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/202512/

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

(It's a wiki, so you are welcome to contribute)

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-pbcore, so that this is still
visible in the BTS web page for this package.

Thanks.
--------------------------------------------------------------------------------
[...]
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pbcore/usr/lib/python3.13/dist-packages/pbcore/io/__init__.py to __init__.cpython-313.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pbcore/usr/lib/python3.13/dist-packages/pbcore/io/base.py to base.cpython-313.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pbcore/usr/lib/python3.13/dist-packages/pbcore/__init__.py to __init__.cpython-313.pyc
running install_egg_info
Copying pbcore.egg-info to /<<PKGBUILDDIR>>/debian/python3-pbcore/usr/lib/python3.13/dist-packages/pbcore-2.2.0.egg-info
Skipping SOURCES.txt
running install_scripts
Installing .open script to /<<PKGBUILDDIR>>/debian/python3-pbcore/usr/bin
I: pybuild pybuild:334: chmod -x /<<PKGBUILDDIR>>/debian/python3-pbcore//usr/lib/python3.13/dist-packages/pbcore/data/datasets/*.xml
   debian/rules execute_before_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p _tmp/usr/share/doc/python3-pbcore
cp -a tests _tmp/usr/share/doc/python3-pbcore
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_install -O--buildsystem=pybuild
   debian/rules execute_after_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mv /<<PKGBUILDDIR>>/debian/python3-pbcore/usr/bin/.open /<<PKGBUILDDIR>>/debian/python3-pbcore/usr/bin/pbopen
rmdir /<<PKGBUILDDIR>>/debian/python-pbcore-doc/usr/share/doc/python3-pbcore/html/_images/
rmdir: failed to remove '/<<PKGBUILDDIR>>/debian/python-pbcore-doc/usr/share/doc/python3-pbcore/html/_images/': No such file or directory
make[1]: *** [debian/rules:30: execute_after_dh_install] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:19: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------

tags 1122324 patch
thanks

Hello.

This one is weird because in theory I fixed it in version 2.1.2+dfsg-13.

Maybe I was mistaken (sorry if that's the case), or maybe some of the
build-dependencies now behave differently. Or maybe I put too much
trust in the salsa job to check this. If I remember well, it does
not work and I had to file a bug against salsa ci for that.

Anyway, my script check-nocheck tells me that this time the bug may be
fixed by dropping <!nocheck> from python3-biopython in d/control
(as in the attached patch).

I leave the upload to you, please double-check.

Thanks.

Hi Santiago,

I've applied your patch since I think this builds fine.  The problem
with the new version of numpy inside autopkgtest remains unfortunately.

Thanks a lot for your contribution in any case
   Andreas.

Am Wed, Dec 10, 2025 at 10:19:02AM +0100 schrieb Santiago Vila:

( several months later :-)

Hello.

I've made an upload to fix this anyway.

I am well aware that the resulting package will not propagate to
testing because of the numpy issue, but at least I will not find the
nocheck bug again in my next archive rebuild.

I'll try to explain in the numpy bug my failed attempt at fixing it,
maybe Étienne or somebody else can make it to work from that.

Thanks.

We believe that the bug you reported is fixed in the latest version of
python-pbcore, 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 1122324@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Santiago Vila <sanvila@debian.org> (supplier of updated python-pbcore 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 ftpmaster@ftp-master.debian.org)
Format: 1.8
Date: Wed, 24 Jun 2026 11:50:00 +0200
Source: python-pbcore
Architecture: source
Version: 2.1.2+dfsg-14
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Santiago Vila <sanvila@debian.org>
Closes: 1122324
Changes:
 python-pbcore (2.1.2+dfsg-14) unstable; urgency=medium
 .
   * Team upload.
 .
   [ Santiago Vila ]
   * Drop <!nocheck> from python3-biopython. Closes: #1122324.
   * Drop "Priority: optional" (default).
   * Update standards-version.
   * Fine-tune salsa-ci.yml.
 .
   [ Michael R. Crusoe ]
   * Update debian/gbp.conf.
 .
   [ Andreas Tille ]
   * Switch watch file to version 5.
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 23cf52104a509c3ab051ccd9c87858b19d4c6e0a 62868 python-pbcore_2.1.2+dfsg-14.debian.tar.xz
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Hi Santiago,

Santiago Vila, on 2026-06-24:

Thanks for your work on this, even if the package does not
migrate, it is a step towards a fully fixed package.

Acknowledged, I saw you comment and the patch you provided in
#1114717.  I don't promise immediate action, but I wrote down to
have a closer look at that in the future.

Have a nice day,  :)