sci-biology/plink: Moved to EAPI=4, add fix for building with gcc-4.7, #424709

Package-Manager: portage-2.2.0_alpha115/cvs/Linux x86_64

4 files changed, 97 insertions, 16 deletions

diff --git a/sci-biology/plink/ChangeLog b/sci-biology/plink/ChangeLog
index ea9fc7da651e..7de52d937314 100644
--- a/sci-biology/plink/ChangeLog
+++ b/sci-biology/plink/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/plink
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/ChangeLog,v 1.11 2011/12/13 23:38:07 ago Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/ChangeLog,v 1.12 2012/07/04 09:31:26 jlec Exp $
+
+  04 Jul 2012; Justin Lecher <jlec@gentoo.org> plink-1.07-r1.ebuild,
+  +files/plink-1.07-gcc47.patch:
+  Moved to EAPI=4, add fix for building with gcc-4.7, #424709
 
   13 Dec 2011; Agostino Sarubbo <ago@gentoo.org> plink-1.07-r1.ebuild:
   Stable for AMD64, wrt bug #392783
diff --git a/sci-biology/plink/Manifest b/sci-biology/plink/Manifest
index c844e4f8290a..4cd6179e16be 100644
--- a/sci-biology/plink/Manifest
+++ b/sci-biology/plink/Manifest
@@ -1,6 +1,18 @@
-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-1.07-r1.ebuild 1195 RMD160 9d959977c7ad8eb4b56f9f6d60e47569ec107e1b SHA1 b5f31d3c6a3ad595777923be085c5d627a23066e SHA256 b9cd0f924b559a1bc67b056e7accca3b892875ecd108919602192b72e4ce6934
-EBUILD plink-1.07.ebuild 940 RMD160 7938cb59bde159119709764e9653933f87e8b987 SHA1 ea449753d041da5da4f18fc1f1c50676f7845dad SHA256 5f25e15a86ff772662d909160fe626389685705a1568cdb70a14e00e49659ee5
-MISC ChangeLog 828 RMD160 8f0bd22fef3bf1d9d1d612a2c4085ee9575c588c SHA1 1f9e1d4bb4401fa0c225ca9b05fd79633089743c SHA256 58846bd2726e5703f5dd5a32380598ebde26fff14e37817a9360c45cf120beda
-MISC metadata.xml 435 RMD160 834e96738664f51a3b8868e863520d4836925c34 SHA1 bff64de8d09c3ffab126a63e3e7ecb795c8c7e9b SHA256 f0fceedb2c7179dbdc908cad4aa34c101e38b3a7eb227c5e19e7fb3829d359e9
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
+AUX 1.07-flags.patch 1021 SHA256 93bdefd7707352ac10b4278064c39adc2a5a8bd94922124a076856b45647e186 SHA512 6ac1190a098b194cbf51351ef67d78d9b12fa18c199d28a6ffa10bd0be6d2095482a4beff17b9fed78f5f2afb73a0368c4c74ba06d06fc7acf359f0cf3361e82 WHIRLPOOL 92356cbf4c6ea8c2dffc4b8e24c592910ac46ef6dd3c118880b8bf460c92fc53d8280bfdaf016d69f1aeb3b49a11dc0b30ddf220bd55eb54038b4101d07e7a2b
+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
+EBUILD plink-1.07-r1.ebuild 1208 SHA256 91c9f0ebaa06e37aa866bd0286e360662fe3ddf0e10197ce16c37d332c29c054 SHA512 3dde7596587f02f97618d8b765938987a2e3921b04283fa1eb6abf7b9b71c0aa17eddb4fe949fd7cb6a075469cb32b9e431ee8aa0891fc2c94f5144373acd652 WHIRLPOOL fbb40252f2d364f7917a290b3591378d89f28b8be98474a460a096b44bc40db1d173b8850cbcaa8eade254b63fa1baa0c02d99c0bb27589e1eb584b8d0885922
+EBUILD plink-1.07.ebuild 940 SHA256 5f25e15a86ff772662d909160fe626389685705a1568cdb70a14e00e49659ee5 SHA512 5c8f4fbd9234c67acbcb2cb8b23cf3a523f2a018caf244a1dab0ce89c08f17206a8cd602b58f298641e3506e1e4a096267f64fde9de059b3ad40731835d01d39 WHIRLPOOL 6c0ec262c9d7cf611f9621422bf4c13caa02cdaba4cff765d5b67d64ede11e94ffdfe72649054eddfd1087a94251a950f4d3e7a7af5d306667c5ac20c975dd6e
+MISC ChangeLog 994 SHA256 48c57a5a2ebcdf5ffe3cf700a333432c04bfeae66d75d8545017d9579f97d58c SHA512 971843546706ea577586138dac78aa7ed294d1af513e0fd2d963f359d42bfa2fa9185e0d1ec30bc07a12a2363f9f4b6e60d8b567c42d2a93bf4646f7ab58bc40 WHIRLPOOL 2147de1f50c5d7623b31a5ca72719b2ce8058315e41a2f6be9a30dfec45572b2d63890e2b7b0227c59a8cb368831f956fe6489c0ce3d15d176f93409d9102fbc
+MISC metadata.xml 435 SHA256 f0fceedb2c7179dbdc908cad4aa34c101e38b3a7eb227c5e19e7fb3829d359e9 SHA512 08fdd61d18e1eb2d8a857f3453de14abeeaf9e1f4ebf3587132d1376865b31b3493f437123673bd3900595c4fd1c776cfc3e6acaa270a125a61ec09a3f8d4af7 WHIRLPOOL 869306cc1f0abddeeb449d5cc8c98b59a57bee314c0d4bbb273414eba10942e032ae3024d091733404d1f981a8e154206857ebd997d76ae6469c4289b26cd725
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.19 (GNU/Linux)
+Comment: GPGTools - http://gpgtools.org
+
+iEYEAREKAAYFAk/0DXQACgkQgAnW8HDreRbnGwCgubb3S2E1fuFHgQLiWmSTTilA
+x9wAoLHy5kcaU/EKEIU+Qj7xKMbw1pA0
+=762O
+-----END PGP SIGNATURE-----
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/plink-1.07-r1.ebuild b/sci-biology/plink/plink-1.07-r1.ebuild
index 96e64d95b785..6f0e5a4233d8 100644
--- a/sci-biology/plink/plink-1.07-r1.ebuild
+++ b/sci-biology/plink/plink-1.07-r1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/plink-1.07-r1.ebuild,v 1.4 2011/12/13 23:38:07 ago Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/plink/plink-1.07-r1.ebuild,v 1.5 2012/07/04 09:31:26 jlec Exp $
 
-EAPI="2"
+EAPI=4
 
 inherit eutils toolchain-funcs
 
@@ -26,7 +26,9 @@ S="${WORKDIR}/${P}-src"
 # Package contains bytecode-only jar gPLINK.jar. Ignored, notified upstream.
 
 src_prepare() {
-	epatch "${FILESDIR}"/${PV}-flags.patch
+	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
@@ -34,11 +36,10 @@ src_prepare() {
 
 src_compile() {
 	emake \
-		CXX_UNIX=$(tc-getCXX) \
-		|| die
+		CXX_UNIX=$(tc-getCXX)
 }
 
 src_install() {
-	newbin plink p-link || die
-	dodoc README.txt || die
+	newbin plink p-link
+	dodoc README.txt
 }