From unknown Sun Jun 22 08:07:17 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#34354] [PATCH] gnu: python-biopython: Update to 1.73. Resent-From: Brett Gilio Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 06 Feb 2019 22:13:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 34354 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 34354@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.15494911275578 (code B ref -1); Wed, 06 Feb 2019 22:13:01 +0000 Received: (at submit) by debbugs.gnu.org; 6 Feb 2019 22:12:07 +0000 Received: from localhost ([127.0.0.1]:36280 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1grVQK-0001Rs-Th for submit@debbugs.gnu.org; Wed, 06 Feb 2019 17:12:07 -0500 Received: from eggs.gnu.org ([209.51.188.92]:52022) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1grVQI-0001RL-0p for submit@debbugs.gnu.org; Wed, 06 Feb 2019 17:12:03 -0500 Received: from lists.gnu.org ([209.51.188.17]:38377) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1grVQC-0002bM-Rl for submit@debbugs.gnu.org; Wed, 06 Feb 2019 17:11:56 -0500 Received: from eggs.gnu.org ([209.51.188.92]:38171) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1grVQB-0005vc-Uv for guix-patches@gnu.org; Wed, 06 Feb 2019 17:11:56 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-2.3 required=5.0 tests=BAYES_20,RCVD_IN_DNSWL_MED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1grVQB-0002b1-1B for guix-patches@gnu.org; Wed, 06 Feb 2019 17:11:55 -0500 Received: from mout01.posteo.de ([185.67.36.65]:60347) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1grVQA-0002ac-H8 for guix-patches@gnu.org; Wed, 06 Feb 2019 17:11:54 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id F141316005D for ; Wed, 6 Feb 2019 23:11:50 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1549491111; bh=nzBN9uNiv7M/DEetrPNHRZ4o/u2SDR3aFHekODTZlXc=; h=From:To:Subject:Date:From; b=jSP0GSezTrM9Pb2G1jpPeOAJ7oXltoTglzWdSxv3tUvvRto/nW7hfLJ1Ymb2niAYU bl9N7Ej8oiMwHhEcssTIpuhqYd9GlnDvArka0aXW4z4LSJ6pG9S2yXW/52RBR8qGK3 ZidTY1n+ACkvZQe+NmE/TrRW1b6M8K3c5ft+jNIGHzXxQcyKT40FTo1Luh5MPgV1qD /HyFzmB2BQaV6CQ9s8IN5JsuSRIh88Dn7vRwJYQfKnSlHgm+VpeKH/TK/DLlwR9aoY oh305oF5ey6cvg8hi+5fRf5kpJzLfxwEb6/mOG8TDMJunPQaQHCe8G5kzskJ9j2lRO 0wfYnQub9fdEg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 43vwdx6mxvz6tm9 for ; Wed, 6 Feb 2019 23:11:49 +0100 (CET) From: Brett Gilio Date: Wed, 06 Feb 2019 16:11:48 -0600 Message-ID: <871s4kzhwb.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/x-patch; charset=utf-8 Content-Disposition: inline; filename=0001-gnu-python-biopython-Update-to-1.73.patch Content-Transfer-Encoding: quoted-printable Content-Description: [PATCH] gnu: python-biopython: Update to 1.73. X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 185.67.36.65 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Spam-Score: 1.0 (+) 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: -0.0 (/) >From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Wed, 6 Feb 2019 16:10:05 -0600 Subject: [PATCH] gnu: python-biopython: Update to 1.73. * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73. --- gnu/packages/bioinformatics.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.= scm index 516a7c1ee..99c205279 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 2019 Brett Gilio ;;; ;;; This file is part of GNU Guix. ;;; @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to do = computational biology.") (define-public python-biopython (package (name "python-biopython") - (version "1.70") + (version "1.73") (source (origin (method url-fetch) ;; use PyPi rather than biopython.org to ease updating (uri (pypi-uri "biopython" version)) (sha256 (base32 - "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a")))) + "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh")))) (build-system python-build-system) (arguments `(#:phases @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, and = more.") (base32 "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) (build-system python-build-system) + (arguments + `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tests (inputs `(("python-biopython" ,python-biopython))) (native-inputs --=20 2.20.1 From unknown Sun Jun 22 08:07:17 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#34354] [PATCH] gnu: python-biopython: Update to 1.73. Resent-From: Brett Gilio Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 06 Feb 2019 22:20:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 34354 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Brett Gilio Cc: 34354@debbugs.gnu.org Received: via spool by 34354-submit@debbugs.gnu.org id=B34354.15494915806364 (code B ref 34354); Wed, 06 Feb 2019 22:20:01 +0000 Received: (at 34354) by debbugs.gnu.org; 6 Feb 2019 22:19:40 +0000 Received: from localhost ([127.0.0.1]:36293 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1grVXf-0001eZ-OQ for submit@debbugs.gnu.org; Wed, 06 Feb 2019 17:19:40 -0500 Received: from mout01.posteo.de ([185.67.36.65]:56873) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1grVXd-0001eG-88 for 34354@debbugs.gnu.org; Wed, 06 Feb 2019 17:19:38 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 0D5C916005E for <34354@debbugs.gnu.org>; Wed, 6 Feb 2019 23:19:30 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1549491571; bh=DtJb3jQLCz6uv/kDkANc++tBCK7hdpSzYYacf3c3TdA=; h=From:To:Cc:Subject:Date:From; b=Zi9DsCdNa5WH9rVgZjK3p0iKE0uX0/zRyiGIUrfNc+/ri2LPgsZZhzh+my7kN/V+e ljStAwaOVsHShtSBNpUXWkS3gKol+okQ02++mZeFBcSAMZ2b7B38mkt5yWfVQczFtu 7lEAxXGY4Lyjflo/IFDQaO/IK0Dh1Xrc3698GNk1JOKmaivpYlmKj9jsKz7itmGY72 U8HasbUXb5mzTI8yCt4kFgSFo52OE4hnthw2eQqEDjYCZ5bZ1g6RNWmb7dXYm5gOEH GxLICRTh1v6TmJnIIRAMs4Jqnw2xsehRy+iT+hhsL9jnus9BCfs2V5gr7HUHKfuOI7 kS3kEmR11L1mg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 43vwpn6xN8z6tm7; Wed, 6 Feb 2019 23:19:29 +0100 (CET) References: <871s4kzhwb.fsf@posteo.net> User-agent: mu4e 1.0; emacs 26.1 From: Brett Gilio In-reply-to: <871s4kzhwb.fsf@posteo.net> Date: Wed, 06 Feb 2019 16:19:28 -0600 Message-ID: <87zhr8y2z3.