[Debian-med-packaging] Bug#960756: Bug#960756: python-biopython FTBFS on 32bit: test_NCBI_BLAST_tools.BlastDB failures

[Étienne Mollier]

Hi Aaron,

Aaron M. Ucko, on 2020-06-09 10:32:20 -0400:
> Andreas Tille <tille at debian.org> writes:
> 
> > On Tue, Jun 09, 2020 at 02:25:58PM +0200, Étienne Mollier wrote:
> >> My current impression is that makeblastdb is unable to work
> >> properly on most 32 bits machines, because the amount of memory
> >> needing to be addressed by the process looks like it might
> >> exceed too easily 32 bits architectural limits.
> 
> That's entirely plausible; upstream tends to assume 64-bit systems
> nowadays.  Explicitly supplying -blastdb_version 4 (the default prior to
> BLAST+ 2.10.x) may help.

It looks good on my eeepc:

	# 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: 06/09/2020 17:20:11
	New DB name:   /tmp/python-biopython/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 0.367298 seconds.
	
	
	# _

And no need for PAE.  :)
Thank you for the workaround!
Thanks Andreas for the forward!
Let's squash that bug.
Cheers everyone,
-- 
Étienne Mollier <etienne.mollier at mailoo.org>
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