Your message dated Tue, 29 Apr 2025 09:25:15 +0000
with message-id <e1u9hdh-0079ag...@fasolo.debian.org>
and subject line Bug#1104289: fixed in openstructure 2.9.3-2
has caused the Debian Bug report #1104289,
regarding openstructure: FTBFS: PermissionError: [Errno 13] Permission denied:
'debian/openstructure/usr/bin/ost-compare-ligand-structures'
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 ow...@bugs.debian.org
immediately.)
--
1104289: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1104289
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:openstructure
Version: 2.9.3-1
Severity: serious
Tags: ftbfs trixie sid
Dear maintainer:
During a rebuild of all packages in trixie, your package failed to build:
[ please read notes at the end ]
--------------------------------------------------------------------------------
[...]
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs
dh_installchangelogs
dh_python3
I: dh_python3 tools:114: replacing shebang in
debian/openstructure/usr/bin/ost-compare-ligand-structures
Traceback (most recent call last):
File "/usr/bin/dh_python3", line 293, in <module>
main()
~~~~^^
File "/usr/bin/dh_python3", line 220, in main
stats = Scanner(interpreter, package, private_dir, options).result
~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/share/dh-python/dhpython/fs.py", line 262, in __init__
self.handle_bin_dir(root, file_names)
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^
File "/usr/share/dh-python/dhpython/fs.py", line 446, in handle_bin_dir
if fix_shebang(fpath, self.options.shebang):
~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/share/dh-python/dhpython/tools.py", line 123, in fix_shebang
with open(fpath, 'wb') as fp:
~~~~^^^^^^^^^^^^^
PermissionError: [Errno 13] Permission denied:
'debian/openstructure/usr/bin/ost-compare-ligand-structures'
make: *** [debian/rules:17: binary] Error 1
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202504/
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 could not 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:openstructure, so that this is still
visible in the BTS web page for this package.
Thanks.
Notes:
- A similar error happens here in unstable:
https://tests.reproducible-builds.org/debian/rbuild/unstable/amd64/openstructure_2.9.3-1.rbuild.log.gz
so it's not trixie-specific.
- Could this be a bug in dh-python? The issue seems related with shebangs,
so it's similar to #1103150, but that one is already fixed and the fix is in
testing.
I'm adding Piotr to X-Debbugs-Cc.
--- End Message ---
--- Begin Message ---
Source: openstructure
Source-Version: 2.9.3-2
Done: Andrius Merkys <mer...@debian.org>
We believe that the bug you reported is fixed in the latest version of
openstructure, 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 1104...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andrius Merkys <mer...@debian.org> (supplier of updated openstructure 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 29 Apr 2025 04:56:31 -0400
Source: openstructure
Architecture: source
Version: 2.9.3-2
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org>
Changed-By: Andrius Merkys <mer...@debian.org>
Closes: 1104289
Changes:
openstructure (2.9.3-2) unstable; urgency=medium
.
* Give write permission for owner of executables (Closes: #1104289)
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