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 011EB139694 for ; Thu, 16 Feb 2017 10:57:12 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id C70AEE0C5C; Thu, 16 Feb 2017 10:57:09 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id A2A65E0C5C for ; Thu, 16 Feb 2017 10:57:08 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id AABBC33D3CE for ; Thu, 16 Feb 2017 10:57:07 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 372DC49BA for ; Thu, 16 Feb 2017 10:57:06 +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: <1487242614.456c869b7e5ae4d6efd1c2293b1181e59a5e6a67.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/freebayes/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/freebayes/freebayes-9999.ebuild X-VCS-Directories: sci-biology/freebayes/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 456c869b7e5ae4d6efd1c2293b1181e59a5e6a67 X-VCS-Branch: master Date: Thu, 16 Feb 2017 10:57:06 +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: 7cfa3f64-b312-4f8c-b40a-06ac6b7ac01e X-Archives-Hash: 86b2dc4cfd571b7bb8f5911623e56f94 commit: 456c869b7e5ae4d6efd1c2293b1181e59a5e6a67 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Thu Feb 16 10:56:54 2017 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Thu Feb 16 10:56:54 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=456c869b sci-biology/freebayes: respect CC/CXX/CFLAGS/CXXFLAGS Package-Manager: Portage-2.3.3, Repoman-2.3.1 sci-biology/freebayes/freebayes-9999.ebuild | 21 +++++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/sci-biology/freebayes/freebayes-9999.ebuild b/sci-biology/freebayes/freebayes-9999.ebuild index 1b1eb89ed..a5e640591 100644 --- a/sci-biology/freebayes/freebayes-9999.ebuild +++ b/sci-biology/freebayes/freebayes-9999.ebuild @@ -4,7 +4,7 @@ EAPI=6 -inherit eutils git-r3 +inherit eutils git-r3 toolchain-funcs DESCRIPTION="Bayesian gen. variant detector to find short polymorphisms" HOMEPAGE="https://github.com/ekg/freebayes" @@ -15,7 +15,7 @@ SLOT="0" KEYWORDS="" IUSE="" -DEPEND="" +DEPEND="dev-util/cmake" RDEPEND="${DEPEND} sci-libs/htslib sci-biology/bamtools @@ -84,6 +84,23 @@ RDEPEND="${DEPEND} # g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../ttmath -I../bamtools/src/ -I../vcflib/src/ -I../vcflib/tabixpp/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/tabixpp/htslib -I../SeqLib -I../SeqLib/htslib -c freebayes.cpp +src_prepare(){ + find . -name Makefile | while read f; do \ + sed -e "s/-O3 -D_FILE_OFFSET_BITS=64/${CFLAGS}/" -i $f || die + sed -e "s/^CFLAGS:= -O3/CFLAGS ?= ${CFLAGS}/" -i $f || die + sed -e "s/^CXX = g++/CXX = $(tc-getCXX)/;s/^CXX=g++/CXX = $(tc-getCXX)/" -i $f || die + sed -e "s/g++ /$(tc-getCXX) /" -i $f || die + sed -e "s/-O3/${CXXFLAGS}/" -i $f || die + sed -e "s/^CC[ ]*=[ ]gcc/CC = $(tc-getCC)/" -i $f || die + sed -e "s/-g -Wall -O2/${CFLAGS}/;s/-g -Wall -Wno-unused-function -O2/${CFLAGS}/" -i $f || die + sed -e "s/-O3 /${CFLAGS}/;s/ -O3/${CFLAGS}/" -i $f || die + done + sed -e "s/^C=gcc/C = $(tc-getCC)/" -i Makefile || die + sed -e "s/gcc/$(tc-getCC)/" -i SeqLib/bwa/Makefile SeqLib/fermi-lite/Makefile || die + sed -e "s/g++/$(tc-getCXX)/" -i SeqLib/src/Makefile.am || die + default +} + src_compile(){ emake -j1 # vcflib/smithwaterman/ sometimes does not compile }