From unknown Sun Aug 17 10:23:09 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#38674 <38674@debbugs.gnu.org> To: bug#38674 <38674@debbugs.gnu.org> Subject: Status: [PATCH] gnu: tophat: Build with GCC 5 Reply-To: bug#38674 <38674@debbugs.gnu.org> Date: Sun, 17 Aug 2025 17:23:09 +0000 retitle 38674 [PATCH] gnu: tophat: Build with GCC 5 reassign 38674 guix-patches submitter 38674 M=C4=83d=C4=83lin Ionel Patra=C8=99cu severity 38674 normal tag 38674 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Thu Dec 19 13:54:32 2019 Received: (at submit) by debbugs.gnu.org; 19 Dec 2019 18:54:32 +0000 Received: from localhost ([127.0.0.1]:45504 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ii0wO-0000fr-DU for submit@debbugs.gnu.org; Thu, 19 Dec 2019 13:54:32 -0500 Received: from lists.gnu.org ([209.51.188.17]:54378) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ii0wM-0000fi-Af for submit@debbugs.gnu.org; Thu, 19 Dec 2019 13:54:26 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:52537) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ii0wK-00027h-3J for guix-patches@gnu.org; Thu, 19 Dec 2019 13:54:25 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,RCVD_IN_DNSWL_NONE, URIBL_BLOCKED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ii0wH-0001uG-NT for guix-patches@gnu.org; Thu, 19 Dec 2019 13:54:23 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:44801) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1ii0wH-0001cS-23 for guix-patches@gnu.org; Thu, 19 Dec 2019 13:54:21 -0500 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id E7F66A009D for ; Thu, 19 Dec 2019 19:54:17 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1576781657; x=1578596058; bh=sVkcH+36rdssSXOm716SHWRN1BqlEpvtECkCOVJGPyw=; b=g226cwZW1ncF Ry7IqcEAEkPKJQ5R5XbfdUYfBkFLiN4slOfE+UGgXfiE5ArvW8wC/IyqOijfztcR fBA114x/p7MmdpZfID1FxPC5UvT94Cd9vtTG692sLt/XHJHHv4Ywz76zLZFNO1gF tyB6Bw6/IOo0Jg6A7O10vDw+4NoQjPQ= Received: from a2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-han.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id uVcj3mLdIXkH for ; Thu, 19 Dec 2019 19:54:17 +0100 (CET) Received: from SW-IT-P-CAS4.mdc-berlin.net (mgw10-4.mdc-berlin.de [141.80.113.59]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Thu, 19 Dec 2019 19:54:17 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.468.0; Thu, 19 Dec 2019 19:54:15 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: Subject: [PATCH] gnu: tophat: Build with GCC 5 Date: Thu, 19 Dec 2019 19:53:31 +0100 Message-ID: <20191219185331.19702-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.24.1 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1684-8.5.1010-25114.002 X-TM-AS-Result: No-1.112600-8.000000-10 X-TMASE-MatchedRID: 6CoZXopK1tC1HHtIgGMIGNqQ6Du6Gk+zNV9S7O+u3KZy220XpoU/hHZM elkn7fiXrdoLblq9S5rt679iIQuulb4br6qTk1yGhKZybi8qfJ8OHw/yNOkRgST7BShWYMvz2gO r1UdaUdYKaIhVI7dKsI1tYtwPvjHZEfIWTKnSZvmdVNZaI2n6/+JNcHLvRNpE1l38M6aWfEgWkH qHAqxWxNQ5SJ8sqjUcmyiLZetSf8my5/tFZu9S3N9pjzubZ2rHwrbXMGDYqV99R4Ss0oUmJ1ew0 xxk05nOAOfqYdKbo4lTFFK3lDO8NwP8pLOcGT+YcuUXh08eDGBMMJnmTJZD8r5+3oOvZ31k9dtg /C2qGRlU7VSLp9mv6nMlKjd7kJW0P2nrhpzTnX4SFeEaqul3aIOFrOPMaJ4V X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.112600-8.000000 X-TMASE-Version: SMEX-12.5.0.1684-8.5.1010-25114.002 X-TM-SNTS-SMTP: A4A0794137C929B258E5BCD6CA3F2D346D56923E56CC80668816AC3A9B37C9BC2000:9 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-Received-From: 194.95.232.172 X-Spam-Score: -1.4 (-) X-Debbugs-Envelope-To: submit Cc: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= 