pytest error #539
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Hello! I've seen this before (we communicated privately about pkgsrc maintainership). I believe the way the tests are integrated in the repository, it is expecting the module to be built "inplace" via In my local pkgsrc repo I have the following This has the unfortunate effect of building this library twice. It is low-priority for me to revamp the build system here. |
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That works, thanks. I don't see a problem with the second build when running "make test". However, several tests are failing on all platforms (Alma, macOS, NetBSD). Results from macOS below. |
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Yeah, thank you. It's a result of a few different versions of
dependencies. The tests should be a bit more resilient :)
…On Thu, Dec 28, 2023, 12:16 Jason Bacon ***@***.***> wrote:
That works, thanks. I don't see a problem with the second build when
running "make test".
However, several tests are failing on all platforms (Alma, macOS, NetBSD).
Results from macOS below.
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED doc/source/tutorial.rst::tutorial.rst
FAILED lib/hmmlearn/tests/test_variational_gaussian.py::TestFull::test_fit_mcgrory_titterington1d[scaling] - AssertionError: array([[-1.20874339],
FAILED lib/hmmlearn/tests/test_variational_gaussian.py::TestFull::test_fit_mcgrory_titterington1d[log] - AssertionError: array([[-1.20874339],
FAILED lib/hmmlearn/tests/test_variational_gaussian.py::TestTied::test_fit_mcgrory_titterington1d[scaling] - AssertionError: array([[ 0.78750943],
FAILED lib/hmmlearn/tests/test_variational_gaussian.py::TestTied::test_fit_mcgrory_titterington1d[log] - AssertionError: array([[ 0.78750943],
FAILED lib/hmmlearn/tests/test_variational_gaussian.py::TestSpherical::test_fit_mcgrory_titterington1d[scaling] - AssertionError: array([[-1.20874339],
FAILED lib/hmmlearn/tests/test_variational_gaussian.py::TestSpherical::test_fit_mcgrory_titterington1d[log] - AssertionError: array([[-1.20874339],
FAILED lib/hmmlearn/tests/test_variational_gaussian.py::TestDiagonal::test_fit_mcgrory_titterington1d[scaling] - AssertionError: array([[-1.20874339],
FAILED lib/hmmlearn/tests/test_variational_gaussian.py::TestDiagonal::test_fit_mcgrory_titterington1d[log] - AssertionError: array([[-1.20874339],
===== 9 failed, 286 passed, 16 xfailed, 10 xpassed, 163 warnings in 16.64s =====
*** Error code 1
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Not sure what this is, but the tutorial.rst test fails on all platforms, and this actually seems to terminate testing in the FreeBSD port. pkgsrc: FreeBSD: |
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Yes, noted as well, and not sure why ci/cd is not catching things. Likely
dependency/version excitement.
Appreciate your eyes on all of this. I can't promise any quick fixes, but
I'll do my beset.
…On Fri, Dec 29, 2023 at 7:11 AM Jason Bacon ***@***.***> wrote:
Not sure what this is, but the tutorial.rst test fails on all platforms,
and this actually seems to terminate testing in the FreeBSD port.
pkgsrc:
collected 321 items
doc/source/tutorial.rst F
lib/hmmlearn/tests/test_base.py ................
FreeBSD:
collected 321 items
doc/source/tutorial.rst ld-elf.so.1: Can't find module with TLS index 1
*** Error code 1
Stop.
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I'm working on a FreeBSD port and a pkgsrc package of hmmlearn 0.3.0 (as a dependency of MACS3), and running into an error importing '_hmmc' when running pytest. The error from pkgsrc is the same on Alma Linux 8, macOS 14.0, and NetBSD 9, and the same in the FreeBSD port. FreeBSD is using python 3.9 and pkgsrc python 3.11.
Below is output from "make test" in the pkgsrc package. The long list of environment variables is just the standard pkgsrc test env. The raw command here is:
cd ${WRKSRC} && ${SETENV} ${TEST_ENV} pytest-${PYVERSSUFFIX}
I'm guessing most of the env variables are irrelevant to pytest, but perhaps one of them is throwing something off?
Any suggestions to help identify the problem would be appreciated.
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