Your message dated Wed, 22 Sep 2021 17:48:55 +0000
with message-id <[email protected]>
and subject line Bug#994714: fixed in kleborate 2.1.0-2
has caused the Debian Bug report #994714,
regarding kleborate: ftbfs on s390x due to architecture dependent blastdbv5
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
994714: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=994714
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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 <[email protected]>
Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
Sent from /dev/pts/9, please excuse my verbosity.
signature.asc
Description: PGP signature
--- End Message ---
--- Begin Message ---
Source: kleborate
Source-Version: 2.1.0-2
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
kleborate, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated kleborate package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 22 Sep 2021 18:54:42 +0200
Source: kleborate
Architecture: source
Version: 2.1.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 994714
Changes:
kleborate (2.1.0-2) unstable; urgency=medium
.
* add bigendian.patch: fixes ftbfs on s390x. (Closes: #994714)
* Standards-Version: 4.6.0 (routine-update)
* Apply multi-arch hints.
+ kleborate-examples: Add Multi-Arch: foreign.
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