[Debichem-devel] Bug#1104289: openstructure: FTBFS: PermissionError: [Errno 13] Permission denied: 'debian/openstructure/usr/bin/ost-compare-ligand-structures'

[Santiago Vila]

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.