Hi Andreas,
Andreas Tille, on 2020-10-03 10:06:59 +0200:
> uploaded. Thanks a lot for caring for the migration of this
> important package
Thank you as well for the upload. Alas the build log still
looks like the run chokes on makeblastdb memory commit issues.
:(
======================================================================
FAIL: test_fasta_db_nucl (test_NCBI_BLAST_tools.BlastDB)
Test makeblastdb wrapper with nucleotide database.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py", line 292, in test_fasta_db_nucl
self.assertTrue(os.path.isfile("GenBank/NC_005816.fna.nhd"))
AssertionError: False is not true
======================================================================
FAIL: test_fasta_db_prot (test_NCBI_BLAST_tools.BlastDB)
Test makeblastdb wrapper with protein database.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py", line 246, in test_fasta_db_prot
self.assertTrue(os.path.isfile("GenBank/NC_005816.faa.phd"))
AssertionError: False is not true
Given the symptoms, I believe the issue is most likely related
to #969608 supplemental messages:
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=969608#30
However I can't be sure, since the buildd environment is based
on a mips64el machine, but do not have any such machine at hand
to dig further:
Machine Architecture: mips64el
Host Architecture: mipsel
Build Architecture: mipsel
I added Aaron in carbon copy for information. The buildd server
is mipsel-osuosl-01.debian.org, the full build log is available
at:
https://buildd.debian.org/status/fetch.php?pkg=python-biopython&arch=mipsel&ver=1.78%2Bdfsg-2&stamp=1601713196&raw=0
I see the buildd uses schroot, but do not know whether Qemu is
needed here, so I'm not sure how the makeblastdb command is
actually affected. On my machine the full build goes through
sucessfully with schroot, qemu and:
Machine Architecture: amd64
Host Architecture: mipsel
Build Architecture: mipsel
Just in case it helps, I wrapped up an override to drop the
memory commit to 3 GiB in python-biopython 1.78+dfsg-3 in the
specific case of mipsel, but fear it is possible that could be
too low as well; this is a (mostly) random shot.
https://salsa.debian.org/med-team/python-biopython
On the great news side, the build on riscv64 went through! :)
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/3, please excuse my verbosity.
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