Fixes for #335975, respecting LDFLAGS/CXXFLAGS, supporting lapack, making R support optional

Package-Manager: portage-2.2.0_alpha5/cvs/Linux x86_64

5 files changed, 84 insertions, 39 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/Manifest b/sci-biology/plink/Manifest
index bfd2fb89e143..1a401819e435 100644
--- a/sci-biology/plink/Manifest
+++ b/sci-biology/plink/Manifest
@@ -1,6 +1,16 @@
-DIST plink-1.06-src.zip 2219294 RMD160 988ef2d3b5806c92b5fe9c75592f0d3e13d13c85 SHA1 2e8c70287a2377cc1c9b6669078c97c2805b9a4c SHA256 d477a0e41493cd32fbf602c7eef73a54a21f73fe21df438217892b23757a2ec1
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 1.07-flags.patch 1021 RMD160 5b80a1c1f3f97f53b527643c292ec4bcb8e1dc9f SHA1 3797f24bb1d3ccd2594897ad3c2cf703799a099b SHA256 93bdefd7707352ac10b4278064c39adc2a5a8bd94922124a076856b45647e186
 DIST plink-1.07-src.zip 2257297 RMD160 ce22e2388fc711ac9938d21ffd3cb68512ba1150 SHA1 d41a2d014ebc02bf11e5235292b50fad6dedd407 SHA256 4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b
-EBUILD plink-1.06.ebuild 936 RMD160 e410adb7ab6dcd5adc36bfea777cd1ed64cb3321 SHA1 f0bbca246f0a994c9115e88e623be2f86f5047eb SHA256 d0dc2b8a185631a6dca71f9f57e5cdfa2d8d6007d12d3f5a3d18f203f636b915
+EBUILD plink-1.07-r1.ebuild 1181 RMD160 dcbcbb0233bbd18a3bc4ef0b21a7cc1f4a7d160b SHA1 8174530536dd5f72e77697f766218be6a80d441e SHA256 65575b684712901efb7395703328c322223ea1367ab111e9056784788e1bac77
 EBUILD plink-1.07.ebuild 940 RMD160 7938cb59bde159119709764e9653933f87e8b987 SHA1 ea449753d041da5da4f18fc1f1c50676f7845dad SHA256 5f25e15a86ff772662d909160fe626389685705a1568cdb70a14e00e49659ee5
-MISC ChangeLog 1257 RMD160 402422975814800e536d62e01061cf31433bfedd SHA1 c25893adafb7dca8837133b976a531e67d4db571 SHA256 61ffe04994c0c87b02ce7b8fb67f8f3ff745cdcbcdf4942f4e013eec9391532c
-MISC metadata.xml 381 RMD160 e48ef6a333ebf961070f902eb0aa29920cbc071e SHA1 14150562fbe14a321272afa502ac029cd1391405 SHA256 44fc0f6729e24f097dfac2b2e0f21de8e2bbc744241806260c62dd9a8376f544
+MISC ChangeLog 464 RMD160 9fd8542ef6ca8cbc6bd91120262552f067c58066 SHA1 2816597b7ffc2bc84254631e2ea5cbf292000cd2 SHA256 9445d14af71e7e5daa1d1bc52c81b2968b5160532b52a8754e813273355eb9b7
+MISC metadata.xml 435 RMD160 0a9a212be109dc94d2c0f1f74b81442cebc43f89 SHA1 fd4927856f7b87a08eb38885e9edc3b140b236fa SHA256 d5ab51d70cd374b8820586ee2e2f0c94c0bd975b5a6005756bc966a5322f41f0
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.16 (GNU/Linux)
+
+iEYEARECAAYFAkzvvMwACgkQgAnW8HDreRYETACfcqa/awyFEKf69dVcXrGmt+pP
+ThIAmwdNoWYBNTZWidVTnxDyCJL++8s/
+=vHFb
+-----END PGP SIGNATURE-----
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
 }