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
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
This package has changed maintainer in Fedora. Reassigning to the new maintainer of this component.
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
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.
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.