Bug 2417960

Summary: openms fails to build with pip 25.3
Product: [Fedora] Fedora Reporter: Miro Hrončok <mhroncok>
Component: openmsAssignee: Antonio T. sagitter <sagitterghostproton.me>
Status: CLOSED ERRATA QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: unspecified Docs Contact:
Priority: unspecified    
Version: rawhide   
Target Milestone: ---   
Target Release: ---   
Hardware: Unspecified   
OS: Unspecified   
Whiteboard:
Fixed In Version: openms-3.5.0-1.20260107git91afebf.fc43 Doc Type: ---
Doc Text:
Story Points: ---
Clone Of: Environment:
Last Closed: 2026-01-17 00:48:15 UTC Type: Bug
Regression: --- Mount Type: ---
Documentation: --- CRM:
Verified Versions: Category: ---
oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
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Embargoed:
Bug Depends On:    
Bug Blocks: 2384424, 2406299    

Description Miro Hrončok 2025-12-01 09:47:36 UTC
Description of problem:
We want to update pip from 25.2 to 25.3 in Rawhide but openms fails to build:

https://copr.fedorainfracloud.org/coprs/churchyard/pip-25.3/package/openms/


[100%] Packaging pyopenms wheel.
cd /builddir/build/BUILD/openms-3.4.1-build/OpenMS-b886c44b4ca0625932f9874613918856774cfd8d/redhat-linux-build/pyOpenMS && /usr/bin/python3 -m pip wheel -w dist --no-deps --no-binary=pyopenms .
Processing /builddir/build/BUILD/openms-3.4.1-build/OpenMS-b886c44b4ca0625932f9874613918856774cfd8d/redhat-linux-build/pyOpenMS
  Installing build dependencies: started
  Installing build dependencies: finished with status 'error'
  error: subprocess-exited-with-error
  
  × installing build dependencies did not run successfully.
  │ exit code: 1
  ╰─> [7 lines of output]
      WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f4b6a3fe660>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')': /simple/setuptools/
      WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f4b6a3cb250>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')': /simple/setuptools/
      WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f4b6a3cb390>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')': /simple/setuptools/
      WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f4b6a3cb4d0>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')': /simple/setuptools/
      WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f4b6a3cb610>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')': /simple/setuptools/
      ERROR: Could not find a version that satisfies the requirement setuptools>=40.8.0 (from versions: none)
      ERROR: No matching distribution found for setuptools>=40.8.0
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed to build 'file:///builddir/build/BUILD/openms-3.4.1-build/OpenMS-b886c44b4ca0625932f9874613918856774cfd8d/redhat-linux-build/pyOpenMS' when installing build dependencies
gmake[3]: Leaving directory '/builddir/build/BUILD/openms-3.4.1-build/OpenMS-b886c44b4ca0625932f9874613918856774cfd8d/redhat-linux-build'
gmake[3]: *** [src/pyOpenMS/CMakeFiles/pyopenms.dir/build.make:74: src/pyOpenMS/CMakeFiles/pyopenms] Error 1
gmake[2]: Leaving directory '/builddir/build/BUILD/openms-3.4.1-build/OpenMS-b886c44b4ca0625932f9874613918856774cfd8d/redhat-linux-build'
gmake[2]: *** [CMakeFiles/Makefile2:1555: src/pyOpenMS/CMakeFiles/pyopenms.dir/all] Error 2
gmake[1]: *** [CMakeFiles/Makefile2:1562: src/pyOpenMS/CMakeFiles/pyopenms.dir/rule] Error 2
gmake[1]: Leaving directory '/builddir/build/BUILD/openms-3.4.1-build/OpenMS-b886c44b4ca0625932f9874613918856774cfd8d/redhat-linux-build'
gmake: *** [Makefile:390: pyopenms] Error 2

error: Bad exit status from /var/tmp/rpm-tmp.P2CzXU (%build)



This looks like the following change in pip:

https://pip.pypa.io/en/stable/news/#v25-3

"""
Remove support for the deprecated setup.py bdist_wheel mechanism. Consequently, --use-pep517 is now always on, and --no-use-pep517 has been removed.
"""

https://github.com/pypa/pip/issues/6334


As a workaround, try building the package with PIP_NO_BUILD_ISOLATION=0 set -- that disables build isolation (which is a tad confusing, see https://github.com/pypa/pip/issues/5735).


Version-Release number of selected component (if applicable): 2:3.4.1-16.20250722gitb886c44

Steps to Reproduce: Build the package from distgit using our copr linked above. E.g.:

fedpkg --release rawhide mockbuild -- --addrepo=https://download.copr.fedorainfracloud.org/results/churchyard/pip-25.3/fedora-rawhide-x86_64

Comment 1 Miro Hrončok 2025-12-01 13:22:30 UTC
I also noticed in the latest Koji build of openms with pip 25.2: https://koji.fedoraproject.org/koji/buildinfo?buildID=2820144

...
Building wheels for collected packages: pyopenms
  DEPRECATION: Building 'pyopenms' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'pyopenms'. Discussion can be found at https://github.com/pypa/pip/issues/6334
  Building wheel for pyopenms (setup.py): started
  Building wheel for pyopenms (setup.py): finished with status 'done'


Upstream fix: https://github.com/OpenMS/OpenMS/commit/36227d14c021cc61b113919bfaf7f6458bb5adeb from https://github.com/OpenMS/OpenMS/pull/8345

Comment 2 Fedora Admin user for bugzilla script actions 2026-01-05 04:10:35 UTC
This package has changed maintainer in Fedora. Reassigning to the new maintainer of this component.

Comment 3 Fedora Update System 2026-01-08 20:12:28 UTC
FEDORA-2026-4d1e0aeb9b (autowrap-0.25.0-2.fc43 and openms-3.5.0-1.20260107git91afebf.fc43) has been submitted as an update to Fedora 43.
https://bodhi.fedoraproject.org/updates/FEDORA-2026-4d1e0aeb9b

Comment 4 Fedora Update System 2026-01-09 01:32:55 UTC
FEDORA-2026-4d1e0aeb9b has been pushed to the Fedora 43 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2026-4d1e0aeb9b`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2026-4d1e0aeb9b

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 5 Fedora Update System 2026-01-17 00:48:15 UTC
FEDORA-2026-4d1e0aeb9b (autowrap-0.25.0-2.fc43 and openms-3.5.0-1.20260107git91afebf.fc43) has been pushed to the Fedora 43 stable repository.
If problem still persists, please make note of it in this bug report.