reinit the tree, so we can have metadata

6 files changed, 234 insertions, 0 deletions

diff --git a/sci-biology/plink/Manifest b/sci-biology/plink/Manifest
new file mode 100644
index 000000000000..5ac9f08542d4
--- /dev/null
+++ b/sci-biology/plink/Manifest
@@ -0,0 +1,9 @@
+AUX 1.07-flags.patch 1024 SHA256 f2427054a2ceecbe6bc4a1d435918a225e71313b454cef02b412d2be5eb3b12c SHA512 6511b08ea740819e2d17bfc2168951f94d8b9ad1165b3ee0966bed8f7a4fe7fb313b9b32994d0405f613c14656125db736757fc7f2a2dd726db4c90e9a13dd6a WHIRLPOOL 4781d59a6c5fe0ea03931a9271b30d5ff41f2a4527135730db00207996d17847cbe8b7f2a06bc628092c485524e5915689e71a0a848e602b355a8c36890f50d2
+AUX plink-1.07-gcc47.patch 1825 SHA256 f3019efb2ea2f979971777b29b449a85dc404ac06771c97adfbed61fbbbda8d9 SHA512 dba53ba4e50bd2352ad2ed604570525b77bc5698259b12f618284c999efb776485e94485a1ad90b8cc1744a0aa004435f77ceb467e1fb9e475065e084938f7fe WHIRLPOOL eb07308a1412753823a65e877a3f7ce3d3e67234d534fee896981347a8f1e37b6c01c9b66c0482f4c4488da89469911fc276bb1d89aa2fd6113bffd3925ce48b
+DIST plink-1.07-src.zip 2257297 SHA256 4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b SHA512 493f9f32ecd9eb20c5d11dc8ac98c47a9e695059cec3d1ad6f17465b71609577032368c0fee0d3d564e9451c3c07761e444717bec0f4628caefc587fceb1f6c3 WHIRLPOOL 01e69f605e1b52c6087dd75b506a7705d3bdb8e7dfdd0158e125f4fc4d962fad70c4ec430a139029b3b4ae91b822eb10123fab062c6552b946ec96ca7caf37da
+DIST plink-1.90_pre140514.zip 822157 SHA256 c6f93153d079b4b7f9ae4a51a3b4dcc7bc5ed60b408d39fce6234b98570b8ea7 SHA512 679f1e136b11f35f1d49636bc44ffd17e72e4e38edc5daa270cd963ca39f7b8a80f31905a94de517059e5b3ea7a6bf518ae34a5c2af8a05c530bd6df771606c4 WHIRLPOOL ebcccc1dc0461afd973aa63313237bfd5d904543785115fa71f3af1925d8bb21da15bd0baf60e38f4da534c8c554202a7af6c642b274ca9a458fc0035c2758d2
+EBUILD plink-1.07-r1.ebuild 1152 SHA256 bc00097a7b578ff3e941ce46755b7e62b0372535246858ec3ba8887baed6f7ef SHA512 eabbb86e94276de320007cc589407800ec29b1a850664c7d3ea74e2a3355a0528c28bf2c8cb416dbcba513e6dc2fe14df3cbfa0fe6678d1029815c62c1822f21 WHIRLPOOL 5152360b69e55e5c9d1d32486e3962ecf56c81aecf13412cc2c22eeb8b9bd96b627f4d5b74fe8cd8b2dfaa369fc97f2919c6006cbfaa54e467f73430624c22ec
+EBUILD plink-1.90_pre140514.ebuild 1129 SHA256 e00e7bcf3f41dcc62bf2731f198c9c747546d8d77ebb7a3426f91bdfacc74f3c SHA512 152653b04caa40c548108bb9cade22c968475faef8fd4af2627462928a6b2b364a8831bba569d467ff4a435e6fe76ce5d9862cb19da9565db1e9b974305fd0e4 WHIRLPOOL f73af35e80d6269c7cae33a10a0707f46e4aa43a9cb4acd9c28ec02eb26f7e48a9be9b27c56dd32da4927d0245ecb693e2631d77690210096c58ea83586be9a7