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) 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: -3.3 (---) Brett Gilio writes: > From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001 > From: Brett Gilio > Date: Wed, 6 Feb 2019 16:10:05 -0600 > Subject: [PATCH] gnu: python-biopython: Update to 1.73. > > * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73. > --- > gnu/packages/bioinformatics.scm | 7 +++++-- > 1 file changed, 5 insertions(+), 2 deletions(-) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatic= s.scm > index 516a7c1ee..99c205279 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 2019 Brett Gilio > ;;; > ;;; This file is part of GNU Guix. > ;;; > @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to d= o computational biology.") > (define-public python-biopython > (package > (name "python-biopython") > - (version "1.70") > + (version "1.73") > (source (origin > (method url-fetch) > ;; use PyPi rather than biopython.org to ease updating > (uri (pypi-uri "biopython" version)) > (sha256 > (base32 > - "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"))= )) > + "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh"))= )) > (build-system python-build-system) > (arguments > `(#:phases > @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, an= d more.") > (base32 > "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) > (build-system python-build-system) > + (arguments > + `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tes= ts > (inputs > `(("python-biopython" ,python-biopython))) > (native-inputs I disabled the tests on package `seqmagick' because after updating biopython to 1.73 it was failing a test on integer iteration. I could not reproduce this failure on the 1.70 version of biopython, so it seems to be a temporary fix to that failure. I'm not sure if this was the "correct" way to fix that issue, but it works. If not, please let me know so I can send a differently modified patch. From unknown Sun Jun 22 08:07:17 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#34354] [PATCH] gnu: python-biopython: Update to 1.73. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 07 Feb 2019 09:33:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 34354 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Brett Gilio Cc: 34354@debbugs.gnu.org Received: via spool by 34354-submit@debbugs.gnu.org id=B34354.154953196229706 (code B ref 34354); Thu, 07 Feb 2019 09:33:02 +0000 Received: (at 34354) by debbugs.gnu.org; 7 Feb 2019 09:32:42 +0000 Received: from localhost ([127.0.0.1]:36559 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1grg2z-0007j3-UE for submit@debbugs.gnu.org; Thu, 07 Feb 2019 04:32:42 -0500 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21033) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1grg2u-0007ir-PA for 34354@debbugs.gnu.org; Thu, 07 Feb 2019 04:32:38 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1549525601; cv=none; d=zoho.com; s=zohoarc; b=d3jfdHPvxigych3lqQnzW/8P/KfDg4sO28f4wIJF5YRqXiSU8ejYuzdZaOcPV3dfTDKDDCOJ+cR83hcsqbIn/kD8GbAwzGWi82Y6fGvoY7mA1Onfp1OB/uYNIH2BaRSDU+jCe4gKNCDPsUQx/n5AYieUJmncy0Dcks73rSkuKyY= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1549525601; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To:ARC-Authentication-Results; bh=GTrprpiqcDioS6RYZYvi9OJCgnRdojCn/aZRQ9ef19Y=; b=YBoNkjV2ZoJCgDP8gKoeh0Vof/bwR4WEU+abYa1ogk9kT1b0eKtOJcAbv2qQ0feIN+Y3jrecC6u+3sB81a/RUMVpAPZZkm1920yVVGDlejm7/o5kzfMcNb3tC3kq1snNZgfSAP8WEdhW1rg2xkVbYzsZtLXsBATkmXELe1Dm5z4= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1549525601; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; l=2713; bh=GTrprpiqcDioS6RYZYvi9OJCgnRdojCn/aZRQ9ef19Y=; b=FdbbR3Le1zP5vboSHmv6fDIS/kUB60JIJ5zz2b14iPMV/ZCWEmtiw8y7VTg+hKcf mMorL8cX+2I2VGgJe4DJYFbEYGjZLQNenfBlcqyxMMpvK6HZOLL7MGc+Hae5ru2mYPY m6nEH7NYO6H178VQZz0R4ACluU3oneSaIllJIjNY= Received: from localhost (p3E9E90DD.dip0.t-ipconnect.de [62.158.144.221]) by mx.zohomail.com with SMTPS id 15495255998851019.2893647958332; Wed, 6 Feb 2019 23:46:39 -0800 (PST) References: <871s4kzhwb.fsf@posteo.net> <87zhr8y2z3.fsf@posteo.net> User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus In-reply-to: <87zhr8y2z3.fsf@posteo.net> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Thu, 07 Feb 2019 08:46:36 +0100 Message-ID: <878sysf3c3.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) 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: -1.0 (-) Hi Brett, > Brett Gilio writes: > >> From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001 >> From: Brett Gilio >> Date: Wed, 6 Feb 2019 16:10:05 -0600 >> Subject: [PATCH] gnu: python-biopython: Update to 1.73. >> >> * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73. >> --- >> gnu/packages/bioinformatics.scm | 7 +++++-- >> 1 file changed, 5 insertions(+), 2 deletions(-) >> >> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformati= cs.scm >> index 516a7c1ee..99c205279 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 2019 Brett Gilio >> ;;; >> ;;; This file is part of GNU Guix. >> ;;; >> @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to = do computational biology.") >> (define-public python-biopython >> (package >> (name "python-biopython") >> - (version "1.70") >> + (version "1.73") >> (source (origin >> (method url-fetch) >> ;; use PyPi rather than biopython.org to ease updating >> (uri (pypi-uri "biopython" version)) >> (sha256 >> (base32 >> - "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a")= ))) >> + "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh")= ))) >> (build-system python-build-system) >> (arguments >> `(#:phases >> @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, a= nd more.") >> (base32 >> "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) >> (build-system python-build-system) >> + (arguments >> + `(#:tests? #f)) ; Updating biopython to 1.73 results in failing te= sts >> (inputs >> `(("python-biopython" ,python-biopython))) >> (native-inputs > > I disabled the tests on package `seqmagick' because after updating > biopython to 1.73 it was failing a test on integer iteration. I could > not reproduce this failure on the 1.70 version of biopython, so it seems > to be a temporary fix to that failure. I'm not sure if this was the > "correct" way to fix that issue, but it works. If the tests are failing it is possibel that seqmagick doesn=E2=80=99t work properly any more. This would be serious. Could you report the test failures to the upstream developers please and add the URL in a comment? Also please separate these two changes. They should not go to the same commit. -- Ricardo From unknown Sun Jun 22 08:07:17 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#34354] [PATCH] gnu: