Your message dated Fri, 24 Oct 2025 18:05:07 +0000
with message-id <[email protected]>
and subject line Bug#1116719: fixed in cctbx 2025.2+ds2+~3.23.0+ds1-1
has caused the Debian Bug report #1116719,
regarding cctbx: FTBFS with the nocheck build profile
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1116719: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1116719
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:cctbx
Version: 2024.10+ds2+~3.22.1+ds1-5
Severity: important
Tags: forky sid ftbfs
User: [email protected]
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.
--------------------------------------------------------------------------------
[...]
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
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: cctbx
Source-Version: 2025.2+ds2+~3.23.0+ds1-1
Done: Roland Mas <[email protected]>
We believe that the bug you reported is fixed in the latest version of
cctbx, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Roland Mas <[email protected]> (supplier of updated cctbx package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 24 Oct 2025 19:38:49 +0200
Source: cctbx
Architecture: source
Version: 2025.2+ds2+~3.23.0+ds1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers
<[email protected]>
Changed-By: Roland Mas <[email protected]>
Closes: 1085414 1116719
Changes:
cctbx (2025.2+ds2+~3.23.0+ds1-1) unstable; urgency=medium
.
[ Picca Frédéric-Emmanuel ]
* New upstream version 2025.2+ds2+~3.23.0+ds1
.
[ Roland Mas ]
* Bug fix: "FTBFS with the nocheck build profile", thanks to Santiago
Vila (Closes: #1116719).
* Bug fix: "Python SyntaxWarning", thanks to Graham Inggs (Closes:
#1085414).
Checksums-Sha1:
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cctbx_2025.2+ds2+~3.23.0+ds1-1.dsc
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cctbx_2025.2+ds2+~3.23.0+ds1.orig-dxtbx.tar.xz
bf97229f39ff1f7e5065409cedc7ef6bd44094b5 23958624
cctbx_2025.2+ds2+~3.23.0+ds1.orig.tar.xz
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cctbx_2025.2+ds2+~3.23.0+ds1-1.debian.tar.xz
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cctbx_2025.2+ds2+~3.23.0+ds1-1_amd64.buildinfo
Checksums-Sha256:
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cctbx_2025.2+ds2+~3.23.0+ds1.orig-dxtbx.tar.xz
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cctbx_2025.2+ds2+~3.23.0+ds1.orig.tar.xz
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cctbx_2025.2+ds2+~3.23.0+ds1-1.debian.tar.xz
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cctbx_2025.2+ds2+~3.23.0+ds1-1_amd64.buildinfo
Files:
cc837fdcb089b419e1f1aaa264728f43 4050 science optional
cctbx_2025.2+ds2+~3.23.0+ds1-1.dsc
2380dd554091f2aa476df013371ae440 379044 science optional
cctbx_2025.2+ds2+~3.23.0+ds1.orig-dxtbx.tar.xz
c5d68253419b1e6fe15068e5e5631334 23958624 science optional
cctbx_2025.2+ds2+~3.23.0+ds1.orig.tar.xz
0941877dab1bc736ff813c8e16a0ac9c 423376 science optional
cctbx_2025.2+ds2+~3.23.0+ds1-1.debian.tar.xz
933b7b1380df019579f85fc9e2d44bdf 22381 science optional
cctbx_2025.2+ds2+~3.23.0+ds1-1_amd64.buildinfo
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