From unknown Sun Jun 15 08:42:23 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#33032] [PATCH] gnu: update python-biopython to 1.72 Resent-From: Brett Gilio Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 13 Oct 2018 03:51:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 33032 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 33032@debbugs.gnu.org Cc: Brett Gilio X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.15394026521394 (code B ref -1); Sat, 13 Oct 2018 03:51:02 +0000 Received: (at submit) by debbugs.gnu.org; 13 Oct 2018 03:50:52 +0000 Received: from localhost ([127.0.0.1]:47651 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gBAwy-0000ML-KV for submit@debbugs.gnu.org; Fri, 12 Oct 2018 23:50:52 -0400 Received: from eggs.gnu.org ([208.118.235.92]:55269) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gBAww-0000M7-9H for submit@debbugs.gnu.org; Fri, 12 Oct 2018 23:50:46 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gBAwq-0000nf-An for submit@debbugs.gnu.org; Fri, 12 Oct 2018 23:50:41 -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 lists.gnu.org ([2001:4830:134:3::11]:57069) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1gBAwq-0000nX-5B for submit@debbugs.gnu.org; Fri, 12 Oct 2018 23:50:40 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:36627) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gBAwp-0002vh-33 for guix-patches@gnu.org; Fri, 12 Oct 2018 23:50:40 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gBAwl-0000jx-Qa for guix-patches@gnu.org; Fri, 12 Oct 2018 23:50:38 -0400 Received: from mout01.posteo.de ([185.67.36.65]:50186) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1gBAwc-0000dC-Cw for guix-patches@gnu.org; Fri, 12 Oct 2018 23:50:29 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id BFD3221259 for ; Sat, 13 Oct 2018 05:50:18 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1539402618; bh=xTKVpojK2xFDVc1ruHTE1n0ovOseZQ8eUcrpbPFVpRU=; h=From:To:Cc:Subject:Date:From; b=mJXyVNi5ZKnS8F+CRg9b6Enya/s/sWTIsdIfAESeGPnb3zptSekLwrZ6IcmvNVvKr DfazLFbGWeIrPfzTAY9tQV6vvKf67cA7IslzlA+V8br+KavW8BSMFuGpmdGEAOctzx 36CH7u1hNrsbrjTbul64JR+QJOw3tYJJYQi+/QyKP5UWVX4Ck1loTGOOMXD62rqRnY PTwkQpwAznqjrAOkvBXIdUJLWQjfSn+lGejUvMhIx7wuJmqkT/ulDNBtl2SnkahSAN pspSkABRoOt8WrB6kxAgNNf8nUtqEiC4Z/anJVcDVFoc7jOMC39X4oiDW4k3WgMFMW z7hdo1unve9kg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 42X9hT5ktNz6tm7; Sat, 13 Oct 2018 05:50:17 +0200 (CEST) From: Brett Gilio Date: Fri, 12 Oct 2018 22:49:45 -0500 Message-Id: <20181013034945.9545-1-brettg@posteo.net> X-Mailer: git-send-email 2.19.1 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-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.0 (----) 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: -5.0 (-----) --- 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 ;;; Copyright =C2=A9 2018 G=C3=A1bor Boskovits ;;; Copyright =C2=A9 2018 M=C4=83d=C4=83lin Ionel Patra=C8=99cu +;;; Copyright =C2=A9 2018 Brett Gilio ;;; ;;; 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 From unknown Sun Jun 15 08:42:23 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#33032] [PATCH] gnu: update python-biopython to 1.72 Resent-From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 21 Oct 2018 21:41:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 33032 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Brett Gilio Cc: 33032@debbugs.gnu.org Received: via spool by 33032-submit@debbugs.gnu.org id=B33032.154015804528529 (code B ref 33032); Sun, 21 Oct 2018 21:41:02 +0000 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?