From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 830B0138334 for ; Tue, 26 Jun 2018 08:15:42 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 6CDD6E08F5; Tue, 26 Jun 2018 08:15:41 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 24637E08F5 for ; Tue, 26 Jun 2018 08:15:40 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 49771335C70 for ; Tue, 26 Jun 2018 08:15:39 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 8455A2C2 for ; Tue, 26 Jun 2018 08:15:37 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1530000928.989059eec92c6fda0890e076cb9fc70fc994ed3f.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/stringtie/, sci-biology/stringtie/files/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/stringtie/files/Makefile.patch sci-biology/stringtie/stringtie-1.2.2.ebuild X-VCS-Directories: sci-biology/stringtie/ sci-biology/stringtie/files/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 989059eec92c6fda0890e076cb9fc70fc994ed3f X-VCS-Branch: master Date: Tue, 26 Jun 2018 08:15:37 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: c753b04a-ce3f-44d3-b935-db50471c619c X-Archives-Hash: 3931e180abf9eaa58ae52f77765ee4f1 commit: 989059eec92c6fda0890e076cb9fc70fc994ed3f Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Tue Jun 26 08:15:28 2018 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Jun 26 08:15:28 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=989059ee sci-biology/stringtie: keep modified bundled copy of samtools-0.1.18 https://github.com/gpertea/stringtie/issues/185#issuecomment-400128090 https://github.com/gpertea/stringtie/issues/186#issuecomment-400131844 Therefore, keep local copy of gclib and samtools. Still it does not compile for me with gcc-7.3.0 Package-Manager: Portage-2.3.40, Repoman-2.3.9 sci-biology/stringtie/files/Makefile.patch | 6 +++--- sci-biology/stringtie/stringtie-1.2.2.ebuild | 18 +++++++----------- 2 files changed, 10 insertions(+), 14 deletions(-) diff --git a/sci-biology/stringtie/files/Makefile.patch b/sci-biology/stringtie/files/Makefile.patch index 7db068985..a7ca43c39 100644 --- a/sci-biology/stringtie/files/Makefile.patch +++ b/sci-biology/stringtie/files/Makefile.patch @@ -2,9 +2,9 @@ +++ stringtie-1.2.2/Makefile 2018-06-26 00:46:43.406712302 +0200 @@ -1,13 +1,15 @@ -BAM := ./samtools-0.1.18 -+BAM_INC = -I$(EPREFIX)/usr/include/bam-0.1-legacy -+BAM_LIB = # or -L/some/path -+BAM_LIBS = -lbam-0.1-legacy ++BAM_INC = -I./samtools-0.1.18 ++BAM_LIB = -L./samtools-0.1.18 ++BAM_LIBS = -lbam #path to the directory where the samtools package was built (in place) #so libbam.a and *.h files MUST be in here diff --git a/sci-biology/stringtie/stringtie-1.2.2.ebuild b/sci-biology/stringtie/stringtie-1.2.2.ebuild index 37c0f26cf..953999e87 100644 --- a/sci-biology/stringtie/stringtie-1.2.2.ebuild +++ b/sci-biology/stringtie/stringtie-1.2.2.ebuild @@ -8,25 +8,21 @@ HOMEPAGE="https://ccb.jhu.edu/software/stringtie https://github.com/gpertea/stringtie" SRC_URI="http://ccb.jhu.edu/software/stringtie/dl/${P}.tar.gz" -LICENSE="Artistic-2" +LICENSE="Artistic-2 MIT" # MIT from bundled samtools-0.1.18 SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -# contains bundled gclib (0.9.8?), well they are just headers -DEPEND=" - sci-biology/gclib - sci-biology/samtools:0.1-legacy" # bundled samtools-0.1.18 +# contains bundled and modified samtools-0.1.18 +# https://github.com/gpertea/stringtie/issues/185#issuecomment-400128090 +# +# contains bundled gclib (0.9.8?), a modified version? +# https://github.com/gpertea/stringtie/issues/186#issuecomment-400131844 +DEPEND="" RDEPEND="${DEPEND}" PATCHES=( "${FILESDIR}"/Makefile.patch ) -src_prepare(){ - default - rm -r samtools-0.1.18 || die - # TODO: `rm -rf ./gclib' and fix Makefile -} - src_compile(){ emake release }