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Bug#1024425: [Debian-med-packaging] Bug#1024425: help needed on pysam ftbfs with python3.11

From Graham Inggs <ginggs@debian.org>
Newsgroups linux.debian.bugs.dist
Subject Bug#1024425: [Debian-med-packaging] Bug#1024425: help needed on pysam ftbfs with python3.11
Date 2022-12-26 22:20 +0100
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References <FttgJ-4NHW-3@gated-at.bofh.it> <FFWwF-cL30-5@gated-at.bofh.it> <FttgJ-4NHW-3@gated-at.bofh.it> <FFWwF-cL30-5@gated-at.bofh.it>
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Hi Étienne

On Fri, 23 Dec 2022 at 20:03, Étienne Mollier <emollier@emlwks999.eu> wrote:
> Hmn, I'm dry on the python-pysam failure to build from source
> with python3.11, and upstream remained silent for now[1].  If I
> were dealing with C code, I would have suspected something like
> an uncaught segmentation fault, or uninitialized memory usage,
> but cython seems to be a slightly different beast, however
> similar it might sound.
>
> [1]: https://github.com/pysam-developers/pysam/issues/1151
>
> As far as I can tell, the purpose of the test is to check the
> behavior of an iterator once it ran out of values, to make sure
> ValueErrors can be sent to callers.  The test code seems to rely
> on the iterator to return NULL once out, or a memory address in
> a normal situation.  But according to the debugger, the address
> obtained is 0x100000000 (or 2^32), and for some reason, I don't
> even manage to get an ugly workaround checking for that value
> running as expected.
>
> so I formally request help on this one,

What about skipping this test for now?

I tried this, and it allowed at least the three reverse-dependencies I
tried (kinetic stools, python-pybedtools, umis) to build with Python
3.11.

Regards
Graham

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Bug#1024425: help needed on pysam ftbfs with python3.11 Étienne Mollier <emollier@emlwks999.eu> - 2022-12-23 21:10 +0100
  Bug#1024425: [Debian-med-packaging] Bug#1024425: help needed on pysam ftbfs with python3.11 Graham Inggs <ginggs@debian.org> - 2022-12-26 22:20 +0100
    Bug#1024425: [Debian-med-packaging] Bug#1024425: help needed on pysam ftbfs with python3.11 Étienne Mollier <emollier@emlwks999.eu> - 2022-12-27 11:20 +0100

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