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: -2.4 (--) * gnu/packages/python-xyz.scm (tophat)[native-inputs]: Add gcc-5. (tophat)[inputs]: Reorder alphabetically the dependencies. (tophat)[home-page]: Swapp to https. --- gnu/packages/bioinformatics.scm | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatic= s.scm index 528b603476..0f6c120687 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,7 +11,7 @@ ;;; Copyright =C2=A9 2017 Arun Isaac ;;; 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, 2019 M=C4=83d=C4=83lin Ionel Patra=C8=99cu ;;; Copyright =C2=A9 2019 Maxim Cournoyer ;;; Copyright =C2=A9 2019 Brian Leung ;;; @@ -1615,7 +1615,7 @@ genome (2.9 GB for paired-end).") #t)))) (build-system gnu-build-system) (arguments - '(#:parallel-build? #f ; not supported + '(#:parallel-build? #f ; not supported #:phases (modify-phases %standard-phases (add-after 'unpack 'use-system-samtools @@ -1639,16 +1639,18 @@ genome (2.9 GB for paired-end).") (("#include ") "#include ") (("#include ") "#include ")) #t))))) + (native-inputs + `(("gcc" ,gcc-5))) ;; doesn't build with later versions (inputs `(("boost" ,boost) ("bowtie" ,bowtie) - ("samtools" ,samtools-0.1) ("ncurses" ,ncurses) - ("python" ,python-2) ("perl" ,perl) - ("zlib" ,zlib) - ("seqan" ,seqan-1))) - (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") + ("python" ,python-2) + ("samtools" ,samtools-0.1) + ("seqan" ,seqan-1) + ("zlib" ,zlib))) + (home-page "https://ccb.jhu.edu/software/tophat/index.shtml") (synopsis "Spliced read mapper for RNA-Seq data") (description "TopHat is a fast splice junction mapper for nucleotide sequence --=20 2.24.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Dec 23 13:32:21 2019 Received: (at 38674-done) by debbugs.gnu.org; 23 Dec 2019 18:32:21 +0000 Received: from localhost ([127.0.0.1]:51663 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ijSVB-0006t6-E6 for submit@debbugs.gnu.org; Mon, 23 Dec 2019 13:32:21 -0500 Received: from eggs.gnu.org ([209.51.188.92]:44582) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ijSV7-0006so-66 for 38674-done@debbugs.gnu.org; Mon, 23 Dec 2019 13:32:20 -0500 Received: from fencepost.gnu.org ([2001:470:142:3::e]:60291) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ijSV1-0008R6-0d; Mon, 23 Dec 2019 13:32:11 -0500 Received: from lns-bzn-56-82-255-208-147.adsl.proxad.net ([82.255.208.147]:35324 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1ijSUz-0002R4-Sg; Mon, 23 Dec 2019 13:32:10 -0500 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#38674] [PATCH] gnu: tophat: Build with GCC 5 References: <20191219185331.19702-1-madalinionel.patrascu@mdc-berlin.de> Date: Mon, 23 Dec 2019 19:32:05 +0100 In-Reply-To: <20191219185331.19702-1-madalinionel.patrascu@mdc-berlin.de> (=?utf-8?B?Ik3Eg2TEg2xpbg==?= Ionel =?utf-8?Q?Patra=C8=99cu=22's?= message of "Thu, 19 Dec 2019 19:53:31 +0100") Message-ID: <87blryj3kq.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (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-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 38674-done Cc: 38674-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: -3.3 (---) Hi, M=C4=83d=C4=83lin Ionel Patra=C8=99cu = skribis: > * gnu/packages/python-xyz.scm (tophat)[native-inputs]: Add gcc-5. > (tophat)[inputs]: Reorder alphabetically the dependencies. > (tophat)[home-page]: Swapp to https. Applied, thanks! Ludo=E2=80=99. From unknown Sun Aug 17 10:23:09 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Tue, 21 Jan 2020 12:24:05 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator