[Debian-med-packaging] Bug#1080479: ncbi-blast+: failure to create blastdb v5 on riscv64

[Étienne Mollier]

Package: ncbi-blast+
Version: 2.16.0+ds-6
Severity: normal

Dear Maintainer,

While working on #1079439, a test failure in python-biopython
that appeared only on riscv64 turns out to be symptomatic of the
following issue:

	$ makeblastdb -dbtype nucl -in GenBank/NC_005816.fna -parse_seqids -hash_index -max_file_sz 20MB -taxid 10
	
	
	Building a new DB, current time: 09/04/2024 20:41:00
	New DB name:   /build/python-biopython-1.83+dfsg1/Tests/GenBank/NC_005816.fna
	New DB title:  GenBank/NC_005816.fna
	Sequence type: Nucleotide
	Keep MBits: T
	Maximum file size: 20000000B
	Adding sequences from FASTA; added 1 sequences in 1.68889 seconds.
	
	No volumes were created.
	
	BLAST Database creation error: LMDB runtime error: mdb_env_open: Operation not supported

Falling back to blastdb version 4 works around the issue:

	# makeblastdb  -blastdb_version 4 -dbtype nucl -in GenBank/NC_005816.fna -parse_seqids -hash_index -max_file_sz 20MB -taxid 10
	
	
	Building a new DB, current time: 09/04/2024 20:43:59
	New DB name:   /build/python-biopython-1.83+dfsg1/Tests/GenBank/NC_005816.fna
	New DB title:  GenBank/NC_005816.fna
	Sequence type: Nucleotide
	Deleted existing Nucleotide BLAST database named /build/python-biopython-1.83+dfsg1/Tests/GenBank/NC_005816.fna
	Keep MBits: T
	Maximum file size: 20000000B
	Adding sequences from FASTA; added 1 sequences in 1.52792 seconds.

As far as I can witness this is machine specific (not accounting
for similar looking symptoms with s390x, although the big endian
factor was not innocent in the matter; we're speaking little
endian in this case):

	$ uname -m 
	riscv64

I plan to skip test_NCBI_BLAST_tools.py in python-biopython in
the meantime: this package is not subject to serious bug or
autoremoval whatsoever, but in its current state it hogs debci
riscv64 runners due to another problem.

Have a nice day,  :)
-- 
  .''`.  Étienne Mollier <emollier at debian.org>
 : :' :  pgp: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
 `. `'   sent from /dev/pts/1, please excuse my verbosity
   `-    on air: Alan Parsons Project - Games People Play
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