Debian Patches
Status for gubbins/3.4-2
| Patch | Description | Author | Forwarded | Bugs | Origin | Last update |
|---|---|---|---|---|---|---|
| do_not_handle_python_by_upstream_build_system.patch | Installation for Python files does not work that way and this is done manually in debian/rules | Andreas Tille <tille@debian.org> | no | 2015-11-19 | ||
| gubbins_exe_in_usr_lib.patch | gubbins executable prints that it is not intended for direct usage While default install procedure installs gubbins executable to /usr/bin it prints that it is intended to be called from run_gubbins. So it makes sense to rather install it to /usr/lib/gubbins instead of /usr/bin. |
Andreas Tille <tille@debian.org> | no | 2015-11-19 | ||
| iqtree2.patch | Adapt test to iqtree2 | Andreas Tille <tille@debian.org> | yes | debian | 2022-02-13 | |
| autoupdate_configure.ac.patch | autoupdate to avoid warnings from configure.ac | Andreas Tille <tille@debian.org> | not-needed | 2023-07-12 | ||
| python3-shebang.patch | fix unversioned Python shebang of a couple of scripts. | Étienne Mollier <emollier@debian.org> | not-needed | 2024-05-22 | ||
| remove-numba-temporarily.patch | disable numba in upstream code. This patch keeps gubbins running while numba is not available in testing. Ideally, numba should be simply recommended, and the code to proceed to numba JIT compilation should be capable of shifting gears to no-optimization in order to support situations where numba is not available. |
Étienne Mollier <emollier@debian.org> | not-needed | debian | 2024-05-22 | |
| numpy2.patch | fix runtime failures with Numpy ≥ 2. This patch fixes the following symptom when running gubbins with Numpy version 2 and more: . Running joint ancestral reconstruction with pyjar Traceback (most recent call last): File "/usr/bin/run_gubbins", line 33, in <module> sys.exit(load_entry_point('gubbins==3.4', 'console_scripts', 'run_gubbins.py')()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^ File "/usr/share/gubbins/gubbins/run_gubbins.py", line 166, in main gubbins.common.parse_and_run(parser.parse_args(), parser.description) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/share/gubbins/gubbins/common.py", line 373, in parse_and_run jar(sequence_names = ordered_sequence_names, # complete polymorphism alignment ~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ base_patterns = base_pattern_bases_array, # array of unique base patterns in alignment ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ...<8 lines>... verbose = input_args.verbose, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ max_pos = max_pos) ^^^^^^^^^^^^^^^^^^ File "/usr/share/gubbins/gubbins/pyjar.py", line 646, in jar node_pij = numpy.full((num_nodes,16), numpy.NINF, dtype=numpy.float32) ^^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 400, in __getattr__ raise AttributeError( ...<3 lines>... ) AttributeError: `np.NINF` was removed in the NumPy 2.0 release. Use `-np.inf` instead. |
Étienne Mollier <emollier@debian.org> | yes | 2025-02-28 |