From debbugs-submit-bounces@debbugs.gnu.org Sun Oct 21 17:40:45 2018 Received: (at 33032) by debbugs.gnu.org; 21 Oct 2018 21:40:45 +0000 Received: from localhost ([127.0.0.1]:34755 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gELSm-0007Q3-SC for submit@debbugs.gnu.org; Sun, 21 Oct 2018 17:40:45 -0400 Received: from eggs.gnu.org ([208.118.235.92]:45081) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gELSk-0007Pq-Uh for 33032@debbugs.gnu.org; Sun, 21 Oct 2018 17:40:43 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gELSe-0002qZ-Cz for 33032@debbugs.gnu.org; Sun, 21 Oct 2018 17:40:37 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:36839) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gELSe-0002qU-95; Sun, 21 Oct 2018 17:40:36 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=33434 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1gELSe-00082A-1J; Sun, 21 Oct 2018 17:40:36 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Brett Gilio Subject: Re: [bug#33032] [PATCH] gnu: update python-biopython to 1.72 References: <20181013034945.9545-1-brettg@posteo.net> Date: Sun, 21 Oct 2018 23:40:34 +0200 In-Reply-To: <20181013034945.9545-1-brettg@posteo.net> (Brett Gilio's message of "Fri, 12 Oct 2018 22:49:45 -0500") Message-ID: <87o9bn6krx.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 33032 Cc: 33032@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) Hi Brett, Brett Gilio 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 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 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: error: Test failed: 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 # =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 `(#)'. 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.