Your message dated Fri, 21 Aug 2026 18:06:56 +0000
with message-id <[email protected]>
and subject line Bug#1144126: fixed in python-biopython 1.88+dfsg-2
has caused the Debian Bug report #1144126,
regarding python-biopython: FTBFS with the nocheck build profile
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1144126: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1144126
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: python-biopython
Source-Version: 1.88+dfsg-2
Done: Karsten Schöke <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-biopython, 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.
Karsten Schöke <[email protected]> (supplier of updated
python-biopython 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: Fri, 21 Aug 2026 19:17:36 +0200
Source: python-biopython
Architecture: source
Version: 1.88+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Karsten Schöke <[email protected]>
Closes: 1144126
Changes:
python-biopython (1.88+dfsg-2) unstable; urgency=medium
.
* Team upload.
* lintian-overrides are no longer needed.
* fix routine-update issue.
* d/rules: Fix FTBR: The second build is invoked with
the `nocheck` option again. (Closes: #1144126)
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