+MISC ChangeLog 2552 SHA256 28a2d8ce7d952a34d2ed8f22e028af25711458c81f2fd449f2058459019c43de SHA512 fc18513555a36255f0e2f8cf30451232550f530c6ff3f706e575a22b7b2be770e924a533fee67d6f2b9f4e996fd5aa231ceb151f247b81c17d9dae6f641e539f WHIRLPOOL f3645112f085ef3fca70324a8c9d6d7973a2b4c62bb68ac6fd9eeb197b9ebb61cf1c8d1d0e83a493cfa5e0bd7770ffda89b20eff78fe10ad63623069c4ca33a8
+MISC ChangeLog-2015 1750 SHA256 b79a87d58ae9d9a8eeaa8bd9c5c6493fc00077f0529defefa109013a5acf1c12 SHA512 382a66511906608ee6ff0890aa8a485613046440f98e78e10646818ad3ace687e83d71687c3e626667c422a9416718657e41278ea1c5bee84d6fa0d46d11e33c WHIRLPOOL 13c54f79b657f444ac22d06b61ae269f8bba84e8f3305c85b0805bc40cef2fdeb4ddda9e0d69832a20bdff068b2109ec766d576fad06b4b23f8df37f550e804b
+MISC metadata.xml 437 SHA256 9e93528414a2dcaba5f262138f36e5abe247d71c74a9b457fd21f0c931b72f19 SHA512 e4161118b7560456cca5ab5f14dfcf2cd3074e6be82dac3ce45b4ccd1d9d018c210d84ce29143c384618445e0a711ab47ed5450a25662dc762e871417c0f1dd4 WHIRLPOOL 05dfae13139466092240e9477113d76056dd05c2d4a82eb32a936e59652078e6d416c4962c214a088d7f4721c09baf631610d3d8eab5c8ae5bf2f3ab632fbc65
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..aa130f29beb2
--- /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/files/plink-1.07-gcc47.patch b/sci-biology/plink/files/plink-1.07-gcc47.patch
new file mode 100644
index 000000000000..6c289edae153
--- /dev/null
+++ b/sci-biology/plink/files/plink-1.07-gcc47.patch
@@ -0,0 +1,64 @@
+ elf.cpp    |    6 +++---
+ idhelp.cpp |    8 ++++----
+ sets.cpp   |    8 ++++----
+ 3 files changed, 11 insertions(+), 11 deletions(-)
+
+diff --git a/elf.cpp b/elf.cpp
+index ec2ed3d..a57665f 100644
+--- a/elf.cpp
++++ b/elf.cpp
+@@ -1175,10 +1175,10 @@ void Plink::elfBaseline()
+ 	  << setw(8) << gcnt << " "
+ 	  << setw(8) << (double)cnt / (double)gcnt << "\n";
+ 
+-      map<int,int>::iterator i = chr_cnt.begin();
+-      while ( i != chr_cnt.end() )
++      map<int,int>::iterator j = chr_cnt.begin();
++      while ( j != chr_cnt.end() )
+ 	{
+-	  int c = i->first;
++	  int c = j->first;
+ 	  int x = chr_cnt.find( c )->second;
+ 	  int y = chr_gcnt.find( c )->second;
+ 	  
+diff --git a/idhelp.cpp b/idhelp.cpp
+index a9244fa..8882097 100644
+--- a/idhelp.cpp
++++ b/idhelp.cpp
+@@ -772,12 +772,12 @@ void IDHelper::idHelp()
+       for (int j = 0 ; j < jointField.size(); j++ )
+ 	{
+ 	  set<IDField*> & jf = jointField[j];
+-	  set<IDField*>::iterator j = jf.begin();
++	  set<IDField*>::iterator k = jf.begin();
+ 	  PP->printLOG(" { ");
+-	  while ( j != jf.end() )
++	  while ( k != jf.end() )
+ 	    {
+-	      PP->printLOG( (*j)->name + " " );
+-	      ++j;
++	      PP->printLOG( (*k)->name + " " );
++	      ++k;
+ 	    }
+ 	  PP->printLOG(" }");
+ 	}
+diff --git a/sets.cpp b/sets.cpp
+index 3a8f92f..66787e8 100644
+--- a/sets.cpp
++++ b/sets.cpp
+@@ -768,11 +768,11 @@ vector_t Set::profileTestScore()
+       //////////////////////////////////////////////
