[Debian-med-packaging] Bug#994714: ncbi-blast+: makeblastdb output dependent of endianness

[Étienne Mollier]

Package: ncbi-blast+
Version: 2.11.0+ds-1
Severity: important

Hi Aaron,

I am currently investigating kleborate failure to migrate to
testing.  The failure is due to build time test suite failure on
s390x [1].

[1]: https://buildd.debian.org/status/fetch.php?pkg=kleborate&arch=s390x&ver=2.1.0-1&stamp=1629929420&raw=0

A recurrent relevant error message in the log is stating errors
on .ndb files, such as:

	BLAST Database error: Invalid db file : /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9/build/test/test_res_alleles/data/CARD_v3.0.8.fasta.ndb

These files are produced at runtime by the execution of a
makeblastdb command within kleborate build time tests scripts.
Here is one of them:

	$ makeblastdb -dbtype nucl -in test/test_res_aac/data/CARD_v3.0.8.fasta

The .fasta file used for producing these databases can be
obtained on Salsa [2].

[2]: https://salsa.debian.org/med-team/kleborate/-/raw/master/test/test_res_aac/data/CARD_v3.0.8.fasta

If I produce these ndb files on big endian, then I have the
following consistent md5sum on s390x and ppc64:

	08bd786ca54ebc4730e5dd42b57c454f  CARD_v3.0.8.fasta.ndb

On amd64 or arm64, the md5sum is:

	8437e0675ad22935790a272be888ff56  CARD_v3.0.8.fasta.ndb

At this point, I strongly suspect that, either makeblastdb does
not output properly blastdb files on big endian systems, or
kleborate is not able to decode properly an eventual blastdb
database with big endian specific layout.

To be honest, I don't know which program is at fault, but if it
is a problem on makeblastdb side, then I thought you would want
to be aware of it.  Otherwise I'm happy with a bug reassigning
(in which case, I suppose I would just skip those test, or ask
for removal from s390x architecture).

Have a nice day,  :)
-- 
Étienne Mollier <emollier at emlwks999.eu>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/9, please excuse my verbosity.
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