new version of ncbi-blast+ causes autopkgtest hangs

Bug #1947645 reported by Steve Langasek
6
This bug affects 1 person
Affects Status Importance Assigned to Milestone
ncbi-blast+ (Ubuntu)
Fix Released
Undecided
Unassigned

Bug Description

After updating ncbi-blast+ to 2.11.0 in proposed, both cct and kleborate autopkgtests fail with timeouts. cct hangs consistently at the same place:

[...]
Warning: [tblastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output
Performing BLAST search for sequence number 105 (orf_105_start=12818;end=12904;strand=1;rf=2).
Warning: [tblastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output
autopkgtest [15:16:05]: ERROR: timed out on command [...]

This is not trivially reproducible by running the autopkgtest locally. Perhaps this is only reproducible in memory-restricted environments.

Steve Langasek (vorlon)
tags: added: update-excuse
Revision history for this message
Steve Langasek (vorlon) wrote :

I was unable to reproduce this failure on a memory-restricted arm64 VM in canonistack.

Revision history for this message
Jeremy Bícha (jbicha) wrote :
Changed in ncbi-blast+ (Ubuntu):
status: New → Fix Released
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