Package: src:python-biopython Version: 1.88+dfsg-1 Severity: serious 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, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202608/ 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 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 cannot 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:python-biopython, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] dh_auto_install install -m0755 -d /<<BUILDDIR>>/python-biopython-1.88\+dfsg/debian/tmp pybuild --install -i python{version} -p "3.13 3.14" --parallel=2 I: pybuild plugin_pyproject:199: Copying package built for python3.13 to destdir I: pybuild pybuild:416: rm -fr /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3*/dist-packages/biopython-*/top_level.txt I: pybuild plugin_pyproject:199: Copying package built for python3.14 to destdir I: pybuild pybuild:416: rm -fr /<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3*/dist-packages/biopython-*/top_level.txt dh_numpy3 -ppython3-biopython Possible precedence problem between ! and pattern match (m//) at /usr/bin/dh_numpy3 line 68. Can't stat debian/python3-biopython: No such file or directory at /usr/bin/dh_numpy3 line 86. dh_numpy3: skipping binary package python3-biopython which does not depend on the NumPy C ABI make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_install -O--buildsystem=pybuild install -m0755 -d debian/python3-biopython//usr/lib/python3.13/dist-packages cp --reflink=auto -a debian/tmp/usr/lib/python3.13/dist-packages/Bio debian/tmp/usr/lib/python3.13/dist-packages/biopython-1.88.dist-info debian/python3-biopython//usr/lib/python3.13/dist-packages/ install -m0755 -d debian/python3-biopython//usr/lib/python3.14/dist-packages cp --reflink=auto -a debian/tmp/usr/lib/python3.14/dist-packages/Bio debian/tmp/usr/lib/python3.14/dist-packages/biopython-1.88.dist-info debian/python3-biopython//usr/lib/python3.14/dist-packages/ install -m0755 -d debian/python3-biopython-sql//usr/lib/python3.13/dist-packages cp --reflink=auto -a debian/tmp/usr/lib/python3.13/dist-packages/BioSQL debian/python3-biopython-sql//usr/lib/python3.13/dist-packages/ install -m0755 -d debian/python3-biopython-sql//usr/lib/python3.14/dist-packages cp --reflink=auto -a debian/tmp/usr/lib/python3.14/dist-packages/BioSQL debian/python3-biopython-sql//usr/lib/python3.14/dist-packages/ rm -f debian/python-biopython-doc.debhelper.log debian/python3-biopython-sql.debhelper.log debian/python3-biopython.debhelper.log debian/rules override_dh_installdocs-indep make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_installdocs -i dh_installdocs: warning: The use of prefix-less debhelper config files is deprecated. dh_installdocs: warning: Please rename "debian/docs" to "debian/python3-biopython.docs" dh_installdocs: warning: Prefix-less debhelper config files will trigger an error in compat 15 or later dh_installdocs: warning: Cannot auto-detect main package for python-biopython-doc. If the default is wrong, please use --doc-main-package or the X-Doc-Main-Package field install -m0755 -d debian/python-biopython-doc/usr/share/doc/python-biopython-doc install -m0755 -d debian/python-biopython-doc/usr/share/doc/python-biopython-doc cd './Doc/_build/html/..' && find 'html' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /<<PKGBUILDDIR>>/debian/python-biopython-doc/usr/share/doc/python-biopython-doc cp --reflink=auto -a ./debian/README.test debian/python-biopython-doc/usr/share/doc/python-biopython-doc cp --reflink=auto -a ./debian/tests/run-unit-test debian/python-biopython-doc/usr/share/doc/python-biopython-doc cd './debian/Tests_fixme/..' && find 'Tests_fixme' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /<<PKGBUILDDIR>>/debian/python-biopython-doc/usr/share/doc/python-biopython-doc chmod -R u\+rw,go=rX debian/python-biopython-doc/usr/share/doc install -p -m0644 debian/copyright debian/python-biopython-doc/usr/share/doc/python-biopython-doc/copyright install -m0755 -d debian/python-biopython-doc/usr/share/doc-base/ install -p -m0644 debian/python-biopython-doc.doc-base debian/python-biopython-doc/usr/share/doc-base/python-biopython-doc.biopython-tutorial install -m0755 -d debian/python3-biopython-sql/usr/share/doc/python3-biopython-sql install -p -m0644 debian/copyright debian/python3-biopython-sql/usr/share/doc/python3-biopython-sql/copyright # dh_installdocs seems to refuse copying zero length files (for # instance Tests/Blast/tab_2226_tblastn_002.txt) but these are # needed for the tests as well cp -a debian/tmp_tests/* /<<PKGBUILDDIR>>/debian/python-biopython-doc/usr/share/doc/python-biopython-doc cp: cannot stat 'debian/tmp_tests/*': No such file or directory make[1]: *** [debian/rules:156: override_dh_installdocs-indep] Error 1 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:64: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 --------------------------------------------------------------------------------
