Hi Aaron, Aaron M. Ucko, on 2020-09-06 23:29:28 -0400: > For #960756, python-biopython worked around a problem with the latest > upstream makeblastdb version on 32-bit architectures by explicitly > reverting to version 4 databases. That problem resurfaced as #969608, > which I've fixed in ncbi-blast+ itself, so python-biopython should be > able to revert that workaround in favor of specifically avoiding > ncbi-blast+ 2.10.0-1. > > Meanwhile, I know 2.10.1 is out upstream, but it will need additional > patching to avoid an FTBFS on non-x86, so I held off on taking it for > now. Thanks for your work on this topic. I attempted to remove the patches to address #960756 in Biopython. While the problem is fixed on i386 without having to fall back on version 4, I hit a very similar issue on amd64 this time. Knowing myself, there's always the possibility that I missed a point, but if someone wants to double check, here is the reproducer using the Biopython test base: $ uname -m x86_64 $ cd python-biopython/Tests $ makeblastdb -dbtype nucl -in GenBank/NC_005816.fna Building a new DB, current time: 09/07/2020 22:36:29 New DB name: /home/emollier/debian/med-team/python-biopython/Tests/GenBank/NC_005816.fna New DB title: GenBank/NC_005816.fna Sequence type: Nucleotide Deleted existing Nucleotide BLAST database named /home/emollier/debian/med-team/python-biopython/Tests/GenBank/NC_005816.fna Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 1 sequences in 0.000201941 seconds. No volumes were created. BLAST Database creation error: mdb_env_open: Cannot allocate memory The version in use should be the proper one, it is today's build: $ makeblastdb -version makeblastdb: 2.10.0+ Package: blast 2.10.0, build Sep 7 2020 03:07:37 As a side note Biopython 1.78 has been released this weekend, so there may be more changes to come in the coming weeks. Kind Regards, -- Étienne Mollier <etienne.mollier@mailoo.org> Old rsa/3072: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d New rsa/4096: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/2, please excuse my verbosity.
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