Initial PKGBUILD version of PLINK.

3 files changed, 117 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..d8017c9d43df
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,18 @@
+pkgbase = plink
+	pkgdesc = Whole genome association analysis toolset
+	pkgver = 1.07
+	pkgrel = 1
+	url = http://pngu.mgh.harvard.edu/~purcell/plink/
+	arch = i686
+	arch = x86_64
+	license = GPL
+	depends = r
+	depends = zlib
+	depends = lapack
+	source = http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-1.07-src.zip
+	source = current_gcc.patch
+	md5sums = 4566376791df4e69459b849bd7078fa3
+	md5sums = 407ef451ca255ff201bffbba37d0a4e2
+
+pkgname = plink
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..c939310d1466
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,32 @@
+# Maintainer: Stunts <f.pinamartins@gmail.com>
+pkgname=plink
+pkgver=1.07
+pkgrel=1
+pkgdesc="Whole genome association analysis toolset"
+arch=('i686' 'x86_64')
+license=('GPL')
+url="http://pngu.mgh.harvard.edu/~purcell/plink/"
+depends=('r' 'zlib' 'lapack')
+source=(http://pngu.mgh.harvard.edu/~purcell/plink/dist/${pkgname}-${pkgver}-src.zip
+        current_gcc.patch)
+md5sums=('4566376791df4e69459b849bd7078fa3'
+         '407ef451ca255ff201bffbba37d0a4e2')
+
+prepare() {
+  cd ${srcdir}/${pkgname}-${pkgver}-src
+  sed -i 's/WITH_LAPACK = /&1/g' Makefile
+  sed -i 's/CXXFLAGS = //' Makefile
+  sed -i 's/FORCE_DYNAMIC = /&1/' Makefile
+  patch -p1 < ../current_gcc.patch
+}
+
+build() {
+  cd ${srcdir}/${pkgname}-${pkgver}-src
+  make
+}
+
+package() {
+    cd ${srcdir}/${pkgname}-${pkgver}-src
+    install -d ${pkgdir}/usr/bin
+    install -D -m 755 plink ${pkgdir}/usr/bin/plink
+}
diff --git a/current_gcc.patch b/current_gcc.patch
new file mode 100644
index 000000000000..1bfef3004f40
--- /dev/null
+++ b/current_gcc.patch
@@ -0,0 +1,67 @@
+diff -rupN plink-1.07-src-orig/elf.cpp plink-1.07-src/elf.cpp
+--- plink-1.07-src-orig/elf.cpp	2009-10-10 17:00:21.000000000 +0100
++++ plink-1.07-src/elf.cpp	2016-04-13 11:43:48.518604345 +0100
+@@ -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 i2 = chr_cnt.begin();
++      while ( i2 != chr_cnt.end() )
+ 	{
+-	  int c = i->first;
++	  int c = i2->first;
+ 	  int x = chr_cnt.find( c )->second;
+ 	  int y = chr_gcnt.find( c )->second;
+ 	  
+@@ -1189,7 +1189,7 @@ void Plink::elfBaseline()
+ 	      << setw(8) << y << " "
+ 	      << setw(8) << (double)x / (double)y << "\n";
+ 	  
+-	  ++i;
++	  ++i2;
+ 	}
+       
+
+diff -rupN plink-1.07-src-orig/idhelp.cpp plink-1.07-src/idhelp.cpp
+--- plink-1.07-src-orig/idhelp.cpp	2009-10-10 17:00:22.000000000 +0100
++++ plink-1.07-src/idhelp.cpp	2016-04-13 11:45:59.860417525 +0100
+@@ -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 j2 = jf.begin();
+ 	  PP->printLOG(" { ");
+-	  while ( j != jf.end() )
++	  while ( j2 != jf.end() )
+ 	    {
+-	      PP->printLOG( (*j)->name + " " );
+-	      ++j;
++	      PP->printLOG( (*j2)->name + " " );
++	      ++j2;
+ 	    }
+ 	  PP->printLOG(" }");
+ 	}
+
+
+diff -rupN plink-1.07-src-orig/sets.cpp plink-1.07-src/sets.cpp
+--- plink-1.07-src-orig/sets.cpp	2009-10-10 17:00:20.000000000 +0100
++++ plink-1.07-src/sets.cpp	2016-04-13 11:42:16.252106931 +0100
+@@ -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 i2 = PP->sample.begin();
++      while ( i2 != PP->sample.end() )
+ 	{
+-	  (*i)->missing = (*i)->flag;
+-	  ++i;
++	  (*i2)->missing = (*i2)->flag;
++	  ++i2;
+ 	}
+ 
+       ////////////////////////////////////////////////