From: ludo@gnu.org (Ludovic Courtès)
To: Brett Gilio <brettg@posteo.net>
Cc: 33032@debbugs.gnu.org
Subject: [bug#33032] [PATCH] gnu: update python-biopython to 1.72
Date: Sun, 21 Oct 2018 23:40:34 +0200 [thread overview]
Message-ID: <87o9bn6krx.fsf@gnu.org> (raw)
In-Reply-To: <20181013034945.9545-1-brettg@posteo.net> (Brett Gilio's message of "Fri, 12 Oct 2018 22:49:45 -0500")
Hi Brett,
Brett Gilio <brettg@posteo.net> skribis:
> ---
> gnu/packages/bioinformatics.scm | 5 +++--
> 1 file changed, 3 insertions(+), 2 deletions(-)
[...]
> (name "python-biopython")
> - (version "1.70")
> + (version "1.72")
I applied the patch and built tried to build the packages that depend on
it, as returned by:
guix refresh -l python-biopython python2-biopython
Unfortunately that triggers a test failure in ‘seqmagic’ (I didn’t see
whether others are failing):
--8<---------------cut here---------------start------------->8---
ERROR: test_dna_protein_nogap_stop (seqmagick.test.test_transform.TranslateTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/tmp/guix-build-seqmagick-0.7.0.drv-0/seqmagick-0.7.0/seqmagick/test/test_transform.py", line 513, in test_dna_protein_nogap_stop
self.assertEqual(expected, [str(i.seq) for i in actual])
File "/tmp/guix-build-seqmagick-0.7.0.drv-0/seqmagick-0.7.0/seqmagick/test/test_transform.py", line 513, in <listcomp>
self.assertEqual(expected, [str(i.seq) for i in actual])
File "/tmp/guix-build-seqmagick-0.7.0.drv-0/seqmagick-0.7.0/seqmagick/transform.py", line 703, in translate
protein = seq.translate(table, to_stop=to_stop)
File "/gnu/store/ng8rrazi7kwchsmnhmhkjdfgjsv3lngv-python-biopython-1.72/lib/python3.6/site-packages/Bio/Seq.py", line 1163, in translate
cds, gap=gap)
File "/gnu/store/ng8rrazi7kwchsmnhmhkjdfgjsv3lngv-python-biopython-1.72/lib/python3.6/site-packages/Bio/Seq.py", line 2543, in _translate_str
dual_coding = [c for c in stop_codons if c in forward_table]
File "/gnu/store/ng8rrazi7kwchsmnhmhkjdfgjsv3lngv-python-biopython-1.72/lib/python3.6/site-packages/Bio/Seq.py", line 2543, in <listcomp>
dual_coding = [c for c in stop_codons if c in forward_table]
File "/tmp/guix-build-seqmagick-0.7.0.drv-0/seqmagick-0.7.0/seqmagick/transform.py", line 663, in __getitem__
elif '-' in codon:
TypeError: argument of type 'int' is not iterable
-------------------- >> begin captured logging << --------------------
root: INFO: Applying translation generator: operation to perform is dna2proteinstop.
--------------------- >> end captured logging << ---------------------
----------------------------------------------------------------------
Ran 164 tests in 1.530s
FAILED (errors=7, skipped=7)
Test failed: <unittest.runner.TextTestResult run=164 errors=7 failures=0>
error: Test failed: <unittest.runner.TextTestResult run=164 errors=7 failures=0>
Backtrace:
5 (primitive-load "/gnu/store/hg9qrk8cr2aw2y4ylxdcnlvpb3y…")
In ice-9/eval.scm:
191:35 4 (_ _)
In srfi/srfi-1.scm:
640:9 3 (for-each #<procedure 94c140 at /gnu/store/5sy3815dpjc…> …)
In /gnu/store/5sy3815dpjcvxhssaba6g2ilxm29va9n-module-import/guix/build/gnu-build-system.scm:
799:31 2 (_ _)
In /gnu/store/5sy3815dpjcvxhssaba6g2ilxm29va9n-module-import/guix/build/python-build-system.scm:
142:8 1 (check #:tests? _ #:test-target _ #:use-setuptools? _)
In /gnu/store/5sy3815dpjcvxhssaba6g2ilxm29va9n-module-import/guix/build/utils.scm:
616:6 0 (invoke _ . _)
/gnu/store/5sy3815dpjcvxhssaba6g2ilxm29va9n-module-import/guix/build/utils.scm:616:6: In procedure invoke:
Throw to key `srfi-34' with args `(#<condition &invoke-error [program: "python" arguments: ("-c" "import setuptools, tokenize;__file__='setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\\r\\n', '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test") exit-status: 1 term-signal: #f stop-signal: #f] 99fec0>)'.
builder for `/gnu/store/a6zljh5pn0agm0rdf8bhx7c8hk9hia1d-seqmagick-0.7.0.drv' failed with exit code 1
--8<---------------cut here---------------end--------------->8---
Could you take a look?
Thank you!
Ludo’.
next prev parent reply other threads:[~2018-10-21 21:42 UTC|newest]
Thread overview: 5+ messages / expand[flat|nested] mbox.gz Atom feed top
2018-10-13 3:49 [bug#33032] [PATCH] gnu: update python-biopython to 1.72 Brett Gilio
2018-10-21 21:40 ` Ludovic Courtès [this message]
2020-09-05 20:36 ` [bug#33032] Update Andreas Enge
2021-09-14 3:32 ` Sarah Morgensen
2022-04-07 12:03 ` bug#33032: [PATCH] gnu: update python-biopython to 1.72 zimoun
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