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Groups > linux.debian.maint.python > #13105
| From | Juhani Numminen <juhaninumminen0@gmail.com> |
|---|---|
| Newsgroups | linux.debian.bugs.dist, linux.debian.maint.python |
| Subject | Bug#980005: lumpy-sv: lumpyexpress fails with no args |
| Date | 2021-01-12 23:10 +0100 |
| Message-ID | <BwA1r-49m-3@gated-at.bofh.it> (permalink) |
| References | <Bwy9k-30B-5@gated-at.bofh.it> <Bwz5o-3yG-15@gated-at.bofh.it> <Bwy9k-30B-5@gated-at.bofh.it> <Bwz5o-3yG-15@gated-at.bofh.it> |
| Organization | linux.* mail to news gateway |
Cross-posted to 2 groups.
Andreas Tille kirjoitti 12.1.2021 klo 23.08:
> Hi,
>
> I confirm I can reproduce the issue in a minimal chroot while the
> lumpyexpress command prints the help screen as expected. This smells
> like a missing dependency but I do not have any idea which one. It
> seems there is a similar known issue here
>
> https://stackoverflow.com/questions/65028261/attributeerror-module-importlib-has-no-attribute-util-ii
>
> but there is no answer here.
>
> Any idea how to fix this?
>
> Kind regards
>
> Andreas.
It's a change made in debian/patches/lumpyexpress.config.patch.
https://salsa.debian.org/med-team/lumpy-sv/-/commit/e64a65545fbf60c5c98965bc1d00d416b2f9582c#6864ced7557ec33a7ee70c7b0c75b076f84f4fac_24_30
- $PYTHON_TEST -c "import imp; imp.find_module('pysam')"
- $PYTHON_TEST -c "import imp; imp.find_module('numpy')"
+ $PYTHON_TEST -c "import importlib; importlib.util.find_spec('pysam')"
+ $PYTHON_TEST -c "import importlib; importlib.util.find_spec('numpy')"
It's not entirely correct even if it worked: the original causes
a visible error message to alert if one of the required modules does
not exist. The current patch will not cause error messages or the
python check to exit non-zero.
Because it's a Debian context we could rely on dpkg dependencies i.e.
just don't perform this check and comment out the two lines.
--
Juhani
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Bug#980005: lumpy-sv: lumpyexpress fails with no args Andreas Tille <andreas@an3as.eu> - 2021-01-12 22:10 +0100
Bug#980005: lumpy-sv: lumpyexpress fails with no args Juhani Numminen <juhaninumminen0@gmail.com> - 2021-01-12 23:10 +0100
Bug#980005: lumpy-sv: lumpyexpress fails with no args Ken Yamaguchi <debian@knowledgesynthesis.com> - 2021-01-13 00:10 +0100
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