=) 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-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. From debbugs-submit-bounces@debbugs.gnu.org Thu Dec 27 06:00:05 2018 Received: (at control) by debbugs.gnu.org; 27 Dec 2018 11:00:06 +0000 Received: from localhost ([127.0.0.1]:38222 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gcTOV-0000W4-59 for submit@debbugs.gnu.org; Thu, 27 Dec 2018 06:00:04 -0500 Received: from hera.aquilenet.fr ([185.233.100.1]:50064) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gcTOR-0000V2-63 for control@debbugs.gnu.org; Thu, 27 Dec 2018 06:00:00 -0500 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 9C1F4B11 for ; Thu, 27 Dec 2018 11:59:58 +0100 (CET) X-Virus-Scanned: Debian amavisd-new at aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 8_GrMIScXl3M for ; Thu, 27 Dec 2018 11:59:58 +0100 (CET) Received: from ribbon (unknown [IPv6:2a01:e0a:1d:7270:af76:b9b:ca24:c465]) by hera.aquilenet.fr (Postfix) with ESMTPSA id E90CC76B for ; Thu, 27 Dec 2018 11:59:57 +0100 (CET) Date: Thu, 27 Dec 2018 11:59:57 +0100 Message-Id: <877efvb5g2.fsf@gnu.org> To: control@debbugs.gnu.org From: =?utf-8?Q?Ludovic_Court=C3=A8s?= Subject: control message for bug #33032 MIME-version: 1.0 Content-type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: control 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: -0.0 (/) tags 33032 moreinfo From unknown Sun Jun 15 08:42:23 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#33032] Update References: <20181013034945.9545-1-brettg@posteo.net> In-Reply-To: <20181013034945.9545-1-brettg@posteo.net> Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 05 Sep 2020 20:37:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 33032 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch moreinfo To: 33032@debbugs.gnu.org Received: via spool by 33032-submit@debbugs.gnu.org id=B33032.159933821813272 (code B ref 33032); Sat, 05 Sep 2020 20:37:01 +0000 Received: (at 33032) by debbugs.gnu.org; 5 Sep 2020 20:36:58 +0000 Received: from localhost ([127.0.0.1]:44184 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kEevi-0003S0-42 for submit@debbugs.gnu.org; Sat, 05 Sep 2020 16:36:58 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:37606) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kEevf-0003Rr-QO for 33032@debbugs.gnu.org; Sat, 05 Sep 2020 16:36:56 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 3BEFBCE78; Sat, 5 Sep 2020 22:36:54 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id lozbVHNa6SX3; Sat, 5 Sep 2020 22:36:53 +0200 (CEST) Received: from jurong (unknown [IPv6:2001:910:103f::610]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 47EF82356; Sat, 5 Sep 2020 22:36:53 +0200 (CEST) Date: Sat, 5 Sep 2020 22:36:39 +0200 From: Andreas Enge Message-ID: <20200905203639.GA24538@jurong> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline X-Spam-Score: 0.7 (/) 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: -0.3 (/) 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 From unknown Sun Jun 15 08:42:23 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#33032] Update Resent-From: Sarah Morgensen Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 14 Sep 2021 03:33:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 33032 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch moreinfo To: Andreas Enge Cc: 33032@debbugs.gnu.org Received: via spool by 33032-submit@debbugs.gnu.org id=B33032.16315903728864 (code B ref 33032); Tue, 14 Sep 2021 03:33:02 +0000 Received: (at 33032) by debbugs.gnu.org; 14 Sep 2021 03:32:52 +0000 Received: from localhost ([127.0.0.1]:47200 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mPzBk-0002Iu-Ao for submit@debbugs.gnu.org; Mon, 13 Sep 2021 23:32:52 -0400 Received: from out0.migadu.com ([94.23.1.103]:65193) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mPzBh-0002Ij-8G for 33032@debbugs.gnu.org; Mon, 13 Sep 2021 23:32:50 -0400 X-Report-Abuse: Please report any abuse attempt to