Ubuntu
ncbi-blast+ package

autopkgtest fails on armhf with Error: mdb_env_open: Cannot allocate memory

Bug #1894218 reported by Iain Lane
6
This bug affects 1 person
Affects Status Importance Assigned to Milestone
kaptive (Ubuntu)
Invalid
Undecided
Unassigned
ncbi-blast+ (Ubuntu)
Fix Released
Medium
Unassigned

Bug Description

See

https://objectstorage.prodstack4-5.canonical.com/v1/AUTH_77e2ada1e7a84929a74ba3b87153c0ac/autopkgtest-groovy/groovy/armhf/n/ncbi-blast+/20200430_223246_71025@/log.gz

autopkgtest [22:32:19]: test run-unit-test: [-----------------------
---Creating Database--

Building a new DB, current time: 04/30/2020 22:32:20
New DB name: /tmp/autopkgtest.Js7A4R/autopkgtest_tmp/testdb
New DB title: testdatabase.fa
Sequence type: Nucleotide
Error: mdb_env_open: Cannot allocate memory
Keep MBits: T
Maximum file size: 1000000000B

No volumes were created.

autopkgtest [22:32:21]: test run-unit-test: -----------------------]
autopkgtest [22:32:23]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - -
run-unit-test FAIL non-zero exit status 253

I found a fix in python-biopython

  https://salsa.debian.org/med-team/python-biopython/-/commit/adceea31e1251bf4bddee8b2e9791239fc26ce55

and ported it to ncbi-blast+.

  https://salsa.debian.org/med-team/ncbi-blastplus/-/merge_requests/1

am not uploading immediately, preferring to wait for a review. But if anyone else (hi, +1-people) wants to, feel free to take it, test it, and upload it if it works.

Iain Lane (laney)
Changed in ncbi-blast+ (Ubuntu):
status: New → Triaged
importance: Undecided → Medium
Revision history for this message
Iain Lane (laney) wrote :

and kaptive is the same via https://salsa.debian.org/med-team/kaptive/-/merge_requests/1/edit

Revision history for this message
Iain Lane (laney) wrote :

https://salsa.debian.org/med-team/kaptive/-/merge_requests/1 (oops)

Revision history for this message
Graham Inggs (ginggs) wrote :

Seems fixed in ncbi-blast+. Sync'd.

ncbi-blast+ (2.10.0-3) unstable; urgency=medium

  * debian/patches/tune_32bit_lmdb_defaults: Tweak default map size expressions.
    - For 64-bit platforms, use an explicit UL suffix on one factor to avoid
      overflow.
    - For 32-bit platforms, avoid tying up quite so much address space, since
      opening a pair of databases is a distinct possibility.
    - Generally parenthesize expressions per best macro practice.

 -- Aaron M. Ucko <email address hidden> Mon, 07 Sep 2020 21:15:02 -0400

ncbi-blast+ (2.10.0-2) unstable; urgency=high

  * debian/patches/support_gcc10: Additionally tweak ncbifile.cpp to avoid
    narrowing errors on some platforms (i386, for one).
  * debian/patches/tune_32bit_lmdb_defaults (new): Conditionalize default
    map size to avoid allocation failures on 32-bit platforms.
    (Closes: #969608.)

 -- Aaron M. Ucko <email address hidden> Sun, 06 Sep 2020 23:07:37 -0400

Graham Inggs (ginggs)
Changed in ncbi-blast+ (Ubuntu):
status: Triaged → Fix Released
Changed in kaptive (Ubuntu):
status: New → Invalid
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