Re: Help needed to package manta which needs samtools >= 1.2 and libbam.a

[Olivier Sallou]

- Mail original -
> De: "Andreas Tille" 
> À: "Debian Med Project List" 
> Envoyé: Mardi 15 Novembre 2016 17:14:33
> Objet: Help needed to package manta which needs samtools >= 1.2 and libbam.a
> 
> Hi folks,
> 
> I have injected manta[1] into packaging Git.  Upstream contains several
> projects as tar.bz2 which are packaged for Debian and rebuilds these in
> the packaging process.  I tried to tweak the cmake input files to
> reference the Debian packaged alternatives.  I was stumbling about
> samtools (manta upstream contains version 1.2 - we just have 1.3 which
> might be a source of failure due to incompatibilities but lets ignore
> this for the moment).  The cmake build system needs a libbam.a which is
> only build by the legacy libbam-dev 0.1.19.  I wonder how we can get
> a libbam.a from recent samtools - or is there any other solution to
> build manta?

don't know how, but if it needs libbam.a, this means you are in static build, 
not using shared libraries, which is not the way Debian does.
So it seems you should tweak the make recipes to build with shared libraries 
instead of static compilation. this will solve your issue and use our .so files.


Olivier 

> 
> Here is the error message the current builds ends with:
> 
> ...
> make[3]: *** No rule to make target '/libhts.a', needed by
> 'src/c++/lib/applications/GenerateSVCandidates/test/manta_unit_test_GenerateSVCandidates'.
> Stop.
> make[3]: Leaving directory '/build/manta-1.0.2+dfsg/obj-x86_64-linux-gnu'
> CMakeFiles/Makefile2:1831: recipe for target
> 'src/c++/lib/applications/GenerateSVCandidates/test/CMakeFiles/manta_unit_test_GenerateSVCandidates.dir/all'
> failed
> ...
> 
> Kind regards
> 
>   Andreas.
> 
> [1] https://anonscm.debian.org/git/debian-med/manta.git
> 
> --
> http://fam-tille.de
> 
> 

Re: [MoM] Bug#843022: ITP: emperor -- new version

[Afif Elghraoui]

Hi, Kerim,

just some comments about this.

email subject: Instead of "new version", you should put the package's
short description.

على الخميس  3 تشرين الثاني 2016 ‫00:44، كتب Kerim Ölçer:
> Subject: ITP: emperor -- new version
> Package: wnpp
> Owner: "Kerim ÖLÇER"  >
> Severity: wishlist
X-Debbugs-Cc: debian-de...@lists.debian.org
^
You would need this line in order for the ITP to be copied to
debian-devel, as mentioned in the Debian Developer's reference [1]. When
reportbug is used with an MTA, it will add this line in the email header
automatically (and you won't see it in the message body), but since you
had to copy this into an email body, you can use the first block to add
pseudo-headers like this one and have the same effect.

You should forward the ITP email to debian-de...@lists.debian.org since
it didn't get automatically sent there by the BTS.

> 
> * Package name: emperor
>   Version : 1.0.0beta5
>   Upstream Author : Vazquez-Baeza Y, Pirrung M, Gonzalez A, Knight R.
> * URL : https://github.com/biocore/emperor
> * License : (MIT)
>   Programming Lang: (Python, Javascript, etc.)

You don't need parentheses here for these fields.

>   Description : Emperor is a next-generation tool for the analysis
> and visualization of large microbial ecology datasets; amongst many
> features Emperor provides a modern user interface that will rapidly
> adjust to your daily workflow.
> 

Looks good.

regards
Afif

1.
https://www.debian.org/doc/manuals/developers-reference/ch05.en.html#newpackage

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Help needed to package manta which needs samtools >= 1.2 and libbam.a

[Andreas Tille]

Hi folks,

I have injected manta[1] into packaging Git.  Upstream contains several
projects as tar.bz2 which are packaged for Debian and rebuilds these in
the packaging process.  I tried to tweak the cmake input files to
reference the Debian packaged alternatives.  I was stumbling about
samtools (manta upstream contains version 1.2 - we just have 1.3 which
might be a source of failure due to incompatibilities but lets ignore
this for the moment).  The cmake build system needs a libbam.a which is
only build by the legacy libbam-dev 0.1.19.  I wonder how we can get
a libbam.a from recent samtools - or is there any other solution to
build manta?