abuse@migadu.com and include these headers. DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=mgsn.dev; s=key1; t=1631590362; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: in-reply-to:in-reply-to:references:references; bh=pXHFC+eb/Rwdqa6dv+etc/fhlFiqUeQjXovoUT8iXO0=; b=MCNMXbyHBIJ6KqJVpWprIbGNY84j8452/0boGFr8yb60ZaV3YaOZNXAkRkis8VB26LWCpW EL48ibgrt85xmWucLN6grcyhJ9AWrAfr6HXOhkn+6hAEL9n9mxiLIX15r7OvuPdBqC0+5B zLf6aqAm+vegXVygFXtOQHlDDjeJRVw= From: Sarah Morgensen References: <20181013034945.9545-1-brettg@posteo.net> <20200905203639.GA24538@jurong> Date: Mon, 13 Sep 2021 20:32:40 -0700 In-Reply-To: <20200905203639.GA24538@jurong> (Andreas Enge's message of "Sat, 5 Sep 2020 22:36:39 +0200 (1 year, 1 week, 1 day ago)") Message-ID: <86o88vj0h3.fsf@mgsn.dev> MIME-Version: 1.0 Content-Type: text/plain X-Migadu-Flow: FLOW_OUT X-Migadu-Auth-User: iskarian@mgsn.dev X-Spam-Score: -0.7 (/) 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: -1.7 (-) Hello, Andreas Enge 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 From unknown Sun Jun 15 08:42:23 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Brett Gilio Subject: bug#33032: closed (Re: bug#33032: [PATCH] gnu: update python-biopython to 1.72) Message-ID: References: <86zgkx2j8x.fsf@gmail.com> <20181013034945.9545-1-brettg@posteo.net> X-Gnu-PR-Message: they-closed 33032 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch moreinfo Reply-To: 33032@debbugs.gnu.org Date: Thu, 07 Apr 2022 12:06:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1649333162-18227-1" This is a multi-part message in MIME format... ------------=_1649333162-18227-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #33032: [PATCH] gnu: update python-biopython to 1.72 which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 33032@debbugs.gnu.org. --=20 33032: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D33032 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1649333162-18227-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 33032-done) by debbugs.gnu.org; 7 Apr 2022 12:05:33 +0000 Received: from localhost ([127.0.0.1]:60063 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncQtI-0004iu-PT for submit@debbugs.gnu.org; Thu, 07 Apr 2022 08:05:33 -0400 Received: from mail-wm1-f47.google.com ([209.85.128.47]:33450) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ncQtE-0004iK-7Z for 33032-done@debbugs.gnu.org; Thu, 07 Apr 2022 08:05:29 -0400 Received: by mail-wm1-f47.google.com with SMTP id l9-20020a05600c4f0900b0038ccd1b8642so4448040wmq.0 for <33032-done@debbugs.gnu.org>; Thu, 07 Apr 2022 05:05:28 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:references:date:in-reply-to:message-id :user-agent:mime-version; bh=MerUY9O8QsPEWv/4PRNpJAWt9cWAa1M92XNbDNzvc4k=; b=UyFPwBrdNKbDyc2xZMtHZXFQyxf4PRNJLdeNA5WkITliBETlRjpNCE80Ny5ocv2cyn v+OMMdD4rEal2b0YXaMorSl5vMrvH92tP5OICsoW9VX/ZRw61NlLttzn9+G9CcjDqAky QqkriRtDHp/lLywMEulYqkOF9a2l8yGRN2UqOesAKOkOzYLqkYKlYc6nDI4KsTwOwtWh WDzW5c9+VFES5NIgeASZIHyRWMOaxA4kaJKLuyGYavZZI6e00EUkM1v5zLhMTSXifDdy bON0z+IUP8mwHeV04B6AIVZrvHj+BfFpDSQAvWQo7i7GhorSqMijEVOmPpi5XgxPG3K3 s0uw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:references:date:in-reply-to :message-id:user-agent:mime-version; bh=MerUY9O8QsPEWv/4PRNpJAWt9cWAa1M92XNbDNzvc4k=; b=6zpxn5TerN1qmvTdBmrCbG1Smj2R1l1fpg0BwigweYLnZeGbK+TpZn5rH9tzHex9Ik tWLvWaMkvm071Odw2znsm3z/sneyP4OnTXsaY9KCMEQ4oBIMxP8CoSow254hlYM+AQDh cKg7naOPZqMsh12CdAe+ed3TWMjj4iBa+6RCLGbn2zrlgH1cVXUPmPV+AGJknhG3qgIA cyaAzt7Zk/sfM6AmK4qlN+tuLeXjMwDtFpJFovtB/cjD4qTx/KfIDHNhgftnDC2Ul99t 3N//TGj3kpE+7c39gpoM/HSI1VijV/mr38Nb4jxiLA5NWQs8rt6ldF5dbQBsl3H5I3LR n4jA== X-Gm-Message-State: AOAM531GtdAHcVlilaqkB76qKLMpa03+zVT/pRRwSvYczuwgHuzMmwXe 1m6chQeP/SLWqzRB+71PhS6MvB1gZcE= X-Google-Smtp-Source: