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.
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[...]
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
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