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 <[email protected]>
: :' : 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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