ABdhPJyF6ExcMeBjro52akyzQPDPxx7nXEgMS/VmUG7YL0bbbe5Gga1rm+oW8uLtWsv0su/MeBiCWQ== X-Received: by 2002:a05:600c:213:b0:38e:6379:af70 with SMTP id 19-20020a05600c021300b0038e6379af70mr11624086wmi.157.1649333122692; Thu, 07 Apr 2022 05:05:22 -0700 (PDT) Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e]) by smtp.gmail.com with ESMTPSA id w1-20020a5d6081000000b002061b616b83sm7614375wrt.39.2022.04.07.05.05.22 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Thu, 07 Apr 2022 05:05:22 -0700 (PDT) From: zimoun To: Brett Gilio Subject: Re: bug#33032: [PATCH] gnu: update python-biopython to 1.72 References: <20181013034945.9545-1-brettg@posteo.net> Date: Thu, 07 Apr 2022 14:03:26 +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: <86zgkx2j8x.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 33032-done Cc: 33032-done@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: -1.0 (-) Hi, Thank for your contribution. Currently Guix provides more recent versions of BioPython. On Fri, 12 Oct 2018 at 22:49, Brett Gilio 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 ------------=_1649333162-18227-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 13 Oct 2018 03:50:52 +0000 Received: from localhost ([127.0.0.1]:47651 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gBAwy-0000ML-KV for submit@debbugs.gnu.org; Fri, 12 Oct 2018 23:50:52 -0400 Received: from eggs.gnu.org ([208.118.235.92]:55269) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1gBAww-0000M7-9H for submit@debbugs.gnu.org; Fri, 12 Oct 2018 23:50:46 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gBAwq-0000nf-An for submit@debbugs.gnu.org; Fri, 12 Oct 2018 23:50:41 -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 lists.gnu.org ([2001:4830:134:3::11]:57069) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1gBAwq-0000nX-5B for submit@debbugs.gnu.org; Fri, 12 Oct 2018 23:50:40 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:36627) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1gBAwp-0002vh-33 for guix-patches@gnu.org; Fri, 12 Oct 2018 23:50:40 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1gBAwl-0000jx-Qa for guix-patches@gnu.org; Fri, 12 Oct 2018 23:50:38 -0400 Received: from mout01.posteo.de ([185.67.36.65]:50186) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1gBAwc-0000dC-Cw for guix-patches@gnu.org; Fri, 12 Oct 2018 23:50:29 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id BFD3221259 for ; Sat, 13 Oct 2018 05:50:18 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1539402618; bh=xTKVpojK2xFDVc1ruHTE1n0ovOseZQ8eUcrpbPFVpRU=; h=From:To:Cc:Subject:Date:From; b=mJXyVNi5ZKnS8F+CRg9b6Enya/s/sWTIsdIfAESeGPnb3zptSekLwrZ6IcmvNVvKr DfazLFbGWeIrPfzTAY9tQV6vvKf67cA7IslzlA+V8br+KavW8BSMFuGpmdGEAOctzx 36CH7u1hNrsbrjTbul64JR+QJOw3tYJJYQi+/QyKP5UWVX4Ck1loTGOOMXD62rqRnY PTwkQpwAznqjrAOkvBXIdUJLWQjfSn+lGejUvMhIx7wuJmqkT/ulDNBtl2SnkahSAN pspSkABRoOt8WrB6kxAgNNf8nUtqEiC4Z/anJVcDVFoc7jOMC39X4oiDW4k3WgMFMW z7hdo1unve9kg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 42X9hT5ktNz6tm7; Sat, 13 Oct 2018 05:50:17 +0200 (CEST) From: Brett Gilio To: guix-patches@gnu.org Subject: [PATCH] gnu: update python-biopython to 1.72 Date: Fri, 12 Oct 2018 22:49:45 -0500 Message-Id: <20181013034945.9545-1-brettg@posteo.net> X-Mailer: git-send-email 2.19.1 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-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.0 (----) X-Debbugs-Envelope-To: submit Cc: Brett Gilio 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: -5.0 (-----) --- 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 ;;; Copyright =C2=A9 2018 G=C3=A1bor Boskovits ;;; Copyright =C2=A9 2018 M=C4=83d=C4=83lin Ionel Patra=C8=99cu +;;; Copyright =C2=A9 2018 Brett Gilio ;;; ;;; 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 ------------=_1649333162-18227-1--