Bug#1116728: dials: FTBFS with the nocheck build profile

[Santiago Vila]

Package: src:dials
Version: 3.25.0+dfsg3-2
Severity: important
Tags: forky sid ftbfs
User: debian-qa at lists.debian.org
Usertags: ftbfs-nocheck-profile

Dear maintainer:

During a rebuild of all packages in unstable using the nocheck build profile,
your package failed to build.

Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202509/

A wiki page discussing how to reproduce bugs in this category and
possible solutions is available here:

https://wiki.debian.org/qa.debian.org/FTBFS/Nocheck

(It's a wiki, so you are welcome to contribute)

[ Note: This is RC, but I will wait at least two weeks before raising
the severities, there are a lot of gcc-15 and CMake 4 bugs open now ].

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:dials, so that this is still
visible in the BTS web page for this package.

Thanks.

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[...]
 debian/rules clean
dh clean --buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
	pybuild --clean -i python{version} -p 3.13
I: pybuild base:311: python3.13 setup.py clean 
/usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!

        ********************************************************************************
        Please consider removing the following classifiers in favor of a SPDX license expression:

        License :: OSI Approved :: BSD License

        See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
        ********************************************************************************

!!
  self._finalize_license_expression()
Found 92 dials dispatchers
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dials/build' (and everything under it)
'build/bdist.linux-x86_64' does not exist -- can't clean it
'build/scripts-3.13' does not exist -- can't clean it
	rm -rf .pybuild/
	find . -name \*.pyc -exec rm {} \;
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/dials.substvars debian/python3-dials.substvars debian/files
	rm -fr -- debian/dials/ debian/tmp/ debian/python3-dials/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
 debian/rules binary
dh binary --buildsystem=pybuild
   dh_update_autotools_config -O--buildsystem=pybuild
   dh_autoreconf -O--buildsystem=pybuild
   dh_auto_configure -O--buildsystem=pybuild
	pybuild --configure -i python{version} -p 3.13
I: pybuild base:311: python3.13 setup.py config 
/usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!

        ********************************************************************************
        Please consider removing the following classifiers in favor of a SPDX license expression:

        License :: OSI Approved :: BSD License

        See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
        ********************************************************************************

!!
  self._finalize_license_expression()
Found 92 dials dispatchers
running config
I: pybuild pybuild:334: cmake -DPython_EXECUTABLE=/usr/bin/python3.13 -S . -B /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dials/build/lib
-- The C compiler identification is GNU 15.2.0
-- The CXX compiler identification is GNU 15.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- 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 Python: /usr/bin/python3.13 (found version "3.13.7") found components: Interpreter Development Development.Module Development.Embed
Error: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dials/build/lib/libtbx_env is not a file
CMake Error at cmake/Modules/FindCCTBX.cmake:109 (message):
  Failed to read environment file:
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dials/build/lib//libtbx_env
Call Stack (most recent call first):
  cmake/Modules/FindCCTBX.cmake:116 (_read_libtbx_env)
  cmake/Modules/FindCCTBX.cmake:263 (_cctbx_read_module)
  CMakeLists.txt:18 (find_package)


-- Configuring incomplete, errors occurred!
E: pybuild pybuild:389: configure: plugin distutils failed with: exit code=1: cmake -DPython_EXECUTABLE=/usr/bin/python3.13 -S . -B /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dials/build/lib
dh_auto_configure: error: pybuild --configure -i python{version} -p 3.13 returned exit code 13
make: *** [debian/rules:22: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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