diff options
| -rw-r--r-- | sci-biology/plink/ChangeLog | 34 | ||||
| -rw-r--r-- | sci-biology/plink/files/1.07-flags.patch | 44 | ||||
| -rw-r--r-- | sci-biology/plink/metadata.xml | 3 | ||||
| -rw-r--r-- | sci-biology/plink/plink-1.07-r1.ebuild (renamed from sci-biology/plink/plink-1.06.ebuild) | 24 |
4 files changed, 70 insertions, 35 deletions
diff --git a/sci-biology/plink/ChangeLog b/sci-biology/plink/ChangeLog index 162e531e4def..243c033443c4 100644 --- a/sci-biology/plink/ChangeLog +++ b/sci-biology/plink/ChangeLog @@ -1,33 +1,11 @@ # ChangeLog for sci-biology/plink # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/ChangeLog,v 1.7 2010/04/05 12:13:23 phajdan.jr Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/ChangeLog,v 1.8 2010/11/26 13:57:26 jlec Exp $ - 05 Apr 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org> plink-1.07.ebuild: - x86 stable wrt bug #311835 +*plink-1.07-r1 (26 Nov 2010) - 29 Mar 2010; Pacho Ramos <pacho@gentoo.org> plink-1.07.ebuild: - amd64 stable, bug 311835 - -*plink-1.07 (27 Jan 2010) - - 27 Jan 2010; Andrey Kislyuk <weaver@gentoo.org> +plink-1.07.ebuild: - Version bump - - 05 Aug 2009; Markus Meier <maekke@gentoo.org> plink-1.06.ebuild: - x86 stable, bug #279345 - - 02 Aug 2009; <chainsaw@gentoo.org> plink-1.06.ebuild: - Marked stable on AMD64 as requested by Andrey "weaver" Kislyuk - <weaver@gentoo.org> in bug #279345. Arch-tested by Chad A. Simmons who - reports he has no test-suite; reporter confirmed and agreed compile-test - was sufficient. - -*plink-1.06 (21 Jun 2009) - - 21 Jun 2009; Andrey Kislyuk <weaver@gentoo.org> - -files/plink-1.05-gcc43.patch, -plink-1.05.ebuild, +plink-1.06.ebuild: - Version bump, change name to follow Debian, and drop old files - - 06 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: - New package, ebuild written by Neil Shephard <nshephard@gmail.com> and me + 26 Nov 2010; Justin Lecher <jlec@gentoo.org> +files/1.07-flags.patch, + -plink-1.06.ebuild, +plink-1.07-r1.ebuild, metadata.xml: + Fixes for #335975, respecting LDFLAGS/CXXFLAGS, supporting lapack, making R + support optional diff --git a/sci-biology/plink/files/1.07-flags.patch b/sci-biology/plink/files/1.07-flags.patch new file mode 100644 index 000000000000..2b5aca74c33b --- /dev/null +++ b/sci-biology/plink/files/1.07-flags.patch @@ -0,0 +1,44 @@ +diff --git a/Makefile b/Makefile +index 172c795..466f09f 100644 +--- a/Makefile ++++ b/Makefile +@@ -26,25 +26,25 @@ WITH_R_PLUGINS = 1 + WITH_WEBCHECK = 1 + FORCE_32BIT = + WITH_ZLIB = 1 +-WITH_LAPACK = +-FORCE_DYNAMIC = ++WITH_LAPACK = 1 ++FORCE_DYNAMIC = 1 + + # Put C++ compiler here; Windows has it's own specific version + CXX_UNIX = g++ + CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe + + # Any other compiler flags here ( -Wall, -g, etc) +-CXXFLAGS = ++CXXFLAGS ?= -O2 + + # Misc +-LIB_LAPACK = /usr/lib/liblapack.so.3 ++LIB_LAPACK = `pkg-config --libs lapack` + + + # -------------------------------------------------------------------- + # Do not edit below this line + # -------------------------------------------------------------------- + +-CXXFLAGS += -O3 -I. ++CXXFLAGS += -I. + OUTPUT = plink + + # Some system specific flags +@@ -151,7 +151,7 @@ OBJ = $(SRC:.cpp=.o) + all : $(OUTPUT) + + $(OUTPUT) : +- $(CXX) $(CXXFLAGS) -o $(OUTPUT) $(OBJ) $(LIB) ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(OUTPUT) $(OBJ) $(LIB) + + $(OBJ) : $(HDR) + diff --git a/sci-biology/plink/metadata.xml b/sci-biology/plink/metadata.xml index 68fb68e6ac6e..0231aa595d4f 100644 --- a/sci-biology/plink/metadata.xml +++ b/sci-biology/plink/metadata.xml @@ -10,5 +10,8 @@ <flag name='webcheck'> add support for online update checking every time the program starts </flag> + <flag name='R'> + add support R language + </flag> </use> </pkgmetadata> diff --git a/sci-biology/plink/plink-1.06.ebuild b/sci-biology/plink/plink-1.07-r1.ebuild index 083aff645ea5..ba55d274f7c7 100644 --- a/sci-biology/plink/plink-1.06.ebuild +++ b/sci-biology/plink/plink-1.07-r1.ebuild @@ -1,20 +1,22 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2010 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/plink-1.06.ebuild,v 1.3 2009/08/05 21:16:10 maekke Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/plink-1.07-r1.ebuild,v 1.1 2010/11/26 13:57:26 jlec Exp $ EAPI="2" +inherit eutils toolchain-funcs + DESCRIPTION="Whole genome association analysis toolset" HOMEPAGE="http://pngu.mgh.harvard.edu/~purcell/plink/" SRC_URI="http://pngu.mgh.harvard.edu/~purcell/plink/dist/${P}-src.zip" LICENSE="GPL-2" SLOT="0" -IUSE="-webcheck" -KEYWORDS="amd64 x86" +IUSE="lapack -webcheck R" +KEYWORDS="~amd64 ~x86" DEPEND="app-arch/unzip" -RDEPEND="" +RDEPEND="lapack? ( virtual/lapack )" S="${WORKDIR}/${P}-src" @@ -22,11 +24,19 @@ S="${WORKDIR}/${P}-src" # Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream. src_prepare() { - sed -i -e '/CXXFLAGS =/ s/^/#/' -e 's/-static//' "${S}/Makefile" || die + epatch "${FILESDIR}"/${PV}-flags.patch use webcheck || sed -i '/WITH_WEBCHECK =/ s/^/#/' "${S}/Makefile" || die + use R || sed -i '/WITH_R_PLUGINS =/ s/^/#/' "${S}/Makefile" || die + use lapack || sed -i '/WITH_LAPACK =/ s/^/#/' "${S}/Makefile" || die +} + +src_compile() { + emake \ + CXX_UNIX=$(tc-getCXX) \ + || die } src_install() { newbin plink p-link || die - dodoc README.txt + dodoc README.txt || die } |