[Debian-med-packaging] sra-toolkit

[Andreas Tille]

Hi Eli,

On Sun, Oct 22, 2017 at 04:23:54PM +0300, E.S. Rosenberg wrote:
> First of thank you for all your hard work! No disrespect was meant in my
> short original mail.

I have not read any disrespect in it.  I was simply trying to explain a
successful "workflow" how we can enhance the cooperation with interested
users.
 
> I don't know much about sra-toolkit either, I hope I'll have some time over
> the next month to look at this....

That would be nice.  I'll keep it on my desk with some lower priority than
other packages (as always any other volunteer is perfectly welcome to be
faster than I ;-) ).

Kind regards

     Andreas.
 
> On Fri, Oct 20, 2017 at 1:27 AM, Andreas Tille <andreas at fam-tille.de> wrote:
> 
> > Hi Eliyahu,
> >
> > thanks for using the packages provided by the Debian Med team.
> >
> > On Thu, Oct 19, 2017 at 10:06:25PM +0300, E.S. Rosenberg wrote:
> > > Are there any plans to update the deb to 2.8.2?
> >
> > I admit there is no real "plan" to update any specific software.  A
> > small team of enthusiasts is struggling very hard to keep way more than
> > 500 packages in the field of bioinformatics up to date.  While you did
> > perfectly right to ask for a certain package which definitely raises
> > our motivation to pick this before other targets I have the following
> > recommendations.
> >
> >    1. Follow the "official" way to ask for new versions which is done
> >       via the bug tracking system:
> >
> >          reportbug sra-toolkit
> >          Bug-Title: New version available
> >          Severity: wishlist
> >
> >       May be you add some extra information about the new features of
> >       this new version.
> >
> >    2. You clone the packaging git as described in Debian Med policy[1]
> >       and try to do the needed stuff in Git.  If you manage to do this
> >       we'll grant you commit permissions so you can contribute directly
> >       to our project.  This will enhance your chances that the package
> >       becomes available sooner drastically.
> >
> > Besides these hints I had a look at the packaging.  The sra-toolkit (and
> > its Build-Depends ncbi-vdb) have manually crafted build systems and I
> > never ever observed a smooth upgrade.  While I managed to build ncbi-vdb
> > 2.8.2-2 after some patching (its just uploading right now) I was ending
> > up to a point with sra-toolkit when it says:
> >
> > ...
> > make[3]: Entering directory '/build/sra-sdk-2.8.2-3+dfsg/test/vdb-config'
> > Testing exit code vdb-config of vdb-config... 2017-10-19T22:11:57
> > vdb-config.2.8.2 err: libs/kfs/unix/sysdir.c:2158:KSysDirOpenDirRead_v1:
> > condition violated while updating node - Warning: normally this application
> > should not be run as root/superuser
> > vdb-config exited with 3 at ./test-vdb-config.pl line 12.
> > Makefile:33: recipe for target 'test-vdb-config' failed
> > make[3]: *** [test-vdb-config] Error 3
> > make[3]: Leaving directory '/build/sra-sdk-2.8.2-3+dfsg/test/vdb-config'
> > /build/sra-sdk-2.8.2-3+dfsg/build/Makefile.targets:90: recipe for target
> > 'vdb-config_runtests' failed
> > make[2]: *** [vdb-config_runtests] Error 2
> > ...
> >
> > I have no idea what to do next and may be I need some sleep now.  Every
> > reader, may be you or somebody else is kindly invited to try fixing the
> > build system.  I admit that I'm pretty bored by this and I really wonder
> > what might make these two toolkits so special that none of the well
> > established build systems should fit their needs. :-(
> >
> > Kind regards
> >
> >         Andreas.
> >
> >
> > [1] https://debian-med.alioth.debian.org/docs/policy.html#source
> >
> > --
> > http://fam-tille.de
> >

-- 
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