Re: Python-pysam 0.12 released, could someone please care?

2017-09-04 Thread Andreas Tille 
Hi Afif,

On Mon, Sep 04, 2017 at 12:00:08AM -0700, Afif Elghraoui wrote:
> 
> Well, the build is still not successful. I've filed an issue upstream for one 
> set of test failures [1] and there is another test failure due to a 
> segmentation fault that needs some investigation.

If it would be only the issues you reported [1] I would not mind to
deactivate the tests temporarily.  A segmentation fault is another
issue thought.
 
> If I move bcftools to Unstable now, we'd need to file an RC bug against it to 
> prevent its migration and breaking of the current pysam version in Testing.

Makes sense even if I'd love to get python-pysam rather sooner than
later into unstable.

Kind regards

  Andreas.
 
> 1. https://github.com/pysam-developers/pysam/issues/534
 

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Re: Python-pysam 0.12 released, could someone please care?

2017-09-04 Thread Afif Elghraoui 
Hi, Andreas,

On September 3, 2017 11:50:05 PM PDT, Andreas Tille  wrote:
>Hi Afif,
>
>I noticed that you commited some promising changes.  They are depending
>from bcftools 1.5 which is only in experimental.  From my point of view
>it makes sense to move bcftools 1.5 to unstable to enable building
>python-pysam in unstable as well.  Any reason to be more carefully and
>stick to experimental?
>

Well, the build is still not successful. I've filed an issue upstream for one 
set of test failures [1] and there is another test failure due to a 
segmentation fault that needs some investigation.

If I move bcftools to Unstable now, we'd need to file an RC bug against it to 
prevent its migration and breaking of the current pysam version in Testing.

regards
Afif

1. https://github.com/pysam-developers/pysam/issues/534

Re: Python-pysam 0.12 released, could someone please care?

2017-09-04 Thread Andreas Tille 
Hi Afif,

On Tue, Aug 29, 2017 at 10:15:00PM -0700, Afif Elghraoui wrote:
> >Could someone please care since I'm a bit offline-ish this week.
> 
> I'll take a look maybe tonight or tomorrow. Thanks for the ping--I hadn't 
> been watching the releases.

I noticed that you commited some promising changes.  They are depending
from bcftools 1.5 which is only in experimental.  From my point of view
it makes sense to move bcftools 1.5 to unstable to enable building
python-pysam in unstable as well.  Any reason to be more carefully and
stick to experimental?

Kind regards

   Andreas.

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http://fam-tille.de

Re: Python-pysam 0.12 released, could someone please care?

2017-08-29 Thread Afif Elghraoui 


On August 29, 2017 2:05:50 PM PDT, Andreas Tille  wrote:
>
>Could someone please care since I'm a bit offline-ish this week.
>

I'll take a look maybe tonight or tomorrow. Thanks for the ping--I hadn't been 
watching the releases.

regards
Afif

Re: Python-pysam 0.12 released, could someone please care?

2017-08-29 Thread Olivier Sallou 


- Mail original -
> De: "Andreas Tille" <andr...@an3as.eu>
> À: "Debian Med Project List" <debian-med@lists.debian.org>
> Envoyé: Mardi 29 Août 2017 23:05:50
> Objet: Python-pysam 0.12 released, could someone please care?

Can't test now, but it seems that config.h should come from htslib, which is 
included in upstream (but we use debian package for build).
config.h is not available in libhts-dev (I think expected from 
HTSLIB_INCLUDE_DIR ind/rules).



Olivier
> 
> Hi,
> 
> I pushed new upstream version to Git but the build failed with:
> 
> 
> ...
> amd64-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes
> -Wno-sign-compare -Wno-error=declaration-after-statement
> bcftools/vcfplugin.c.pysam.c:27:10: fatal error: config.h: No such file or
> directory
>  #include "config.h"
>   ^~
> compilation terminated.
> error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
> E: pybuild pybuild:283: build: plugin distutils failed with: exit code=1:
> /usr/bin/python setup.py build
> ...
> 
> 
> Could someone please care since I'm a bit offline-ish this week.
> 
> Kind regards
> 
>   Andreas.
> 
> - Forwarded message from Andreas Tille <ti...@debian.org> -
> 
> Date: Tue, 29 Aug 2017 21:04:00 +
> From: Andreas Tille <ti...@debian.org>
> To: debian-med-com...@lists.alioth.debian.org
> Subject: [python-pysam] branch master updated (63edbcb -> 1c15d8e)
> 
> This is an automated email from the git hooks/post-receive script.
> 
> tille pushed a change to branch master
> in repository python-pysam.
> 
>   from  63edbcb   New upstream version
>new  1c15d8e   Patch applied upstream
> 
> The 1 revisions listed above as "new" are entirely new to this
> repository and will be described in separate emails.  The revisions
> listed as "adds" were already present in the repository and have only
> been added to this reference.
> 
> 
> Summary of changes:
>  debian/patches/no-usage-test-without-tty.patch | 19 ---
>  debian/patches/series  |  1 -
>  2 files changed, 20 deletions(-)
>  delete mode 100644 debian/patches/no-usage-test-without-tty.patch
>  delete mode 100644 debian/patches/series
> 
> --
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> --
> http://fam-tille.de
> 
>

Python-pysam 0.12 released, could someone please care?

2017-08-29 Thread Andreas Tille 
Hi,

I pushed new upstream version to Git but the build failed with:


...
amd64-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes 
-Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/vcfplugin.c.pysam.c:27:10: fatal error: config.h: No such file or 
directory
 #include "config.h"
  ^~
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
E: pybuild pybuild:283: build: plugin distutils failed with: exit code=1: 
/usr/bin/python setup.py build 
...


Could someone please care since I'm a bit offline-ish this week.

Kind regards

  Andreas.

- Forwarded message from Andreas Tille  -

Date: Tue, 29 Aug 2017 21:04:00 +
From: Andreas Tille 
To: debian-med-com...@lists.alioth.debian.org
Subject: [python-pysam] branch master updated (63edbcb -> 1c15d8e)

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository python-pysam.

  from  63edbcb   New upstream version
   new  1c15d8e   Patch applied upstream

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 debian/patches/no-usage-test-without-tty.patch | 19 ---
 debian/patches/series  |  1 -
 2 files changed, 20 deletions(-)
 delete mode 100644 debian/patches/no-usage-test-without-tty.patch
 delete mode 100644 debian/patches/series

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