python-biopython: Update to 1.73. Resent-From: Brett Gilio Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 07 Feb 2019 20:07:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 34354 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ricardo Wurmus Cc: 34354@debbugs.gnu.org, Brett Gilio Received: via spool by 34354-submit@debbugs.gnu.org id=B34354.15495699713904 (code B ref 34354); Thu, 07 Feb 2019 20:07:02 +0000 Received: (at 34354) by debbugs.gnu.org; 7 Feb 2019 20:06:11 +0000 Received: from localhost ([127.0.0.1]:38648 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1grpw2-00010t-LQ for submit@debbugs.gnu.org; Thu, 07 Feb 2019 15:06:10 -0500 Received: from mout01.posteo.de ([185.67.36.65]:54967) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1grpw0-00010g-3C for 34354@debbugs.gnu.org; Thu, 07 Feb 2019 15:06:09 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 9C0BF16005E for <34354@debbugs.gnu.org>; Thu, 7 Feb 2019 21:06:01 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1549569961; bh=1DDdgT0L7yj1IE2QFRJ4Qp49FUemOIS/mvi8cxwDOe0=; h=From:To:Cc:Subject:Date:From; b=cm7Wrqa99Y2pGeF5uiEteHBz6Tsz/aMd46ABanx9axbkd9wQDOEoNBeOXE1dVBmCj JhaQ0qjw4dbPGNh7jgVBS1wEMWvfK3tNwVvuqcvDVmP3FnTyg3kygo5OO1QsFkwoNQ Zj8n4eZ7xC3gzty30a0+YzCMs76CqH/dyXDGs2I2WKQJ8H0nwq6ZKH8RAn10eVe0NF lnf2KyQ4ME7vqB4jKjSLLG2ogHDG8wq9wqdh6HUsHlr2qA3Taxnjd4PmRdNNFqcAYz /5EFI0ouEi792xQljM8a+fJ4h/UChgbMOEnFLMY63cHrN+Bw/O1kTzCwhS76VwzmCw YyrBjYoKlSUTA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 43wTpJ0hGWz6tmP; Thu, 7 Feb 2019 21:05:59 +0100 (CET) References: <871s4kzhwb.fsf@posteo.net> <87zhr8y2z3.fsf@posteo.net> <878sysf3c3.fsf@elephly.net> User-agent: mu4e 1.0; emacs 26.1 From: Brett Gilio In-reply-to: <878sysf3c3.fsf@elephly.net> Date: Thu, 07 Feb 2019 14:05:58 -0600 Message-ID: <87mun7qs7t.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) 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: -3.3 (---) Ricardo Wurmus writes: > Hi Brett, > >> Brett Gilio writes: >> >>> From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001 >>> From: Brett Gilio >>> Date: Wed, 6 Feb 2019 16:10:05 -0600 >>> Subject: [PATCH] gnu: python-biopython: Update to 1.73. >>> >>> * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73. >>> --- >>> gnu/packages/bioinformatics.scm | 7 +++++-- >>> 1 file changed, 5 insertions(+), 2 deletions(-) >>> >>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformat= ics.scm >>> index 516a7c1ee..99c205279 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 2019 Brett Gilio >>> ;;; >>> ;;; This file is part of GNU Guix. >>> ;;; >>> @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to= do computational biology.") >>> (define-public python-biopython >>> (package >>> (name "python-biopython") >>> - (version "1.70") >>> + (version "1.73") >>> (source (origin >>> (method url-fetch) >>> ;; use PyPi rather than biopython.org to ease updating >>> (uri (pypi-uri "biopython" version)) >>> (sha256 >>> (base32 >>> - "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"= )))) >>> + "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh"= )))) >>> (build-system python-build-system) >>> (arguments >>> `(#:phases >>> @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, = and more.") >>> (base32 >>> "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) >>> (build-system python-build-system) >>> + (arguments >>> + `(#:tests? #f)) ; Updating biopython to 1.73 results in failing t= ests >>> (inputs >>> `(("python-biopython" ,python-biopython))) >>> (native-inputs >> >> I disabled the tests on package `seqmagick' because after updating >> biopython to 1.73 it was failing a test on integer iteration. I could >> not reproduce this failure on the 1.70 version of biopython, so it seems >> to be a temporary fix to that failure. I'm not sure if this was the >> "correct" way to fix that issue, but it works. > > If the tests are failing it is possibel that seqmagick doesn=E2=80=99t wo= rk > properly any more. This would be serious. > > Could you report the test failures to the upstream developers please and > add the URL in a comment? > > Also please separate these two changes. They should not go to the same > commit. Ricardo, Understood. I will do exactly that and reply again later with a revised patch series. Brett Gilio From unknown Sun Jun 22 08:07:17 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#34354] [PATCH] gnu: python-biopython: Update to 1.73. Resent-From: Maxim Cournoyer Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 13 Jul 2021 13:33:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 34354 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Brett Gilio Cc: Ricardo Wurmus , 34354@debbugs.gnu.org Received: via spool by 34354-submit@debbugs.gnu.org id=B34354.162618314627798 (code B ref 34354); Tue, 13 Jul 2021 13:33:02 +0000 Received: (at 34354) by debbugs.gnu.org; 13 Jul 2021 13:32:26 +0000 Received: from localhost ([127.0.0.1]:39820 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m3IWO-0007EH-TX for submit@debbugs.gnu.org; Tue, 13 Jul 2021 09:32:26 -0400 Received: from mail-qt1-f176.google.com ([209.85.160.176]:35550) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m3IWL-0007E3-03 for 34354@debbugs.gnu.org; Tue, 13 Jul 2021 09:32:24 -0400 Received: by mail-qt1-f176.google.com with SMTP id g12so16596467qtb.2 for <34354@debbugs.gnu.org>; Tue, 13 Jul 2021 06:32:20 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:references:date:in-reply-to:message-id :user-agent:mime-version:content-transfer-encoding; bh=Yte+Es4cb00Fn7ESy6SYtBIVT1qz/Q+9l/6OV638R2k=; b=gj/+fsD+RBFKTi+88Y4JoXfKiJWq6f834pPZdPgNgymunrKqZTszXHrNPmDu+4/lju Z4sNswoYsD3iQu1X1arVBud93M7p+LJPZMblAfX2LzHrFg6YRXqbkDviX3riFa0+ezp+ BmxPC1S0gIGfNGnjPsZ4tmrhINEECqF5NjX9XjRM7KwXg01S4EbTA2FZJsfdHIV0g9ra c2smXKZZiZjRbVgISuVD2v5BX3iYauLdSBGJhhncx3DTgonYfTR1nLybM7wVOnweOGvX Gt2Z29YYChYnw/AvfagJAM3omvKcVeqzHw2cDLc0qOW7akNRzNKRfNa3OzkBUhNAntwi XMLw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:references:date:in-reply-to :message-id:user-agent:mime-version:content-transfer-encoding; bh=Yte+Es4cb00Fn7ESy6SYtBIVT1qz/Q+9l/6OV638R2k=; b=C3SMMHt5c0v4Hf6zY5fhlw2Yioae9mKShFmxXJlhcNvyZBjuNcEVCO4h0K9Omx1Vsz ZDP44ixlkR8sfHcXz7EzCrk86TS0ryOUEsiDMBkrUd1J7SE+fL1027sGj+zxCUMLLNvl AV/GwYLftU0kZ+vBCJNhYCQIiUrzY6cb/HRr89IdJJHd3JINY3PQXvrkroNEj5r0GNVh