipping

+------------------------------------------------------------------------------+
| Cleanup                                      Fri, 29 Aug 2025 16:51:35 +0000 |
+------------------------------------------------------------------------------+

Purging /build/reproducible-path
Not cleaning session: cloned chroot in use
E: dsc: arm64 not in arch list or does not match any arch wildcards: amd64 -- skipping

+------------------------------------------------------------------------------+
| Summary                                      Fri, 29 Aug 2025 16:51:39 +0000 |
+------------------------------------------------------------------------------+

Build Architecture: arm64
Build Type: binary
Build-Space: n/a
Build-Time: 0
Distribution: sid
Fail-Stage: arch-check
Host Architecture: arm64
Install-Time: 254
Job: /tmp/debusine-fetch-exec-upload-83wclll8/dials_3.22.1+dfsg3-1.dsc
Machine Architecture: arm64
Package: dials
Package-Time: 0
Source-Version: 3.22.1+dfsg3-1
Space: n/a
Status: skipped
Version: 3.22.1+dfsg3-1
--------------------------------------------------------------------------------
Finished at 2025-08-29T16:46:45Z
Build needed 00:00:00, no disk space

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

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/2391122/

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/152697/

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

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