Here is the error message the current builds ends with:

...
make[3]: *** No rule to make target '/libhts.a', needed by 
'src/c++/lib/applications/GenerateSVCandidates/test/manta_unit_test_GenerateSVCandidates'.
  Stop.
make[3]: Leaving directory '/build/manta-1.0.2+dfsg/obj-x86_64-linux-gnu'
CMakeFiles/Makefile2:1831: recipe for target 
'src/c++/lib/applications/GenerateSVCandidates/test/CMakeFiles/manta_unit_test_GenerateSVCandidates.dir/all'
 failed
...

Kind regards

  Andreas.

[1] https://anonscm.debian.org/git/debian-med/manta.git

-- 
http://fam-tille.de

Re: [Debian-med-packaging] Bug#841560: Could anybody please check the issue in python-skbio

[Ghislain Vaillant]

On 15/11/16 11:58, Kevin Murray wrote:

Hi Andreas,

On 12:13 15/11, Andreas Tille wrote:

On Tue, Nov 15, 2016 at 07:15:03PM +1100, Kevin Murray wrote:

There are also old binary packages preventing a testing transition,
which I'm not sure how to deal with.


If you want to get old package versions removed for certain architectures
you file a bug:


Thanks for the tip! Sorry for being a bit thick, but I'm not 100% sure which
package needs removing. From the "testing excuses" page for skbio, "missing
build on i386: python-skbio, python-skbio-doc, python3-skbio (from 0.4.1-1)".
Does this mean that the i386 packages from testing (or sid?) should be removed
(via the method you suggest)?

Or should the python-skbio (binary, python2) package be removed for all
architectures, as it is no longer provided? (this would be done with a bug
against release.debian.org, right?)


Just file a removal bug [1] for python-skbio asking for a removal from 
i386 only. Use reportbug for this, it will ask you the right questions 
to fill the initial template of the email.


[1] https://wiki.debian.org/ftpmaster_Removals

Ghis

Re: [Debian-med-packaging] Bug#841560: Could anybody please check the issue in python-skbio

[Andreas Tille]

On Tue, Nov 15, 2016 at 07:15:03PM +1100, Kevin Murray wrote:
> On 08:49 15/11, Andreas Tille wrote:
> > could anybody check the issue in the skbio test suite?
> 
> I've packaged the latest upstream, and uploaded. Let's see if this fixes the
> build. I will also (but haven't yet) see if I can get it to build against
> libssw. There are also old binary packages preventing a testing transition,
> which I'm not sure how to deal with.

If you want to get old package versions removed for certain architectures
you file a bug:

reportbug other
ftpmaster  (I think item 10 in the list)
ROM
package python-skbio
 for the release
remove only certain architectures: YES
Add a space separated list of architectures

 Write some explanation text

Hope this helps

   Andreas.

-- 
http://fam-tille.de

Re: [Debian-med-packaging] Bug#841560: Bug#841560: Could anybody please check the issue in python-skbio

[Kevin Murray]

Hi Andreas,

On 19:15 15/11, Kevin Murray wrote:
> I will also (but haven't yet) see if I can get it to build against libssw.

Well that turned out to be far easier than I expected. I've pushed a patch that
uses libssw from debian. So let's see if this fixes the build. And we also need
to remove the old binary pkgs from the archive, I think (or whatever the reason
is for the package being stuck in sid).

Cheers,
K

---
Kevin Murray

Re: [Debian-med-packaging] Bug#841560: Could anybody please check the issue in python-skbio

[Kevin Murray]

Hi Andreas,

On 08:49 15/11, Andreas Tille wrote:
> could anybody check the issue in the skbio test suite?

I've packaged the latest upstream, and uploaded. Let's see if this fixes the
build. I will also (but haven't yet) see if I can get it to build against
libssw. There are also old binary packages preventing a testing transition,
which I'm not sure how to deal with.

Cheers,
K

---
Kevin Murray