Your message dated Tue, 06 Jan 2026 18:34:17 +0000
with message-id <[email protected]>
and subject line Bug#1119699: fixed in cctbx 2025.12+ds2+~3.26.0+ds1-1
has caused the Debian Bug report #1119699,
regarding cctbx: ftbfs with pip 25.3
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.
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--
1119699: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1119699
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: cctbx
Severity: serious
Tags: ftbfs
Justification: ftbfs
Dear Maintainer,
cctbx currently fails to build from source in sid with the
following symptom:
Obtaining
file:///build/reproducible-path/cctbx-2025.2%2Bds2%2B~3.23.0%2Bds1/dxtbx
Checking if build backend supports build_editable: started
Checking if build backend supports build_editable: finished with
status 'done'
ERROR: Project
file:///build/reproducible-path/cctbx-2025.2%2Bds2%2B~3.23.0%2Bds1/dxtbx uses a
build backend that is missing the 'build_editable' hook, so it cannot be
installed in editable mode. Consider using a build backend that supports PEP
660.
Processing:
"/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/cctbx/libtbx_refresh.py"
Generating C++ files in:
"/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/cctbx/eltbx"
Generating C++ files in:
"/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include/cctbx/boost_python"
Processing:
"/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/crys3d/libtbx_refresh.py"
Processing:
"/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/smtbx/libtbx_refresh.py"
Generating C++ files in:
"/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/include/smtbx/boost_python"
Processing:
"/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/iotbx/libtbx_refresh.py"
Using fable to convert iotbx/pdb/hybrid_36_f.f
Writing: iotbx/pdb/hybrid_36_fem.cpp
Processing:
"/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx/libtbx_refresh.py"
Traceback (most recent call last):
File
"/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/libtbx/configure.py",
line 33, in <module>
if not run():
~~~^^
File
"/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/libtbx/configure.py",
line 28, in run
libtbx.env_config.cold_start(sys.argv)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^
File
"/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/libtbx/env_config.py",
line 2980, in cold_start
env.refresh()
~~~~~~~~~~~^^
File
"/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/libtbx/env_config.py",
line 2195, in refresh
module.process_libtbx_refresh_py()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File
"/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/libtbx/env_config.py",
line 2508, in process_libtbx_refresh_py
exec(to_str(fh.read()), global_vars)
~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<string>", line 113, in <module>
File "<string>", line 35, in _install_setup_readonly_fallback
File "/usr/lib/python3.13/subprocess.py", line 577, in run
raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['/usr/bin/python3.13', '-m',
'pip', 'install', '--prefix',
'/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/.pybuild/cpython3_3.13/build_/dxtbx',
'--no-build-isolation', '--no-deps', '--ignore-installed', '-e',
'/build/reproducible-path/cctbx-2025.2+ds2+~3.23.0+ds1/dxtbx']' returned
non-zero exit status 1.
The error looks to be related to the following deprecation
warning when attempting to build cctbx in testing/forky,
appearing in place of the above error:
Obtaining
file:///build/reproducible-path/cctbx-2024.10%2Bds2%2B~3.22.1%2Bds1/dxtbx
Checking if build backend supports build_editable: started
Checking if build backend supports build_editable: finished with
status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Installing collected packages: dxtbx
DEPRECATION: Legacy editable install of dxtbx==3.22.0
from
file:///build/reproducible-path/cctbx-2024.10%2Bds2%2B~3.22.1%2Bds1/dxtbx
(setup.py develop) is deprecated. pip 25.3 will enforce this
behaviour change. A possible replacement is to add a
pyproject.toml or enable --use-pep517, and use setuptools >=
64. If the resulting installation is not behaving as expected,
try using --config-settings editable_mode=compat. Please consult
the setuptools documentation for more information. Discussion
can be found at https://github.com/pypa/pip/issues/11457
Running setup.py develop for dxtbx
Successfully installed dxtbx
[…]
In hope this helps,
--
.''`. Étienne Mollier <[email protected]>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/4, please excuse my verbosity
`- on air: IZZ - Into the Sun
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Description: PGP signature
--- End Message ---
--- Begin Message ---
Source: cctbx
Source-Version: 2025.12+ds2+~3.26.0+ds1-1
Done: Picca Frédéric-Emmanuel <[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.
Picca Frédéric-Emmanuel <[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: Tue, 06 Jan 2026 19:00:31 +0100
Source: cctbx
Architecture: source
Version: 2025.12+ds2+~3.26.0+ds1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers
<[email protected]>
Changed-By: Picca Frédéric-Emmanuel <[email protected]>
Closes: 1119699
Changes:
cctbx (2025.12+ds2+~3.26.0+ds1-1) unstable; urgency=medium
.
* New upstream version 2025.12+ds2+~3.26.0+ds1
* d/patches: refresh series for new upstream version
* d/control: Added B-D
* d/install-cctbx.sh: Added a few files for test
* Bug fix: "ftbfs with pip 25.3", thanks to Étienne Mollier (Closes:
#1119699).
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