[Debian-med-packaging] Bug#958840: kmer: autopkgtest regression: No module named 'localAlignerInterface'

[Andreas Tille]

On Mon, May 18, 2020 at 01:27:52AM +0000, Antoni Villalonga wrote:
> For some reason I din't included all my previous work on my merge request.

I suspect this "some reason" was that salsa and other infrastructure of
Debian went offline at that day for several hours.
 
> I've recovered most of it from a binary package I've found on my machine. And
> after lot of hours I've found the python module naming issue (see d/rules
> changes).
> 
> All changes are now included on:
>  https://salsa.debian.org/med-team/kmer/-/merge_requests/4

I've merged this and tried a test build including running autopkgtest in
my pbuilder environment.  Unfortunately the latter test is now failing with

...
autopkgtest [06:48:10]: test atac-unit-test: [-----------------------
Rewriting '/tmp/autopkgtest.jgVuO6/autopkgtest_tmp/GCF_000195855.1_ASM19585v1_genomic.fna' to '/tmp/autopkgtest.jgVuO6/autopkgtest_tmp/meryldir/Lepr.fasta', removing newlines.
Rewriting '/tmp/autopkgtest.jgVuO6/autopkgtest_tmp/GCF_000195955.2_ASM19595v2_genomic.fna' to '/tmp/autopkgtest.jgVuO6/autopkgtest_tmp/meryldir/Tuber.fasta', removing newlines.

/usr/bin/meryl -B -C -threads 2 -m 20 -s /tmp/autopkgtest.jgVuO6/autopkgtest_tmp/meryldir/Lepr.fasta -o /tmp/autopkgtest.jgVuO6/autopkgtest_tmp/meryldir/Lepr.ms20 

fastaFile::constructIndex()-- magic mismatch.
fastaFile::constructIndex()-- magic mismatch.
bitPackedFile::bitPackedFile()-- failed to open and truncate '/tmp/autopkgtest.jgVuO6/autopkgtest_tmp/meryldir/Lepr.ms20.batch0.mcidx': No such file or directory
Failed to count mers in Lepr
autopkgtest [06:48:10]: test atac-unit-test: -----------------------]
autopkgtest [06:48:11]: test atac-unit-test:  - - - - - - - - - - results - - - - - - - - - -
atac-unit-test       FAIL non-zero exit status 2
...


I admit I personally have no idea why this fails.

> Sorry for the long delay and the childish mistake.

No need to sorry here and there are no childish mistakes.  Your
contribution is perfectly welcome and absolutely helpful.

> Best regrads,
> 
> PS: d/changelog is unmodified in my last MR. Probably should include a
> reference to close this bug.

I added an according changelog entry.  Thanks for the hint.

Kind regards and thanks again for your contribution

      Andreas.

-- 
http://fam-tille.de