W54b6UAgsi+FSUT1vy4b3CKeVLlUvZAdv+3vu+uvvEZEOHWNJUdEziSFWgMllEh7JJv5 1TDFrSuL+ivl/+PsnOcoYv2xA5GUyXKUeS6QvxJmNAjAXbpqOk+rfTXU1EUnLZJbajCh s85Q== X-Gm-Message-State: AOAM530/A+M4eZ2LxhCaNSDBgMhlub1oYGGAHCsLjTm7yehYsuL1GHpB pTSgKdzrxbC2NpApMtE3kqAvMaIyh/BkA4iW X-Google-Smtp-Source: ABdhPJzaRVMrVyFTa2AM3ce8ELUimFdUYVjv+ual8hZvPtU3AkgUWrvA5y6WrsqPIVKDaDZmNobDMA== X-Received: by 2002:ac8:5f52:: with SMTP id y18mr4033600qta.153.1626183135087; Tue, 13 Jul 2021 06:32:15 -0700 (PDT) Received: from hurd (dsl-10-136-19.b2b2c.ca. [72.10.136.19]) by smtp.gmail.com with ESMTPSA id bm24sm4494128qkb.47.2021.07.13.06.32.14 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 13 Jul 2021 06:32:14 -0700 (PDT) From: Maxim Cournoyer References: <871s4kzhwb.fsf@posteo.net> <87zhr8y2z3.fsf@posteo.net> <878sysf3c3.fsf@elephly.net> <87mun7qs7t.fsf@posteo.net> Date: Tue, 13 Jul 2021 09:32:14 -0400 In-Reply-To: <87mun7qs7t.fsf@posteo.net> (Brett Gilio's message of "Thu, 07 Feb 2019 14:05:58 -0600") Message-ID: <875yxes5k1.fsf_-_@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) 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: -1.0 (-) Hello, Brett Gilio writes: > Ricardo Wurmus writes: > >> Hi Brett, >> >>> Brett Gilio writes: >>> >>>> From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001 >>>> From: Brett Gilio >>>> Date: Wed, 6 Feb 2019 16:10:05 -0600 >>>> Subject: [PATCH] gnu: python-biopython: Update to 1.73. >>>> >>>> * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73. >>>> --- >>>> gnu/packages/bioinformatics.scm | 7 +++++-- >>>> 1 file changed, 5 insertions(+), 2 deletions(-) >>>> >>>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinforma= tics.scm >>>> index 516a7c1ee..99c205279 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 2019 Brett Gilio >>>> ;;; >>>> ;;; This file is part of GNU Guix. >>>> ;;; >>>> @@ -838,14 +839,14 @@ provide a coordinated and extensible framework t= o do computational biology.") >>>> (define-public python-biopython >>>> (package >>>> (name "python-biopython") >>>> - (version "1.70") >>>> + (version "1.73") >>>> (source (origin >>>> (method url-fetch) >>>> ;; use PyPi rather than biopython.org to ease updating >>>> (uri (pypi-uri "biopython" version)) >>>> (sha256 >>>> (base32 >>>> - "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a= ")))) >>>> + "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh= ")))) >>>> (build-system python-build-system) >>>> (arguments >>>> `(#:phases >>>> @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment,= and more.") >>>> (base32 >>>> "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) >>>> (build-system python-build-system) >>>> + (arguments >>>> + `(#:tests? #f)) ; Updating biopython to 1.73 results in failing = tests >>>> (inputs >>>> `(("python-biopython" ,python-biopython))) >>>> (native-inputs >>> >>> I disabled the tests on package `seqmagick' because after updating >>> biopython to 1.73 it was failing a test on integer iteration. I could >>> not reproduce this failure on the 1.70 version of biopython, so it seems >>> to be a temporary fix to that failure. I'm not sure if this was the >>> "correct" way to fix that issue, but it works. >> >> If the tests are failing it is possibel that seqmagick doesn=E2=80=99t w= ork >> properly any more. This would be serious. >> >> Could you report the test failures to the upstream developers please and >> add the URL in a comment? >> >> Also please separate these two changes. They should not go to the same >> commit. > > Ricardo, > > Understood. I will do exactly that and reply again later with a revised > patch series. > > Brett Gilio Any news on this? Thanks, Maxim From unknown Sun Jun 22 08:07:17 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#34354: closed (Re: bug#34354: [PATCH] gnu: python-biopython: Update to 1.73.) Message-ID: References: <871r4ujjj4.fsf@systemreboot.net> <871s4kzhwb.fsf@posteo.net> X-Gnu-PR-Message: they-closed 34354 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 34354@debbugs.gnu.org Date: Sat, 09 Oct 2021 15:39:01 +0000 Content-Type: multipart/mixed; boundary="----------=_1633793941-2345-1" This is a multi-part message in MIME format... ------------=_1633793941-2345-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #34354: [PATCH] gnu: python-biopython: Update to 1.73. 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 34354@debbugs.gnu.org. --=20 34354: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D34354 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1633793941-2345-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 34354-done) by debbugs.gnu.org; 9 Oct 2021 15:38:24 +0000 Received: from localhost ([127.0.0.1]:54013 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mZEQa-0000b0-Fb for submit@debbugs.gnu.org; Sat, 09 Oct 2021 11:38:24 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:54620) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mZEQX-0000an-Kz for 34354-done@debbugs.gnu.org; Sat, 09 Oct 2021 11:38:23 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Type:MIME-Version:Message-ID:Date: References:Subject:Cc:To:From:Sender:Reply-To:Content-Transfer-Encoding: Content-ID:Content-Description:Resent-Date:Resent-From:Resent-Sender: Resent-To:Resent-Cc:Resent-Message-ID:In-Reply-To:List-Id:List-Help: List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=yv9vO/i0gnfFDhLWGtCAbX3//PqQcLfWEb6PmK9tHCw=; b=lvg6/t26eiV4fYJh+o1GsNucjO WS9leNefEG36d5/mi8mIpRC5RUO8hlhD1XT0AdSPbrR48I7afBQEuWHpydBivuaw1Pg/qig5jDyLN vxS+qObEJH96Aa7MSTYI92Kr3xlsYRTtdhrpwQls8k82fArKfnrUZFnV6+KIdGy+8IyqRpBOwF9Ce dRHLjI+y01fLFv31nRnRGSljKsSH08zqRxZqBu34b+4N1n4sexf7RoNyMIbCgevTokLMAzUKMXZDV 5O28XnRG0mca4E+W2nPMVu2zkl18f6CSQF2EPpWQy1+NzsdUMT0MO86x3AlzWPFMAQGj6HTGW/6/c sVG5HdZg==; Received: from [192.168.2.1] (port=47868 helo=steel) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.94.2) (envelope-from ) id 1mZEQN-000Kh9-NB; Sat, 09 Oct 2021 21:08:11 +0530 From: Arun Isaac To: Maxim Cournoyer Subject: Re: bug#34354: [PATCH] gnu: python-biopython: Update to 1.73. References: <871s4kzhwb.fsf@posteo.net> <87zhr8y2z3.fsf@posteo.net> <878sysf3c3.fsf@elephly.net> <87mun7qs7t.fsf@posteo.net> <875yxes5k1.fsf_-_@gmail.com> Date: Sat, 09 Oct 2021 21:08:07 +0530 Message-ID: <871r4ujjj4.fsf@systemreboot.net> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 34354-done Cc: Ricardo Wurmus , 34354-done@debbugs.gnu.org, 