Control: tags -1 + confirmed Hi Reinhard,
Thanks for your time investigating this issue! On the good news front, I confirm I can reproduce the problem with qemu-user, so this facilitate debugging even without direct access to the real hardware. Reinhard Tartler, on 2024-08-23: > test_Align_clustal ... ok […] > This tells me that there is unlikely a single test that could be disabled get > the build unstuck. Probably yes. The next test would be test_Align_codonalign, and it does not hang during the test suite execution with minimal dependencies set (test-name=dependencies). It only occurs with the test-name=full_suite which includes all build dependencies. > Rather, the issue seems triggered by the run_tests.py, and > might require a change to either run_tests.py [1] or the python interpreter on > riscv64? > > [1] > https://sources.debian.org/src/python-biopython/1.83%2Bdfsg1-3/Tests/run_tests.py/ The test would hang somewhere in this loop: start_time = time.time() for test in self.tests: ok = self.runTest(test) if not ok: failures += 1 total = len(self.tests) which would point fingers to the runTest method, which does all sorts of things beyond triggering each test. Assuming output is properly flushed, I think we hang someplace in the following hunk: def runTest(self, name): from Bio import MissingPythonDependencyError from Bio import MissingExternalDependencyError result = self._makeResult() output = StringIO() # Restore the language and thus default encoding (in case a prior # test changed this, e.g. to help with detecting command line tools) global SYSTEM_LANG os.environ["LANG"] = SYSTEM_LANG # Always run tests from the Tests/ folder where run_tests.py # should be located (as we assume this with relative paths etc) os.chdir(self.testdir) try: stdout = sys.stdout sys.stdout = output if name.startswith("test_"): # It's a unittest sys.stderr.write(f"{name} ... ") I'm at loss reasoning about the _makeResult method for now. Maybe there is something off about output handling by StringIO? I haven't dug further for the moment. Upstream recently released Biopython 1.84. It seems to have a couple of cosmetic changes to the run_test.py script. It could be worth a shot too. Have a nice day, :) -- .''`. Étienne Mollier <emoll...@debian.org> : :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/1, please excuse my verbosity `-
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