Re: sra-sdk is lacking libngs

[Andreas Tille <tille@debian.org>]

Hi Aaron,

Am Thu, Oct 14, 2021 at 12:24:29PM -0400 schrieb Aaron M. Ucko:
> Andreas Tille <tille@debian.org> writes:
> 
> > Ahhhm my failure.  Usually I do it in this sequence.
> 
> No problem; thanks for getting ngs-sdk now.

:-)
 
> I'll push fixes for both complications shortly.

Thanks a lot.  Unfortunately there are some remaining problems
with the test suite.  Salsa CI fails to build[1]:


Run VDB_CONFIG=/builds/med-team/sra-sdk/debian/output/source_dir/test/fastq-loader /builds/med-team/sra-sdk/debian/output/source_dir/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/test-bin/test-id2name
Running 14 test cases...
Init_NullSelf (0 s)
Whack_NullSelf (0 s)
Init_Whack (0 s)
Add_NullSelf (0 s)
Add_NullName (0 s)
Get_NullSelf (0 s)
Get_NullRes (0 s)
Get_Empty (0 s)
Get_Found (0 s)
Get_NotFound (0 s)
AddMultiple_Get (0 s)
AddRealloc (0 s)
Killed
make[4]: *** [/builds/med-team/sra-sdk/debian/output/source_dir/build/Makefile.env:380: runtests] Error 137
make[4]: Leaving directory '/builds/med-team/sra-sdk/debian/output/source_dir/test/fastq-loader'


However, this works in my local pbuilder, where I get:

Run VDB_CONFIG=/build/sra-sdk-2.11.2+dfsg/test/fastq-loader /build/sra-sdk-2.11.2+dfsg/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/test-bin/test-id2name
Running 14 test cases...
Init_NullSelf (0 s)
Whack_NullSelf (0 s)
Init_Whack (0 s)
Add_NullSelf (0 s)
Add_NullName (0 s)
Get_NullSelf (0 s)
Get_NullRes (0 s)
Get_Empty (0 s)
Get_Found (0 s)
Get_NotFound (0 s)
AddMultiple_Get (0 s)
AddRealloc (0 s)
MiltipleBuffers (6 s)
NameTooLong (345 s)

*** No errors detected (352 s total)


Any idea what might be wrong here?

I was checking Salsa CI since in my local pbuilder autopkgtest fails
later (but this was due to some 

  2021-10-15T05:11:56 vdb-config.2.11.2 err: condition violated while updating node - Warning: normally this application should not be run as root/superuser

... which is most probably a flaw of running autopkgtest in the
pbuilder chroot.  Thus I expect autopkgtest in Salsa CI passing
... once it builds there.

Kind regards

    Andreas.

[1] https://salsa.debian.org/med-team/sra-sdk/-/jobs/2074700#L1700 

-- 
http://fam-tille.de