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: -1.0 (-) --=-=-= Content-Type: text/plain Hi, Efraim updated python-biopython to 1.73 in 309b38bed61c21ce8ba559a679592ecc1c94dbfc. So, I'm closing this issue. Thanks! Arun --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQFPBAEBCAA5FiEEf3MDQ/Lwnzx3v3nTLiXui2GAK7MFAmFht18bHGFydW5pc2Fh Y0BzeXN0ZW1yZWJvb3QubmV0AAoJEC4l7othgCuzkssH/AhcEzO3PGuC45RNDFCv ueoxfxMXAB4rurLUZDnijAAUbGz1hYzuu/QLseLqVqP94gAE3PuNpVUl2GK51d/m zV5H63gEqVQEqaqKoAcGiUsFuXdHBUQpmbFb/wSsxB+ltsEY9mL8Jqf7y9L1Cefs EeHGzbyONVBHpcMtgFFGhcAfp8tFwauoACzXQk1DkbJffMWtri3s68sOuWk+3WsX 3a5ib5sS0QGfgPYXc8WAD5tEEkC3P+7XMwgt869yPBChSkfm+vLTJtjSddmZ4Ect yNF0OdUmmQhnQpC0hHpQUkG06+N/ezd2+u2sob6AFFz/PN8bmCj8FFhIuKsoycEE lc4= =Wzv5 -----END PGP SIGNATURE----- --=-=-=-- ------------=_1633793941-2345-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 6 Feb 2019 22:12:07 +0000 Received: from localhost ([127.0.0.1]:36280 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1grVQK-0001Rs-Th for submit@debbugs.gnu.org; Wed, 06 Feb 2019 17:12:07 -0500 Received: from eggs.gnu.org ([209.51.188.92]:52022) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1grVQI-0001RL-0p for submit@debbugs.gnu.org; Wed, 06 Feb 2019 17:12:03 -0500 Received: from lists.gnu.org ([209.51.188.17]:38377) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1grVQC-0002bM-Rl for submit@debbugs.gnu.org; Wed, 06 Feb 2019 17:11:56 -0500 Received: from eggs.gnu.org ([209.51.188.92]:38171) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1grVQB-0005vc-Uv for guix-patches@gnu.org; Wed, 06 Feb 2019 17:11:56 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-2.3 required=5.0 tests=BAYES_20,RCVD_IN_DNSWL_MED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1grVQB-0002b1-1B for guix-patches@gnu.org; Wed, 06 Feb 2019 17:11:55 -0500 Received: from mout01.posteo.de ([185.67.36.65]:60347) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1grVQA-0002ac-H8 for guix-patches@gnu.org; Wed, 06 Feb 2019 17:11:54 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id F141316005D for ; Wed, 6 Feb 2019 23:11:50 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1549491111; bh=nzBN9uNiv7M/DEetrPNHRZ4o/u2SDR3aFHekODTZlXc=; h=From:To:Subject:Date:From; b=jSP0GSezTrM9Pb2G1jpPeOAJ7oXltoTglzWdSxv3tUvvRto/nW7hfLJ1Ymb2niAYU bl9N7Ej8oiMwHhEcssTIpuhqYd9GlnDvArka0aXW4z4LSJ6pG9S2yXW/52RBR8qGK3 ZidTY1n+ACkvZQe+NmE/TrRW1b6M8K3c5ft+jNIGHzXxQcyKT40FTo1Luh5MPgV1qD /HyFzmB2BQaV6CQ9s8IN5JsuSRIh88Dn7vRwJYQfKnSlHgm+VpeKH/TK/DLlwR9aoY oh305oF5ey6cvg8hi+5fRf5kpJzLfxwEb6/mOG8TDMJunPQaQHCe8G5kzskJ9j2lRO 0wfYnQub9fdEg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 43vwdx6mxvz6tm9 for ; Wed, 6 Feb 2019 23:11:49 +0100 (CET) From: Brett Gilio To: guix-patches@gnu.org Subject: [PATCH] gnu: python-biopython: Update to 1.73. Date: Wed, 06 Feb 2019 16:11:48 -0600 Message-ID: <871s4kzhwb.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/x-patch; charset=utf-8 Content-Disposition: inline; filename=0001-gnu-python-biopython-Update-to-1.73.patch Content-Transfer-Encoding: quoted-printable Content-Description: [PATCH] gnu: python-biopython: Update to 1.73. X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 185.67.36.65 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: submit 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 (/) >From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Wed, 6 Feb 2019 16:10:05 -0600 Subject: [PATCH] gnu: python-biopython: Update to 1.73. * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73. --- gnu/packages/bioinformatics.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.= scm index 516a7c1ee..99c205279 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 2019 Brett Gilio ;;; ;;; This file is part of GNU Guix. ;;; @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to do = computational biology.") (define-public python-biopython (package (name "python-biopython") - (version "1.70") + (version "1.73") (source (origin (method url-fetch) ;; use PyPi rather than biopython.org to ease updating (uri (pypi-uri "biopython" version)) (sha256 (base32 - "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a")))) + "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh")))) (build-system python-build-system) (arguments `(#:phases @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, and = more.") (base32 "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) (build-system python-build-system) + (arguments + `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tests (inputs `(("python-biopython" ,python-biopython))) (native-inputs --=20 2.20.1 ------------=_1633793941-2345-1-- From unknown Sun Jun 22 08:07:17 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#34354] (no subject) References: <871s4kzhwb.fsf@posteo.net> In-Reply-To: <871s4kzhwb.fsf@posteo.net> Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 09 Oct 2021 16:14:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 34354 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: control@debbugs.gnu.org Cc: 34354@debbugs.gnu.org, Ricardo Wurmus , Brett Gilio , Maxim Cournoyer Received: via spool by 34354-submit@debbugs.gnu.org id=B34354.16337959955610 (code B ref 34354); Sat, 09 Oct 2021 16:14:01 +0000 Received: (at 34354) by debbugs.gnu.org; 9 Oct 2021 16:13:15 +0000 Received: from localhost ([127.0.0.1]:54034 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mZEyJ-0001SP-1E for submit@debbugs.gnu.org; Sat, 09 Oct 2021 12:13:15 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:54622) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mZEyE-0001SB-BQ; Sat, 09 Oct 2021 12:13:13 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Type:MIME-Version:Message-ID:Date:Cc :To:From:Sender:Reply-To:Subject:Content-Transfer-Encoding:Content-ID: Content-Description:Resent-Date:Resent-From:Resent-Sender:Resent-To:Resent-Cc :Resent-Message-ID:In-Reply-To:References:List-Id:List-Help:List-Unsubscribe: List-Subscribe:List-Post:List-Owner:List-Archive; bh=t9fAtVd7p9M6pbbUjN4Y5dj2pcR564vmUf3+tQniJaU=; b=SV+GnDkSuIRAh2VgXQpavjRIH8 XRpebZFmRj437U2nV5Z4jYOcKMJ20rhD9Bgd93Ls/N/AzGvpj0WvWFozbtkF1oQeUL+LDNBP+nfzH /l26TW/CxMiQymYySnbGN/6V679Cge5NBR614ZAJYcaPAhDJVv+BG0jVU0YLhq9Qt+CSgE97ytg+I 7NGdipkFQNZeive+lXMBgbpMDsaduygkWY75/4EaPqEUzNKeYKM/7adtyq2vpV7/yvacm4qWEJrYt 6niVKpvs/PiUEbnDpvxLOlf6oVJSC4aXNnb6sDkOLoayrIQsQtydSs0xLKy0AjNK1ZLGbjmgAXOsD