GNU bug report logs -
#33032
[PATCH] gnu: update python-biopython to 1.72
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Reported by: Brett Gilio <brettg <at> posteo.net>
Date: Sat, 13 Oct 2018 03:51:02 UTC
Severity: normal
Tags: moreinfo, patch
Done: zimoun <zimon.toutoune <at> gmail.com>
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bug#33032
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(Sat, 13 Oct 2018 03:51:02 GMT)
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(Sat, 13 Oct 2018 03:51:02 GMT)
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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
---
gnu/packages/bioinformatics.scm | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 91bb94c54..2f59211ab 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12,6 +12,7 @@
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua <at> nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits <at> gmail.com>
;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
+;;; Copyright © 2018 Brett Gilio <brettg <at> posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -732,14 +733,14 @@ provide a coordinated and extensible framework to do computational biology.")
(define-public python-biopython
(package
(name "python-biopython")
- (version "1.70")
+ (version "1.72")
(source (origin
(method url-fetch)
;; use PyPi rather than biopython.org to ease updating
(uri (pypi-uri "biopython" version))
(sha256
(base32
- "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"))))
+ "18p5dk9hdjq1p8sz3fgld0yajsdf0bb28gbv4rk0rfdd8cj4jsxb"))))
(build-system python-build-system)
(arguments
`(#:phases
--
2.19.1
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(Sun, 21 Oct 2018 21:41:02 GMT)
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Message #8 received at 33032 <at> debbugs.gnu.org (full text, mbox):
Hi Brett,
Brett Gilio <brettg <at> 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’.
Added tag(s) moreinfo.
Request was from
Ludovic Courtès <ludo <at> gnu.org>
to
control <at> debbugs.gnu.org
.
(Thu, 27 Dec 2018 11:00:11 GMT)
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(Sat, 05 Sep 2020 20:37:01 GMT)
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Message #13 received at 33032 <at> debbugs.gnu.org (full text, mbox):
Hello,
I just updated seqmagick to 0.8.0.
Then I tried to update python-biopython to the latest version, 1.78. With it,
seqmagick fails to compile with the following message:
mportError: cannot import name 'triefind' from 'Bio' (/gnu/store/9cr6885z39yb5x3pbanva5h9nacmlkvz-python-biopython-1.78/lib/python3.8/site-packages/Bio/__init__.py)
======================================================================
ERROR: Failure: ImportError (Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.)
Andreas
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(Tue, 14 Sep 2021 03:33:02 GMT)
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Message #16 received at 33032 <at> debbugs.gnu.org (full text, mbox):
Hello,
Andreas Enge <andreas <at> enge.fr> writes:
> Hello,
>
> I just updated seqmagick to 0.8.0.
>
> Then I tried to update python-biopython to the latest version, 1.78. With it,
> seqmagick fails to compile with the following message:
>
> mportError: cannot import name 'triefind' from 'Bio'
> (/gnu/store/9cr6885z39yb5x3pbanva5h9nacmlkvz-python-biopython-1.78/lib/python3.8/site-packages/Bio/__init__.py)
>
> ======================================================================
> ERROR: Failure: ImportError (Bio.Alphabet has been removed from Biopython. In
> many cases, the alphabet can simply be ignored and removed from scripts. In a
> few cases, you may need to specify the ``molecule_type`` as an annotation on a
> SeqRecord for your script to work correctly. Please see
> https://biopython.org/wiki/Alphabet for more information.)
I think this may be fixed by updating seqmagick to 0.8.1 (current
release 0.8.4) and packaging its new dependency, pygtrie, which provides
that removed functionality.
--
Sarah
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zimoun <zimon.toutoune <at> gmail.com>
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You have taken responsibility.
(Thu, 07 Apr 2022 12:06:02 GMT)
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Brett Gilio <brettg <at> posteo.net>
:
bug acknowledged by developer.
(Thu, 07 Apr 2022 12:06:02 GMT)
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Message #21 received at 33032-done <at> debbugs.gnu.org (full text, mbox):
Hi,
Thank for your contribution. Currently Guix provides more recent
versions of BioPython.
On Fri, 12 Oct 2018 at 22:49, Brett Gilio <brettg <at> posteo.net> wrote:
> (name "python-biopython")
> - (version "1.70")
> + (version "1.72")
--8<---------------cut here---------------start------------->8---
$ guix show python-biopython | recsel -C -p version
version: 1.76
version: 1.73
--8<---------------cut here---------------end--------------->8---
Therefore, closing!
Cheers,
simon
bug archived.
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(Fri, 06 May 2022 11:24:05 GMT)
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This bug report was last modified 1 year and 354 days ago.
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