[Debian-med-packaging] sra-toolkit

[Andreas Tille]

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

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