fh0PIeMw==; Received: from [192.168.2.1] (port=47466 helo=steel) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.94.2) (envelope-from ) id 1mZExw-000Kis-2D; Sat, 09 Oct 2021 21:42:52 +0530 From: Arun Isaac Date: Sat, 09 Oct 2021 21:42:44 +0530 Message-ID: <87wnmmi3cz.fsf@systemreboot.net> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: 2.0 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: reopen 34354 retitle 34354 Update python-biopython to 1.79, seqmagick to 0.8.4 thanks Oops, it seems I closed this bug without realizing that seqmagick is still broken! I have fixed this problem (on my local machine) by updating both python-biopython and seqmagick. I will send patches [...] Content analysis details: (2.0 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.0 SPF_PASS SPF: sender matches SPF record 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record 1.8 MISSING_SUBJECT Missing Subject: header 0.2 NO_SUBJECT Extra score for no subject 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 (+) --=-=-= Content-Type: text/plain reopen 34354 retitle 34354 Update python-biopython to 1.79, seqmagick to 0.8.4 thanks Oops, it seems I closed this bug without realizing that seqmagick is still broken! I have fixed this problem (on my local machine) by updating both python-biopython and seqmagick. I will send patches soon. Thanks! --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQFPBAEBCAA5FiEEf3MDQ/Lwnzx3v3nTLiXui2GAK7MFAmFhv30bHGFydW5pc2Fh Y0BzeXN0ZW1yZWJvb3QubmV0AAoJEC4l7othgCuznPAH/07c6O61imuWfu73OIxB CswyZ74JMRLo+plqxGBmHmExOFvUuiXPiCJUxZ38YY8lYjBjHCN4hvKHFdeGEiH9 NWAdQ188qCFZWuEs6K2FR6pU8ZaZq+aFWd1atoGO3Bb259sSyTBCROUSHNG62kp2 bC43E9mm3p3cG1wfb7GhmdiYxe/bj9605JqgEPniC7yBB+YgR5tOydJJ+SVGcEt8 PugB5KgQRWKhUY5dBPR16tASN9aY9gKXFIfTebJWCCP2loNjCIpdYuouZ4OsCw/U OCn2M8fOJ8RdhAgwkI6OCnoQ4ZW5S6MlfdHy8VTELsu6KKT5vWFvvfo1gJKSFPQo Zl4= =IbNT -----END PGP SIGNATURE----- --=-=-=-- From unknown Sun Jun 22 08:07:17 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#34354] Update python-biopython to 1.79, seqmagick to 0.8.4 In-Reply-To: <871s4kzhwb.fsf@posteo.net> Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 16 Oct 2021 11:45:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 34354 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 34354@debbugs.gnu.org Cc: Ricardo Wurmus , Brett Gilio , Maxim Cournoyer Received: via spool by 34354-submit@debbugs.gnu.org id=B34354.163438469125777 (code B ref 34354); Sat, 16 Oct 2021 11:45:02 +0000 Received: (at 34354) by debbugs.gnu.org; 16 Oct 2021 11:44:51 +0000 Received: from localhost ([127.0.0.1]:41054 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mbi7P-0006hh-Is for submit@debbugs.gnu.org; Sat, 16 Oct 2021 07:44:51 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:50228) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1mbi7M-0006hW-2u for 34354@debbugs.gnu.org; Sat, 16 Oct 2021 07:44:50 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Type:MIME-Version:Message-ID:Date: References:Subject:Cc:To:From:Sender:Reply-To:Content-Transfer-Encoding: Content-ID:Content-Description:Resent-Date:Resent-From:Resent-Sender: Resent-To:Resent-Cc:Resent-Message-ID:In-Reply-To:List-Id:List-Help: List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=0H2qm2ZvZk+hSzvFhwYwVDc9whq1UvXZMuPomrry3oM=; b=Aa99+oeJ2kq5QCb8qwukPK6X1J DUECUc/xdkmAG7Dl/Lq9yo/uVKQeQDaw1NM+3+hiIc8WgLDJKelGA/NesktsFDJt3BZ9o3obnzJOl x0kUwYzOTQPDt/5vUItbVMPqcO0HJKT7xXOI/lJiQWyw6Ubx2hgh30Og843/rSDQ+DhP4cP4ISfR2 sIq4JrpdUcPfZvAXZpuTNU8jkl9mrxQQgLHCNqW6N2OQTvjBOluOKMONhiQEwMhcZFo2JPWYecxb8 S8SgssfMV0MHdPqQw5kLdgywLlAnsTGMC3ux4vfjFc7+E8Ci1t19z04YJ6A3kpN5pHkuTDjV++FOi b65TaQJw==; Received: from [192.168.2.1] (port=16260 helo=steel) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.94.2) (envelope-from ) id 1mbi73-000CHz-Jr; Sat, 16 Oct 2021 17:14:29 +0530 From: Arun Isaac References: <871s4kzhwb.fsf@posteo.net> <87wnmmi3cz.fsf@systemreboot.net> Date: Sat, 16 Oct 2021 17:14:23 +0530 Message-ID: <8735p1ry7c.fsf@systemreboot.net> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) 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: -1.0 (-) --=-=-= Content-Type: text/plain > I have fixed this problem (on my local machine) by updating both > python-biopython and seqmagick. I will send patches soon. It turns out that updating python-biopython breaks too many other dependent packages. And, some of them take too long to reasonably build on my machine of relatively humble specifications. So, I'm afraid I have to bail out on this promise. Sorry! Regards, Arun --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQFPBAEBCAA5FiEEf3MDQ/Lwnzx3v3nTLiXui2GAK7MFAmFquxcbHGFydW5pc2Fh Y0BzeXN0ZW1yZWJvb3QubmV0AAoJEC4l7othgCuz0DEIAJ2XTCIEP3BxE7y4RfaY XilF/RoyMxrOKYdNGw3hRqJQTa1mboGe9hkXpAJpa9vLWQMtJi/roSTst1t0ive/ zJF38ubadHC28FMNjv5aA51dSK3kQj9tkgEAGNhZ/Ou/Fz/+Jq4I22rE3G2JBtbv H+6LxpYksKeQMOohpD6Eh+np8ETuq8waD9w/SvXYdoGwMDX790cjeby7nStDTLKg X6vKzMjnNoQTMzXgoKY9kS/v5o6nI6JdusnC0KutsVNzB3ToZRtBo61offzIeryS pJrK9ND3LpAgNgQDqQEoQ9TcleDjvHGAqcI8yOkmjNhOvXCdt4DTw4AHImgJFozH GYY= =OKHw -----END PGP SIGNATURE----- --=-=-=-- From unknown Sun Jun 22 08:07:17 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#34354] Update python-biopython to 1.79, seqmagick to 0.8.4 Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 12 Apr 2022 10:15:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 34354 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Arun Isaac Cc: 34354@debbugs.gnu.org, Ricardo Wurmus , Brett Gilio , Maxim Cournoyer Received: via spool by 34354-submit@debbugs.gnu.org id=B34354.164975847029595 (code B ref 34354); Tue, 12 Apr 2022 10:15:02 +0000 Received: (at 34354) by debbugs.gnu.org; 12 Apr 2022 10:14:30 +0000 Received: from localhost ([127.0.0.1]:47606 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1neDXa-0007hG-3B for submit@debbugs.gnu.org; Tue, 12 Apr 2022 06:14:30 -0400 Received: from mail-wr1-f41.google.com ([209.85.221.41]:46613) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1neDXY-0007gu-BM for 34354@debbugs.gnu.org; Tue, 12 Apr 2022 06:14:28 -0400 Received: by mail-wr1-f41.google.com with SMTP id i20so13866881wrb.13 for <34354@debbugs.gnu.org>; Tue, 12 Apr 2022 03:14:28 -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=ilVhONFp6wT5Q/m5J1A1ePWh1sor7g64ZaQF6VSvnvY=; b=eHSRydemde6nk9ppgsjLrzeQRJp6ESboqfvB/SrWlS03+YPPywfe2ecoBMshSroazN