gentoo resync : 15.12.2019

5 files changed, 1 insertions, 168 deletions

diff --git a/sci-biology/plink/Manifest b/sci-biology/plink/Manifest
index d6102d8c41a6..8922b631e9c0 100644
--- a/sci-biology/plink/Manifest
+++ b/sci-biology/plink/Manifest
@@ -1,7 +1,3 @@
-AUX 1.07-flags.patch 1024 BLAKE2B 6b47f8782653d70eb86c4ebe7f06295f4b093fb17737b6ee9ab8f56fb02313049d5189ce0fa11d0ee8eb8d5c029f9d4432fb7aa0198282f56ba174bff2363b4f SHA512 6511b08ea740819e2d17bfc2168951f94d8b9ad1165b3ee0966bed8f7a4fe7fb313b9b32994d0405f613c14656125db736757fc7f2a2dd726db4c90e9a13dd6a
-AUX plink-1.07-gcc47.patch 1825 BLAKE2B 696f30be55c9fc26204041d255eea3c44675e51c1ad021fcfda105d40c04e312ac27514b297ed42d2c30bc2978a7d6a3a1bd29e44b9c0b1b186c496b2a4a6386 SHA512 dba53ba4e50bd2352ad2ed604570525b77bc5698259b12f618284c999efb776485e94485a1ad90b8cc1744a0aa004435f77ceb467e1fb9e475065e084938f7fe
-DIST plink-1.07-src.zip 2257297 BLAKE2B 572daeec24ec53daa017de9d4326c5db316f94fdcb40fb3d6a889643a5b5c60208a9424246e70414982a4659dd9c9bae5115d7ba3dc45183b521d1809fe2f00b SHA512 493f9f32ecd9eb20c5d11dc8ac98c47a9e695059cec3d1ad6f17465b71609577032368c0fee0d3d564e9451c3c07761e444717bec0f4628caefc587fceb1f6c3
 DIST plink-1.90_pre140514.zip 822157 BLAKE2B 3c29670862de99c9715bc37d8cffc2b02c0cb25ad746975f253ca1e8094b24668cc6739943c68bfa407471f30835a74c6ad027eaa56a92f13445e0a02854cad3 SHA512 679f1e136b11f35f1d49636bc44ffd17e72e4e38edc5daa270cd963ca39f7b8a80f31905a94de517059e5b3ea7a6bf518ae34a5c2af8a05c530bd6df771606c4
-EBUILD plink-1.07-r1.ebuild 1152 BLAKE2B 929aad0e5b3946e5b35f068b21c7549e22b7039dca8d053f8bd71d1fafa0171e093131a9b2591429184558438562ff8d1adaa4485e996b50f75f0e22ade7261a SHA512 eabbb86e94276de320007cc589407800ec29b1a850664c7d3ea74e2a3355a0528c28bf2c8cb416dbcba513e6dc2fe14df3cbfa0fe6678d1029815c62c1822f21
 EBUILD plink-1.90_pre140514.ebuild 1129 BLAKE2B ded7a69c8a040d4b4e2bcb2bb931adf6eeeccd6168d78dc7285322490f1744f7b4ae6c7e112e62a00ab0663227896cb3088c607a5a4a1d3903a080806618d6d7 SHA512 152653b04caa40c548108bb9cade22c968475faef8fd4af2627462928a6b2b364a8831bba569d467ff4a435e6fe76ce5d9862cb19da9565db1e9b974305fd0e4
-MISC metadata.xml 437 BLAKE2B a02d4418454b418b43b68ac394b2b08a196ca660d5b7cc5709e8750f6045f6a032700168bc5550557217f7af0f762ae7a4d24456ca3440e02674df6c604b161e SHA512 e4161118b7560456cca5ab5f14dfcf2cd3074e6be82dac3ce45b4ccd1d9d018c210d84ce29143c384618445e0a711ab47ed5450a25662dc762e871417c0f1dd4
+MISC metadata.xml 261 BLAKE2B 3768c926bca545090342a947ba83e706a8954c51b99a5e7b3476ba5198cd326fe1c3b8efb51dfd6be1800682556b8ceea065e388981463ab32f3d687951872f3 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a
diff --git a/sci-biology/plink/files/1.07-flags.patch b/sci-biology/plink/files/1.07-flags.patch
deleted file mode 100644
index aa130f29beb2..000000000000
--- a/sci-biology/plink/files/1.07-flags.patch
+++ /dev/null
@@ -1,44 +0,0 @@
-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
deleted file mode 100644
index 6c289edae153..000000000000
--- a/sci-biology/plink/files/plink-1.07-gcc47.patch
+++ /dev/null
@@ -1,64 +0,0 @@
- 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
index c281934d9943..8417d1580d40 100644
--- a/sci-biology/plink/metadata.xml
+++ b/sci-biology/plink/metadata.xml
@@ -5,12 +5,4 @@
 		<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
deleted file mode 100644
index 3e1d4d5b0b43..000000000000
--- a/sci-biology/plink/plink-1.07-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# 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
-}