From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([209.51.188.92]:54774) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1grg3N-0007Pb-IN for guix-patches@gnu.org; Thu, 07 Feb 2019 04:33:06 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1grg3M-00075S-KI for guix-patches@gnu.org; Thu, 07 Feb 2019 04:33:05 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:37278) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1grg3K-00073y-CM for guix-patches@gnu.org; Thu, 07 Feb 2019 04:33:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1grg3K-0007jf-8X for guix-patches@gnu.org; Thu, 07 Feb 2019 04:33:02 -0500 Subject: [bug#34354] [PATCH] gnu: python-biopython: Update to 1.73. Resent-Message-ID: References: <871s4kzhwb.fsf@posteo.net> <87zhr8y2z3.fsf@posteo.net> From: Ricardo Wurmus In-reply-to: <87zhr8y2z3.fsf@posteo.net> 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 List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: Brett Gilio Cc: 34354@debbugs.gnu.org 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