GNU bug report logs - #33032
[PATCH] gnu: update python-biopython to 1.72

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Package: guix-patches; Reported by: Brett Gilio <brettg@HIDDEN>; Keywords: patch; dated Sat, 13 Oct 2018 03:51:02 UTC; Maintainer for guix-patches is guix-patches@HIDDEN.

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From: ludo@HIDDEN (Ludovic =?utf-8?Q?Court=C3=A8s?=)
To: Brett Gilio <brettg@HIDDEN>
Subject: Re: [bug#33032] [PATCH] gnu: update python-biopython to 1.72
References: <20181013034945.9545-1-brettg@HIDDEN>
Date: Sun, 21 Oct 2018 23:40:34 +0200
In-Reply-To: <20181013034945.9545-1-brettg@HIDDEN> (Brett Gilio's message
 of "Fri, 12 Oct 2018 22:49:45 -0500")
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Hi Brett,

Brett Gilio <brettg@HIDDEN> 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 =E2=80=98seqmagic=E2=80=99 (I=
 didn=E2=80=99t see
whether others are failing):

--8<---------------cut here---------------start------------->8---
ERROR: test_dna_protein_nogap_stop (seqmagick.test.test_transform.Translate=
TestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/guix-build-seqmagick-0.7.0.drv-0/seqmagick-0.7.0/seqmagick/tes=
t/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/tes=
t/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/tra=
nsform.py", line 703, in translate
    protein =3D seq.translate(table, to_stop=3Dto_stop)
  File "/gnu/store/ng8rrazi7kwchsmnhmhkjdfgjsv3lngv-python-biopython-1.72/l=
ib/python3.6/site-packages/Bio/Seq.py", line 1163, in translate
    cds, gap=3Dgap)
  File "/gnu/store/ng8rrazi7kwchsmnhmhkjdfgjsv3lngv-python-biopython-1.72/l=
ib/python3.6/site-packages/Bio/Seq.py", line 2543, in _translate_str
    dual_coding =3D [c for c in stop_codons if c in forward_table]
  File "/gnu/store/ng8rrazi7kwchsmnhmhkjdfgjsv3lngv-python-biopython-1.72/l=
ib/python3.6/site-packages/Bio/Seq.py", line 2543, in <listcomp>
    dual_coding =3D [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/tra=
nsform.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 dna2pro=
teinstop.
--------------------- >> end captured logging << ---------------------

----------------------------------------------------------------------
Ran 164 tests in 1.530s

FAILED (errors=3D7, skipped=3D7)
Test failed: <unittest.runner.TextTestResult run=3D164 errors=3D7 failures=
=3D0>
error: Test failed: <unittest.runner.TextTestResult run=3D164 errors=3D7 fa=
ilures=3D0>
Backtrace:
           5 (primitive-load "/gnu/store/hg9qrk8cr2aw2y4ylxdcnlvpb3y=E2=80=
=A6")
In ice-9/eval.scm:
   191:35  4 (_ _)
In srfi/srfi-1.scm:
    640:9  3 (for-each #<procedure 94c140 at /gnu/store/5sy3815dpjc=E2=80=
=A6> =E2=80=A6)
In /gnu/store/5sy3815dpjcvxhssaba6g2ilxm29va9n-module-import/guix/build/gnu=
-build-system.scm:
   799:31  2 (_ _)
In /gnu/store/5sy3815dpjcvxhssaba6g2ilxm29va9n-module-import/guix/build/pyt=
hon-build-system.scm:
    142:8  1 (check #:tests? _ #:test-target _ #:use-setuptools? _)
In /gnu/store/5sy3815dpjcvxhssaba6g2ilxm29va9n-module-import/guix/build/uti=
ls.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: "pyt=
hon" arguments: ("-c" "import setuptools, tokenize;__file__=3D'setup.py';f=
=3Dgetattr(tokenize, 'open', open)(__file__);code=3Df.read().replace('\\r\\=
n', '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test") exit-st=
atus: 1 term-signal: #f stop-signal: #f] 99fec0>)'.
builder for `/gnu/store/a6zljh5pn0agm0rdf8bhx7c8hk9hia1d-seqmagick-0.7.0.dr=
v' failed with exit code 1
--8<---------------cut here---------------end--------------->8---

Could you take a look?

Thank you!

Ludo=E2=80=99.




Information forwarded to guix-patches@HIDDEN:
bug#33032; Package guix-patches. Full text available.

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From: Brett Gilio <brettg@HIDDEN>
To: guix-patches@HIDDEN
Subject: [PATCH] gnu: update python-biopython to 1.72
Date: Fri, 12 Oct 2018 22:49:45 -0500
Message-Id: <20181013034945.9545-1-brettg@HIDDEN>
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---
 gnu/packages/bioinformatics.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatic=
s.scm
index 91bb94c54..2f59211ab 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12,6 +12,7 @@
 ;;; Copyright =C2=A9 2018 Joshua Sierles, Nextjournal <joshua@nextjourna=
l.com>
 ;;; Copyright =C2=A9 2018 G=C3=A1bor Boskovits <boskovits@HIDDEN>
 ;;; Copyright =C2=A9 2018 M=C4=83d=C4=83lin Ionel Patra=C8=99cu <madalin=
ionel.patrascu@HIDDEN>
+;;; Copyright =C2=A9 2018 Brett Gilio <brettg@HIDDEN>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -732,14 +733,14 @@ provide a coordinated and extensible framework to d=
o 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
--=20
2.19.1





Acknowledgement sent to Brett Gilio <brettg@HIDDEN>:
New bug report received and forwarded. Copy sent to guix-patches@HIDDEN. Full text available.
Report forwarded to guix-patches@HIDDEN:
bug#33032; Package guix-patches. Full text available.
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