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Re: [PATCH 2/3] gnu: Add python-pyxb.
From: |
Marius Bakke |
Subject: |
Re: [PATCH 2/3] gnu: Add python-pyxb. |
Date: |
Mon, 26 Sep 2016 19:32:03 +0100 |
Ben Woodcroft <address@hidden> writes:
> On 24/09/16 13:15, Marius Bakke wrote:
>> Ben Woodcroft <address@hidden> writes:
>>
>>>> Htslib is propagated because it
>>>> is included by the installed samtools and bcftools headers; at least one
>>>> of pysams dependencies failed to build when it was a regular input.
>>> Ah, I see. Can this be avoided with patchelf?
>> I don't think so. The htslib headers need to be propagated for anything
>> that uses header files from pysam, since they contain contain code such
>> as "include <htslib/foo.h>". Perhaps you can update the comment to make
>> it more clear?
>>
>> Patchelf is probably what made that work when htslib was bundled.
> Ah, ok I see, so the problem is that python-plastid requires the .h
> files during build. Given that this is the only package that has an
> issue, and perhaps pysam doesn't intend to provide these .h files as
> part of it's "interface", I think it might be best to simply put htslib
> as an input to python-plastid.
I'm not sure, we would have to do this with every package that uses
the pysam cython interface. This particular issue is described in the
manual:
https://www.gnu.org/software/guix/manual/html_node/package-Reference.html
The propagated-inputs section says "For example this is necessary when a
C/C++ library needs headers of another library to compile, or when a
pkg-config file refers to another one via its Requires field.".
So I think it's a pretty common propagation scenario. See e.g. 618089f9
for a less convoluted case (C++ library that propagates zlib headers).
Perhaps a "propagated-build-inputs" functionality would be useful, so
that libraries are only propagated at build time and not to the profile.
If we don't do propagation, at least add a comment to python-plastid
explaining that htslib is there to avoid propagating from pysam, since
the plastid code contains no direct references to htslib.
Your other changes LGTM.
Thanks!
Marius
- Re: [PATCH 2/3] gnu: Add python-pyxb., (continued)
- Re: [PATCH 2/3] gnu: Add python-pyxb., Ben Woodcroft, 2016/09/20
- Re: [PATCH 2/3] gnu: Add python-pyxb., Marius Bakke, 2016/09/21
- Re: [PATCH 2/3] gnu: Add python-pyxb., Ben Woodcroft, 2016/09/21
- Re: [PATCH 2/3] gnu: Add python-pyxb., Marius Bakke, 2016/09/22
- Re: [PATCH 2/3] gnu: Add python-pyxb., Ben Woodcroft, 2016/09/22
- Re: [PATCH 2/3] gnu: Add python-pyxb., Marius Bakke, 2016/09/23
- Re: [PATCH 2/3] gnu: Add python-pyxb., Marius Bakke, 2016/09/23
- Re: [PATCH 2/3] gnu: Add python-pyxb., Ben Woodcroft, 2016/09/23
- Re: [PATCH 2/3] gnu: Add python-pyxb., Marius Bakke, 2016/09/23
- Re: [PATCH 2/3] gnu: Add python-pyxb., Ben Woodcroft, 2016/09/26
- Re: [PATCH 2/3] gnu: Add python-pyxb.,
Marius Bakke <=
- Re: [PATCH 2/3] gnu: Add python-pyxb., Ben Woodcroft, 2016/09/27
- Re: [PATCH 2/3] gnu: Add python-pyxb., Ludovic Courtès, 2016/09/30
[PATCH 3/3] gnu: python2-pbcore: Update to 1.2.10., Marius Bakke, 2016/09/17