Re: RFS: simpleitk/1.0.1-1 [ITP]

[Afif Elghraoui]

Hi, Ghislain,

على الثلاثاء 31 تشرين الأول 2017 ‫15:04، كتب Ghislain Vaillant:
> Hi all,
> 
> Could someone from the team sponsor the initial upload for simpleitk 
> [1]. Perhaps Gert (cc'd), since he is also involved with packaging ITK?
> 

Based on the Python policy, the python3-dev build-dependency should be
either python3-all-dev, or specific to a minor version of python3 (like
python3.5-dev) [2].

My reading of the BuildProfileSpec wiki page suggests to me that the
`googletest` build dependency should be qualified as `googletest
`. And I'm not sure that there is need to wrap the
override_dh_auto_test rule to look for `nocheck` in `DEB_BUILD_OPTIONS`,
but I've posted a question about this to -devel [3] since I've seen
similar code get added to python-pysam as well [4].


Thanks and regards
Afif

> [1] https://anonscm.debian.org/cgit/debian-med/simpleitk.git
> 

2.
https://www.debian.org/doc/packaging-manuals/python-policy/build_dependencies.html
3. https://lists.debian.org/debian-devel/2017/11/msg3.html
4.
https://anonscm.debian.org/cgit/debian-med/python-pysam.git/tree/debian/rules?id=5897693255ab6a36fb69cfc5bc096c65973f5f47#n25

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

EDFbrowser 1.61 (new version available)

[Teunis van Beelen]

EDFbrowser 1.61 is available at:

https://www.teuniz.net/edfbrowser/

or

https://github.com/Teuniz/EDFbrowser/


Kind Regards,

Teunis van Beelen

-- 
"C'è qualcosa nella nebbia! Qualcosa nella nebbia ha preso John Lee!"

Re: [Outreachy] Hi all!

[ka lou]

Dear all,

I am sorry for the long absence , i had unexpected turnarounds with the
experiment i am running for my thesis ;)

However in my free time i kept  trying to build the above mentioned
packages from source - and i think i am more successful than before.

Running

sudo apt-get source bwa
cd bwa-0.7.12
sudo apt-get build-dep bwa
sudo apt-get upgrade
debuild -i -us -uc -b

produced the desired bwa_0.7.12-5_amd64.deb file. I also build the other
the packages ' primer3'  ,  'maq'  and 'tophat' (which builds fine as well)
for some more practice.

However , i cannot find the */debian/tests/' file - i'm running the  'apt-file
list bwa_0.7.12-5_amd64.deb' command - so maybe there is still some mistake
in the build? Or maybe i should use another command?

Thank you all again for your help :)

Kind regards,
Kate

On Fri, Oct 20, 2017 at 11:28 AM, Andreas Tille  wrote:

> Hi Katerina,
>
> On Thu, Oct 19, 2017 at 07:05:39PM +0300, ka lou wrote:
> > I am sorry for the late answer!  This is just an update on my last tries
> to
> > get the source of tophat and run a test with sbuild ;)
>
> Good you hit the list with your question.
>
> > As Diane suggested in the last email , i downloaded and installed (at
> least
> > tried too) the sbuild package on my linux mint machine. I followed the
> > instructions of the Debian wiki
> >  c793b4a7db_1>
> > and
> > i also installed the libsbuild-dev
> > . Things
> > seemed to work up until that point.
>
> Good.  I admit I *personally* was never happy with sbuild (in contrast
> to others who like it) since I was always running into trouble.
>
> > I then followed the commands  'apt source tophat' , 'apt build-dep
> > tophat',  'cd usr/source/tophat',  'dpkg-buildpackage', which went also
> > well.
>
> Are you sure that you went to usr/source/tophat?  Apt source extracts the
> source to
>
> ./tophat-
>
> at this point I would suggest to use debuild (from devscripts package).
> This is the most simple way to create a Debian package on your local
> machine.  For this to work you did right with `apt build-dep tophat`
> (which is not needed in a chroot as sbuild is creating).
>
> Could you confirm that this creates a tophat*.deb package?
>
> > However, when i tried 'sudo sbuild -d unstable' , after running for a
> while
> > i get an error : ​ 'E: Build failure (dpkg-buildpackage died)'.
> > I think the error connected to that (last lines of the log) is that :
> > '/usr/include/c++/7/bits/stl_pair.h:519:5: note:   template argument
> > deduction/substitution failed:
> > tophat_reports.cpp:2707:128: note:   cannot convert ‘junction_stat’ (type
> > ‘JunctionStats’) to type ‘JunctionStats&&’
> >  gtf_junctions.insert(make_pair > JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense),
> > junction_stat));'
>
> I admit I'm not aware that tophat fails to build from source.  To save you
> some trouble from this actual package which was a pretty random example
> here are some other example packages featuring autopkgtests.  Just forget
> tophat and use either
>
>  bwa
>  primer3
>  maq
>
> as examples.  There is no point in wasting your time with tophat.
>
> > I can also send you more details if you wish (e.g the summary) , i am
> sorry
> > i do not know very well how to report all these.
> >
> > Finally , i would like to tell you that since my PhD thesis deadline is
> > postponed to the end of January , i will probably won't make it to apply
> to
> > the Outreach program for this round... which is really sad. However ,
> with
> > your permission, i would like to keep on working on running tests and get
> > more familiar with the whole process. And hopefully i will be able to
> apply
> > for Outreach's next round!
>
> There is absolutely no need to ask for permission to help inside the
> Debian Med team.  Everybody is perfectly welcome to join the project and
> help us making the best operating system for life sciences and medicine.
>
> Kind regards
>
>   Andreas.
>
> --
> http://fam-tille.de
>
>

htsjdk and picard tools updated

[olivier sallou]

Hi,
I uploaded patched version of htsjdk and picard-tools to fix serious bugs
and prevent their removal (and removal of their reverse dependencies)

I switched bugs severity to normal but keep bugs open as a reminder as part
of the fix is to disable unit tests (due to gradle 3.2 issue that will be
solved when gradle 3.4 is available in debian).

Once gradle is fixed, we should re-introduce unit tests in those packages.

As a note, I kept htsjdk to version 2.8 and created a debian/2.8.1 branch
for this as version 2.12 breaks API and is not compatible with picard-tools
2.8.

Olivier