xNBZ2yrqM6j0XIL7p+TlXrNAeZAhQsnhjJJ4i+YGaZGZ6+2xWUA0sSm1rZkrPiSFHJcd ro3xk0kZsq/nRTXR567GKCzMreSkZcVX7vjwh0tU7Os0NvRvTGB0Qi2S7HVq1iUVmIeb GVdG8i4fyHfmaCHzXMR4txXZU2ePh62JwMZ749UXvobBEXhEeeoHtEqSXPF/5pYYBZZA +tQ9nrQNCep1r8JkugG3nMjTHYS6aKWGftFsAs9imG7097EklfQEfABQXtddb+xeLmSG 7f1w== 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=ilVhONFp6wT5Q/m5J1A1ePWh1sor7g64ZaQF6VSvnvY=; b=fWoWtY1h2DfgBeQXxHIckfHd2hljlmmHc7qzFJENjZL5CIMTfYJj8qltGHtC/NfAAF juwW2zMEi/AsOSYA3ckzX5Lw9prhkiWGJQF8q16WeZT8S5KgkW2SR0RvBaHkmBnbdL8a Zq5TA5pKkeSaooxAoRUDXbyNzHgpt2Er1x+JlZW0nNwGLptq0/ARGm1NVXTmnS/68PdM 93x5eztdoHkDyjt8SY4bGSi/TmbnL5ukcj8qeV3eu483J61SrzeB4ySafEsWq3zWpFIA NXr7fgPWhUIluyqrDrKouxHHFkC2mMXS5CN1exnwMaux/54enFfHuLbIPx2sf1dpqfwy 13oQ== X-Gm-Message-State: AOAM531sm9mf7jC3SkU6X5uzW8uyMofx5Jo1zvw31VfDPhJ8Kx/DPrZ9 zB3NRRS3oz9tnJJ6DnqvlmA= X-Google-Smtp-Source: ABdhPJxor1ZjTlctz+GzknKR2blDzzYRe1j3sr2ysQNv9YYxvohJwitHyKYA2LBHT9R4hMoCL648Jg== X-Received: by 2002:adf:f00b:0:b0:207:9956:48c5 with SMTP id j11-20020adff00b000000b00207995648c5mr15261913wro.693.1649758462548; Tue, 12 Apr 2022 03:14:22 -0700 (PDT) Received: from lili (roam-nat-fw-prg-194-254-61-45.net.univ-paris-diderot.fr. [194.254.61.45]) by smtp.gmail.com with ESMTPSA id m2-20020a056000008200b00207a6f32833sm5517056wrx.117.2022.04.12.03.14.21 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 12 Apr 2022 03:14:22 -0700 (PDT) From: zimoun References: <871s4kzhwb.fsf@posteo.net> <87wnmmi3cz.fsf@systemreboot.net> <8735p1ry7c.fsf@systemreboot.net> Date: Tue, 12 Apr 2022 12:04:04 +0200 In-Reply-To: <8735p1ry7c.fsf@systemreboot.net> (Arun Isaac's message of "Sat, 16 Oct 2021 17:14:23 +0530") Message-ID: <86v8ve39ez.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-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 Arun, On Sat, 16 Oct 2021 at 17:14, Arun Isaac wrote: >> I have fixed this problem (on my local machine) by updating both >> python-biopython and seqmagick. I will send patches soon. > > It turns out that updating python-biopython breaks too many other > dependent packages. And, some of them take too long to reasonably build > on my machine of relatively humble specifications. So, I'm afraid I have > to bail out on this promise. Sorry! Do we close this patch submission? Since it was initially an update for 1.73 which is older than the current version. And the update of 1.79 requires more work. Therefore, is it worth to keep this submission open? I guess the update to 1.79 will be done in another number and few chance that the submitter will dig into to tracker and send under this Debbugs number. :-) Closing? Cheers, simon From unknown Sun Jun 22 08:07:17 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#34354: closed (Re: bug#34354: Update python-biopython to 1.79, seqmagick to 0.8.4) Message-ID: References: <87r162xz7o.fsf@elephly.net> <871s4kzhwb.fsf@posteo.net> X-Gnu-PR-Message: they-closed 34354 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 34354@debbugs.gnu.org Date: Tue, 12 Apr 2022 12:29:01 +0000 Content-Type: multipart/mixed; boundary="----------=_1649766541-29935-1" This is a multi-part message in MIME format... ------------=_1649766541-29935-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #34354: Update python-biopython to 1.79, seqmagick to 0.8.4 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 34354@debbugs.gnu.org. --=20 34354: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D34354 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1649766541-29935-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 34354-done) by debbugs.gnu.org; 12 Apr 2022 12:28:53 +0000 Received: from localhost ([127.0.0.1]:47906 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1neFdd-0007mS-8q for submit@debbugs.gnu.org; Tue, 12 Apr 2022 08:28:53 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21104) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1neFdb-0007mI-E1 for 34354-done@debbugs.gnu.org; Tue, 12 Apr 2022 08:28:52 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1649766528; cv=none; d=zohomail.com; s=zohoarc; b=ZopJ2R8nWjhp+vGwAyfj8hi4MzbcwVBIxWIeUV2YG69fjzJwljxjKqzjpUtCYSe/luzNk4zbzrjELbAxqHjjNGeCqMeqow1HRRUdzaUgbAJgIoCuQE+cuDeoKyuOqTcUAEUmNUuJiMUj1BHd5+/5PyFVD04LQaR6cHxMTNuJmYw= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1649766528; h=Content-Type:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=IWOn8Lgwg4UTgMnPfGIN4MSWkPzWF/3b0D9qhgzp5to=; b=d2Av98zI51k8iDfA35TbivatrB0X/415QDzc4NY3tJr8RZse9g21k1n9tze7HG+AhipP2VannK6/JFGB38zQUGdRpEQhi+rOMLZkntSRwprDImmWGOTcgk/ICwoWoQwrRzMZ7q3SJIrrSDb0QB8eA2XzWz2zFdP3qIyN9syBKE4= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1649766528; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To; bh=IWOn8Lgwg4UTgMnPfGIN4MSWkPzWF/3b0D9qhgzp5to=; b=GwpPEdVW0LgPQli99OahUhwi00SXHx0SlvQpLpssMPF8Fj4Sve8zmBzWBxIwQtTq kEURIzqLf/QZlkHhYCV8lR4IbLZ/iH1wHr1Ds8jLO1LnldB3U6ePKmweIVppBX0oQxQ Ij83bpOElTkQknZMHY4bsC72goLm+6YlJOlr4pFw= Received: from localhost (i5E862C83.versanet.de [94.134.44.131]) by mx.zohomail.com with SMTPS id 1649766526972283.70105027235286; Tue, 12 Apr 2022 05:28:46 -0700 (PDT) References: <871s4kzhwb.fsf@posteo.net> <87wnmmi3cz.fsf@systemreboot.net> <8735p1ry7c.fsf@systemreboot.net> <86v8ve39ez.fsf_-_@gmail.com> User-agent: mu4e 1.6.10; emacs 28.0.50 From: Ricardo Wurmus To: zimoun Subject: Re: bug#34354: Update python-biopython to 1.79, seqmagick to 0.8.4 Date: Tue, 12 Apr 2022 14:28:22 +0200 In-reply-to: <86v8ve39ez.fsf_-_@gmail.com> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <87r162xz7o.