+       // Reset original missing status
+ 
+-      vector<Individual*>::iterator i = PP->sample.begin();
+-      while ( i != PP->sample.end() )
++      vector<Individual*>::iterator j = PP->sample.begin();
++      while ( j != PP->sample.end() )
+ 	{
+-	  (*i)->missing = (*i)->flag;
+-	  ++i;
++	  (*j)->missing = (*j)->flag;
++	  ++j;
+ 	}
+ 
+       ////////////////////////////////////////////////
diff --git a/sci-biology/plink/metadata.xml b/sci-biology/plink/metadata.xml
new file mode 100644
index 000000000000..c281934d9943
--- /dev/null
+++ b/sci-biology/plink/metadata.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<use>
+		<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-1.07-r1.ebuild b/sci-biology/plink/plink-1.07-r1.ebuild
new file mode 100644
index 000000000000..3e1d4d5b0b43
--- /dev/null
+++ b/sci-biology/plink/plink-1.07-r1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=4
+
+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="lapack -webcheck R"
+KEYWORDS="amd64 x86"
+
+DEPEND="
+	app-arch/unzip
+	lapack? ( virtual/pkgconfig )"
+RDEPEND="
+	sys-libs/zlib
+	lapack? ( virtual/lapack )"
+
+S="${WORKDIR}/${P}-src"
+
+# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian.
+# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}-flags.patch \
+		"${FILESDIR}"/${P}-gcc47.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/^/#/' "${S}/Makefile" || die
+	tc-export PKG_CONFIG
+}
+
+src_compile() {
+	emake \
+		CXX_UNIX=$(tc-getCXX)
+}
+
+src_install() {
+	newbin plink p-link
+	dodoc README.txt
+}
diff --git a/sci-biology/plink/plink-1.90_pre140514.ebuild b/sci-biology/plink/plink-1.90_pre140514.ebuild
new file mode 100644
index 000000000000..9abd1604abc4
--- /dev/null
+++ b/sci-biology/plink/plink-1.90_pre140514.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+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/static/bin/plink140514/plink_src.zip -> ${P}.zip"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="
+	app-arch/unzip
+	virtual/pkgconfig"
+RDEPEND="
+	sys-libs/zlib
+	virtual/cblas
+	virtual/lapack
+	"
+
+S="${WORKDIR}/"
+
+# Package collides with net-misc/putty. Renamed to p-link following discussion with Debian.
+# Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
+
+src_prepare() {
+	sed \
+		-e 's:zlib-1.2.8/zlib.h:zlib.h:g' \
+		-i *.{c,h} || die
+
+	sed \
+		-e 's:g++:$(CXX):g' \
+		-e 's:gcc:$(CC):g' \
+		-e 's:gfortran:$(FC):g' \
+		-i Makefile || die
+	tc-export PKG_CONFIG
+}
+
+src_compile() {
+	emake \
+		CXX=$(tc-getCXX) \
+		CFLAGS="${CFLAGS}" \
+		ZLIB="$($(tc-getPKG_CONFIG) --libs zlib)" \
+		BLASFLAGS="$($(tc-getPKG_CONFIG) --libs lapack cblas)"
+}
+
+src_install() {
+	newbin plink p-link
+}