Bug#1116719: cctbx: FTBFS with the nocheck build profile

[Santiago Vila]

Package: src:cctbx
Version: 2024.10+ds2+~3.22.1+ds1-5
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:cctbx, 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
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cp -f debian/setup.py setup.py
cp -r debian/annlib_adaptbx annlib_adaptbx
mkdir annlib
cp -r debian/ccp4io_adaptbx ccp4io_adaptbx
mkdir ccp4io
cp -r debian/gui_resources gui_resources
dh_auto_clean
	pybuild --clean -i python{version} -p 3.13
I: pybuild base:311: python3.13 setup.py clean 
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/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 {} \;
find . -name __pycache__ -type d -exec rm -rf {} \;
rm -f setup.py
rm -rf annlib annlib_adaptbx
rm -rf ccp4io ccp4io_adaptbx
rm -rf gui_resources
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/libcctbx0.substvars debian/libcctbx-dev.substvars debian/python3-cctbx.substvars debian/files
	rm -fr -- debian/libcctbx0/ debian/tmp/ debian/libcctbx-dev/ debian/python3-cctbx/
	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
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cp -f debian/setup.py setup.py
cp -r debian/annlib_adaptbx annlib_adaptbx
mkdir annlib
cp -r debian/ccp4io_adaptbx ccp4io_adaptbx
mkdir ccp4io
cp -r debian/gui_resources gui_resources
# configure the cctbx python modules
dh_auto_configure
	pybuild --configure -i python{version} -p 3.13
I: pybuild base:311: python3.13 setup.py config 
running config
# configure dxtbx python modules
dh_auto_configure --sourcedirectory=dxtbx
	pybuild --configure -i python{version} -p 3.13 --dir dxtbx
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 21 dxtbx dispatchers
Found 140 Format classes
running config
# configure the cctbx libtbx build system
dh_auto_configure -- -s custom --configure-args="mkdir -p {build_dir}_ && cd {build_dir}_ \
	&& {interpreter} /<<PKGBUILDDIR>>/libtbx/configure.py --build=debug --use_environment_flags --cxxstd=c++14 annlib_adaptbx boost_adaptbx cbflib_adaptbx ccp4io_adaptbx cctbx cma_es crys3d dxtbx fable gltbx iotbx libtbx mmtbx omptbx rstbx scitbx serialtbx smtbx spotfinder tbxx wxtbx annlib ccp4io"
	pybuild --configure -i python{version} -p 3.13 -s custom --configure-args="mkdir -p {build_dir}_ && cd {build_dir}_ 	&& {interpreter} /<<PKGBUILDDIR>>/libtbx/configure.py --build=debug --use_environment_flags --cxxstd=c++14 annlib_adaptbx boost_adaptbx cbflib_adaptbx ccp4io_adaptbx cctbx cma_es crys3d dxtbx fable gltbx iotbx libtbx mmtbx omptbx rstbx scitbx serialtbx smtbx spotfinder tbxx wxtbx annlib ccp4io"
I: pybuild base:311: mkdir -p '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build'_ && cd '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build'_ 	&& python3.13 /<<PKGBUILDDIR>>/libtbx/configure.py --build=debug --use_environment_flags --cxxstd=c++14 annlib_adaptbx boost_adaptbx cbflib_adaptbx ccp4io_adaptbx cctbx cma_es crys3d dxtbx fable gltbx iotbx libtbx mmtbx omptbx rstbx scitbx serialtbx smtbx spotfinder tbxx wxtbx annlib ccp4io

******************************************************************************
FATAL: For Python 2/3 compatibility, CCTBX currently requires the six and
  future modules.
To install, please use pip or conda (if available)
  pip install six future
  conda install six future
******************************************************************************

E: pybuild pybuild:389: configure: plugin custom failed with: exit code=1: mkdir -p '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build'_ && cd '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build'_ 	&& python3.13 /<<PKGBUILDDIR>>/libtbx/configure.py --build=debug --use_environment_flags --cxxstd=c++14 annlib_adaptbx boost_adaptbx cbflib_adaptbx ccp4io_adaptbx cctbx cma_es crys3d dxtbx fable gltbx iotbx libtbx mmtbx omptbx rstbx scitbx serialtbx smtbx spotfinder tbxx wxtbx annlib ccp4io
dh_auto_configure: error: pybuild --configure -i python{version} -p 3.13 -s custom --configure-args="mkdir -p {build_dir}_ && cd {build_dir}_ 	&& {interpreter} /<<PKGBUILDDIR>>/libtbx/configure.py --build=debug --use_environment_flags --cxxstd=c++14 annlib_adaptbx boost_adaptbx cbflib_adaptbx ccp4io_adaptbx cctbx cma_es crys3d dxtbx fable gltbx iotbx libtbx mmtbx omptbx rstbx scitbx serialtbx smtbx spotfinder tbxx wxtbx annlib ccp4io" returned exit code 13
make[1]: *** [debian/rules:54: override_dh_auto_configure] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:24: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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