[Debian-med-packaging] Bug#951944: ariba: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.7 returned exit code 13

[Andreas Tille]

Hi again,

> I need to inspect the spades issue (may be my local environment is not
> totally clean regarding spades!) but it seems that changes in fermi-lite
> between 0.1-5 and latest fermi-lite are responsible for most of the test
> suite errors.  There might be a chance to "bisect" fermi-lite package
> uploads (= checking 0.1-7 and depending from the result 0.1-6 or 0.1-8)
> to find out what actual change might have caused the failures.  But
> may be Michael or Sascha (both in CC have a more direct idea about the
> changes that might affect the test.

I've did a test build with fermi-lite 0.1-7[1].  I can confirm that ariba
builds nicely against this version.  *All* build-time tests are running.
I guess the spades test did not fail since spades is not in Build-Depends
(hmmm, is it a bug that spades is neither in Build-Depends nor Depends or
Recommends? Its not in the documentation but there are some references
inside the code!)

However, despite the build-time tests are running there are issues in
autopkgtest.  While debci logs also report an issue in unstable[2] this
is rather connected to Python 3.8 transition.

In the autopkgtest log of my pbuilder chroot I get:

...
Python packages OK: True

Everything looks OK: False
Some dependencies not satisfied. Cannot continue.
Running ARIBA on test data...
-------------------------------------------------------------------------------
|=============================================================================|
|                            Preparing input data                             |
|=============================================================================|
-------------------------------------------------------------------------------
Made output directory ./foo. Copying test data files into it:
    copied ref_seqs.fa
    copied metadata.tsv
    copied reads_1.fq
    copied reads_2.fq
-------------------------------------------------------------------------------
|=============================================================================|
|                        Try running ariba prepareref                         |
|=============================================================================|
-------------------------------------------------------------------------------

Running ariba prepareref with:
/usr/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF


Something went wrong. See above for error message(s). Return code was 1
...


No idea what this might mean yet.  If there will be no further ideas
I'll do a build check with fermi-lite 0.1-8 tomorrow.

Kind regards

       Andreas.

[1] https://snapshot.debian.org/package/fermi-lite/0.1-7/
[2] https://ci.debian.net/packages/a/ariba/

-- 
http://fam-tille.de