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 34354-done Cc: 34354-done@debbugs.gnu.org, Arun Isaac , Brett Gilio , Maxim Cournoyer 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 (-) zimoun writes: > And the update of 1.79 requires more work. Therefore, is it worth to > keep this submission open? I guess the update to 1.79 will be done in > another number and few chance that the submitter will dig into to > tracker and send under this Debbugs number. :-) > > Closing? Yes. -- Ricardo ------------=_1649766541-29935-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 6 Feb 2019 22:12:07 +0000 Received: from localhost ([127.0.0.1]:36280 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1grVQK-0001Rs-Th for submit@debbugs.gnu.org; Wed, 06 Feb 2019 17:12:07 -0500 Received: from eggs.gnu.org ([209.51.188.92]:52022) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1grVQI-0001RL-0p for submit@debbugs.gnu.org; Wed, 06 Feb 2019 17:12:03 -0500 Received: from lists.gnu.org ([209.51.188.17]:38377) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1grVQC-0002bM-Rl for submit@debbugs.gnu.org; Wed, 06 Feb 2019 17:11:56 -0500 Received: from eggs.gnu.org ([209.51.188.92]:38171) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1grVQB-0005vc-Uv for guix-patches@gnu.org; Wed, 06 Feb 2019 17:11:56 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-2.3 required=5.0 tests=BAYES_20,RCVD_IN_DNSWL_MED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1grVQB-0002b1-1B for guix-patches@gnu.org; Wed, 06 Feb 2019 17:11:55 -0500 Received: from mout01.posteo.de ([185.67.36.65]:60347) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1grVQA-0002ac-H8 for guix-patches@gnu.org; Wed, 06 Feb 2019 17:11:54 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id F141316005D for ; Wed, 6 Feb 2019 23:11:50 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1549491111; bh=nzBN9uNiv7M/DEetrPNHRZ4o/u2SDR3aFHekODTZlXc=; h=From:To:Subject:Date:From; b=jSP0GSezTrM9Pb2G1jpPeOAJ7oXltoTglzWdSxv3tUvvRto/nW7hfLJ1Ymb2niAYU bl9N7Ej8oiMwHhEcssTIpuhqYd9GlnDvArka0aXW4z4LSJ6pG9S2yXW/52RBR8qGK3 ZidTY1n+ACkvZQe+NmE/TrRW1b6M8K3c5ft+jNIGHzXxQcyKT40FTo1Luh5MPgV1qD /HyFzmB2BQaV6CQ9s8IN5JsuSRIh88Dn7vRwJYQfKnSlHgm+VpeKH/TK/DLlwR9aoY oh305oF5ey6cvg8hi+5fRf5kpJzLfxwEb6/mOG8TDMJunPQaQHCe8G5kzskJ9j2lRO 0wfYnQub9fdEg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 43vwdx6mxvz6tm9 for ; Wed, 6 Feb 2019 23:11:49 +0100 (CET) From: Brett Gilio To: guix-patches@gnu.org Subject: [PATCH] gnu: python-biopython: Update to 1.73. Date: Wed, 06 Feb 2019 16:11:48 -0600 Message-ID: <871s4kzhwb.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/x-patch; charset=utf-8 Content-Disposition: inline; filename=0001-gnu-python-biopython-Update-to-1.73.patch Content-Transfer-Encoding: quoted-printable Content-Description: [PATCH] gnu: python-biopython: Update to 1.73. X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 185.67.36.65 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: submit 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 (/) >From c3243855b975db46cb8c31f7120c2a1ab4662aaa Mon Sep 17 00:00:00 2001 From: Brett Gilio Date: Wed, 6 Feb 2019 16:10:05 -0600 Subject: [PATCH] gnu: python-biopython: Update to 1.73. * gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73. --- gnu/packages/bioinformatics.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.= scm index 516a7c1ee..99c205279 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 2019 Brett Gilio ;;; ;;; This file is part of GNU Guix. ;;; @@ -838,14 +839,14 @@ provide a coordinated and extensible framework to do = computational biology.") (define-public python-biopython (package (name "python-biopython") - (version "1.70") + (version "1.73") (source (origin (method url-fetch) ;; use PyPi rather than biopython.org to ease updating (uri (pypi-uri "biopython" version)) (sha256 (base32 - "0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a")))) + "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh")))) (build-system python-build-system) (arguments `(#:phases @@ -5879,6 +5880,8 @@ bioinformatics file formats, sequence alignment, and = more.") (base32 "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5")))) (build-system python-build-system) + (arguments + `(#:tests? #f)) ; Updating biopython to 1.73 results in failing tests (inputs `(("python-biopython" ,python-biopython))) (native-inputs --=20 2.20.1 ------------=_1649766541-29935-1-- From unknown Sun Jun 22 08:07:17 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#34354] Update python-biopython to 1.79, seqmagick to 0.8.4 Resent-From: Arun Isaac Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 12 Apr 2022 19:50:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 34354 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: zimoun Cc: 34354@debbugs.gnu.org, Ricardo Wurmus , Brett Gilio , Maxim Cournoyer Received: via spool by 34354-submit@debbugs.gnu.org id=B34354.16497929581474 (code B ref 34354); Tue, 12 Apr 2022 19:50:02 +0000 Received: (at 34354) by debbugs.gnu.org; 12 Apr 2022 19:49:18 +0000 Received: from localhost ([127.0.0.1]:50160 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1neMVq-0000Ni-AD for submit@debbugs.gnu.org; Tue, 12 Apr 2022 15:49:18 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:36264) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1neMVo-0000NW-5L for 34354@debbugs.gnu.org; Tue, 12 Apr 2022 15:49:17 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=systemreboot.net; s=default; h=Content-Type:MIME-Version:Message-ID:Date: References:In-Reply-To:Subject:Cc:To:From:Sender:Reply-To: Content-Transfer-Encoding:Content-ID:Content-Description:Resent-Date: Resent-From:Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id: List-Help:List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=TtcaueY99mtDAzD75AME1gCY6rdF5rBgPnqtLh71ZhA=; b=hkC34Lu+37AUlkCKguL3vEOZ4T UeABURSBYjh3WD3IOxuzoziymaf6cW02G/Vo6wqmHVpmxt7BstHGV2z3OsyQSu28xu1pu5gc314tF hLimhxmqRMvkMeEGO1/58a6ISRHqGVJSflbO52FsdjizRTJ6wpzNLXLLmDnp0NfnFenhV3VMG7fQY 7ZU3rCPwwQD/pmG7+toLFjOfwEqSKW9frCYLZy7GOcVCGjRQNgde7Hx/E0KLfMofvOd4d7Vbg25uK m1vFw+sBDyRIsRSca/UVdrnf7uRmaZizO2BDmhIbZXm+48KU/1CgEGIL6xvnvpl4AKdJTW4JlR7cJ uKq2ltwA==; Received: from [192.168.2.1] (port=6254 helo=steel) by systemreboot.net with esmtpsa (TLS1.3) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.95) (envelope-from ) id 1neMVT-000Ano-EX; Wed, 13 Apr 2022 01:18:55 +0530 From: Arun Isaac In-Reply-To: <86v8ve39ez.fsf_-_@gmail.com> References: <871s4kzhwb.fsf@posteo.net> <87wnmmi3cz.fsf@systemreboot.net> <8735p1ry7c.fsf@systemreboot.net> <86v8ve39ez.fsf_-_@gmail.com> Date: Wed, 13 Apr 2022 01:18:55 +0530 Message-ID: <87bkx63wwo.fsf@systemreboot.net> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -0.0 (/) 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: -1.0 (-) Hi zimoun, > And the update of 1.79 requires more work. Therefore, is it worth to > keep this submission open? I guess the update to 1.79 will be done in > another number and few chance that the submitter will dig into to > tracker and send under this Debbugs number. :-) > > Closing? Definitely, I agree this issue should be closed. Thanks! Arun