Hi Brett,
Brett Gilio <brettg@posteo.net> skribis:
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> ---> gnu/packages/bioinformatics.scm | 5 +++--> 1 file changed, 3 insertions(+), 2 deletions(-)
[...]
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> (name "python-biopython")> - (version "1.70")> + (version "1.72")
I applied the patch and built tried to build the packages that depend onit, as returned by:
guix refresh -l python-biopython python2-biopython
Unfortunately that triggers a test failure in ‘seqmagic’ (I didn’t seewhether others are failing):
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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
Could you take a look?
Thank you!
Ludo’.