[Debian-med-packaging] sra-toolkit

[E.S. Rosenberg]

Hi Andreas,
First of thank you for all your hard work! No disrespect was meant in my
short original mail.

I don't know much about sra-toolkit either, I hope I'll have some time over
the next month to look at this....
Thanks again,
Eli

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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