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[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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1626183191; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=Yte+Es4cb00Fn7ESy6SYtBIVT1qz/Q+9l/6OV638R2k=; b=FZMcvR8I/wOE/uUg6KDtt19pae/LthrEX7E4e3hilTJj6qXrnh8Og76diTyxRxN7FeRL2I DOBN6RyWZ7c4VFIWmfWIje7+F/cC9d1guiBC49WKqH8bQYtsThlO6Zko1BiMsnbHDDddbj vPLTXYkDbd7PgrohiQoTZh+C+7zHmA1DXaA5KuqLJWckkAmp8KaJr8Q1w6O9YowxgKhyva 7SMXV/dsffnJZktWbGekZ2t8tv1PW8rrOVO5uRmfIaA76diPulwL+W86FCpHxGmlvtaIdz 6c2/G4rhv47teBMQbxKRcqKGGuXiEBtyohAem45S7z3p9rAVXW+csdb2tzjNNA== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1626183191; a=rsa-sha256; cv=none; b=c1aB2vJQZaSQTfoWc3Q0HtucTjpd/C58F1AMNVJ8wnCVsuMRFSaDrE++UXWtk0J6tqFAGI pYQDRrJmjnBJS7b2LlrBNzK8sEM4GZp0k53oKv4e1+OpyrYTSwN+h4F6pC3gTN2ztqK6hy cRZuvzwpk7tmp3v7mbM88nrGRzaXFGPyKGTwbyKXSJZdawlNYwKLFKD9qOrmdUsEQ3GH6n TH85w70ub3qOukY36iz1GT8DcBgorod/HpuRhKeDsh49kiNU0kzPqjQrkjSCJATJXizKeC DjMwzjtveom/5zQqEdQBjfltTXffrJSdtV2evEF/b8mhbSynE19pdCIYhiGP9w== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b="gj/+fsD+"; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: 0.20 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b="gj/+fsD+"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: E64862FC27 X-Spam-Score: 0.20 X-Migadu-Scanner: scn0.migadu.com X-TUID: alFQp5ZQwBpu 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