Added patch to allow compilation with gcc-4.3 (bug #228121).

Package-Manager: portage-2.1.4.4

4 files changed, 27 insertions, 4 deletions

diff --git a/sci-chemistry/pdb2pqr/ChangeLog b/sci-chemistry/pdb2pqr/ChangeLog
index 9e0e2b29e758..698875659358 100644
--- a/sci-chemistry/pdb2pqr/ChangeLog
+++ b/sci-chemistry/pdb2pqr/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-chemistry/pdb2pqr
 # Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.11 2008/02/06 15:14:10 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/ChangeLog,v 1.12 2008/06/19 13:02:12 markusle Exp $
+
+  19 Jun 2008; Markus Dittrich <markusle@gentoo.org>
+  +files/pdb2pqr-1.3.0-gcc4.3.patch, pdb2pqr-1.3.0.ebuild:
+  Added patch to allow compilation with gcc-4.3 (bug #228121).
 
 *pdb2pqr-1.3.0 (06 Feb 2008)
 
diff --git a/sci-chemistry/pdb2pqr/Manifest b/sci-chemistry/pdb2pqr/Manifest
index cda314b7403b..4a2008710c78 100644
--- a/sci-chemistry/pdb2pqr/Manifest
+++ b/sci-chemistry/pdb2pqr/Manifest
@@ -1,5 +1,6 @@
 AUX pdb2pqr-1.1.2-fpic-gentoo.patch 668 RMD160 e076ebcfe1e0fd39ca7b2219b6d9938b6f4870c8 SHA1 38018f5494b21296dfabe02c61824d0af6d6ce36 SHA256 6455be2583ded00bea43f49789cde72cdd240858f187db6d59ed67c87163af45
 AUX pdb2pqr-1.1.2-gcc4-gentoo.patch 1104 RMD160 87d7c92e4f24be4f205379acafdc9c41b8e99a9b SHA1 346ed354808f2d902a2d4076e9c41690a83995f5 SHA256 164ae1a21de69ea97f5439a15004d1441fc7d11cbd79cf1c5ab777363b1e3019
+AUX pdb2pqr-1.3.0-gcc4.3.patch 349 RMD160 a7e241b288738faaee678609c61968dba990b9a3 SHA1 95e0dcb30e926f0bab2068bff550427a1a3a623e SHA256 4e65916b3370bc3c4690ca9424629a928f9753879939f0ebb881304331fab946
 AUX pdb2pqr-gcc4-gentoo.patch 627 RMD160 293cd6faa4c9d9a20ca8a708187652c79f106927 SHA1 bad480b23ad7d5e65b3e9c3e249538a180083609 SHA256 afcfb33b59d4feb18f35ebcafea3d759bcb8ba7211dca2b8694df2c9f179363f
 AUX pdb2pqr-propka-gentoo.patch 383 RMD160 aba20c68558d3131b9f04b4188c70e42611f013e SHA1 4bfd930bdfd719d22d8f8576949eb68dd35e0036 SHA256 5f75dfd2a72861b46685568ea6c55be0ed055ab5d72d231e328f7f482252101a
 DIST pdb2pqr-1.1.2.tar.gz 653600 RMD160 40510384a6b03213d6c857a270d508d4bbefa884 SHA1 89ae9b50e64fc3bbd2a868af01da708fb3f45395 SHA256 ea45ec40b420044e5c7a11744a5db867c544b93d25a8bccf27ebac43cd7d6f94
@@ -7,6 +8,6 @@ DIST pdb2pqr-1.2.1.tar.gz 2090993 RMD160 647aa616703208f81396917b805be1daf3adf18
 DIST pdb2pqr-1.3.0.tar.gz 2641989 RMD160 469b38457a10e93ce96c7ea4e580cb4656ba3218 SHA1 e2095a7130ff6114d15466b009cc8ed335d8ffd1 SHA256 7e8a733aacdb76ec8f920b6827ebbc86712044a10c50363535978bc22b7fd413
 EBUILD pdb2pqr-1.1.2.ebuild 1848 RMD160 e56dd0be66205cee302fc5c2a8c0caca8adb17ab SHA1 07cc0856bfb50c1648ba4dd1b6c2cb9103943d6d SHA256 995a2a2940b97a7daf18c8a487f5381c2019285b57fe03982969d6406974f1a2
 EBUILD pdb2pqr-1.2.1.ebuild 1717 RMD160 a47593b7d6a5a206ed34544719ccc603f9cf5196 SHA1 db42c2869b3bb57f68a51a8efed5871db71a9079 SHA256 8c97db05b9e2bb337d4d8f19eb74119b1bf0edf9882089493ccefd2727ac4c7a
-EBUILD pdb2pqr-1.3.0.ebuild 1822 RMD160 19c8f34d483d90fcc277dc561a2a470f571a2958 SHA1 3a5bfd569b74bac48568284da67262848f0ef515 SHA256 130cdb2a05250d6e515966e70224e844184eec2af46870d4040bc2e30b44fb95
-MISC ChangeLog 1748 RMD160 39de74828142c7f80935eeac0ee50bcf0ae9ac03 SHA1 665ad679317d74ff627fe6eeeff53bf5c3f9bab4 SHA256 ce32a255a4bfba526102b6891edfbd0e20e16198e53aba9dc26db3549b020c2f
+EBUILD pdb2pqr-1.3.0.ebuild 1904 RMD160 4e4651aab2e32d5c63e5646e64e7ca8b13a9076a SHA1 005366ea17064d38b4bf3094a474c14759835f4d SHA256 ae20708a4f1c21b0a807cd29baf258fb699dfea9b4c793e7ddc9d6881a69257a
+MISC ChangeLog 1924 RMD160 e739cdb86160f6ccc3707fe5371c238cecee1809 SHA1 940dec9ac7e86165d868c3f805fd26ee090b6779 SHA256 8fc78ea4cfec2baabebe60bcae6aeff8e0a607d2e0354f4b58257aa8ebf123be
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
diff --git a/sci-chemistry/pdb2pqr/files/pdb2pqr-1.3.0-gcc4.3.patch b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.3.0-gcc4.3.patch
new file mode 100644
index 000000000000..2ccd01785213
--- /dev/null
+++ b/sci-chemistry/pdb2pqr/files/pdb2pqr-1.3.0-gcc4.3.patch
@@ -0,0 +1,12 @@
+diff -Naur pdb2pqr-1.3.0/pdb2pka/pMC_mult.cpp pdb2pqr-1.3.0.new/pdb2pka/pMC_mult.cpp
+--- pdb2pqr-1.3.0/pdb2pka/pMC_mult.cpp	2006-12-05 20:35:43.000000000 -0500
++++ pdb2pqr-1.3.0.new/pdb2pka/pMC_mult.cpp	2008-06-19 08:53:22.000000000 -0400
+@@ -8,6 +8,8 @@
+ //
+ //
+ 
++#include <cstdlib>
++
+ void MC::reformat_arrays() {
+   //
+   // Reformat the matrix
diff --git a/sci-chemistry/pdb2pqr/pdb2pqr-1.3.0.ebuild b/sci-chemistry/pdb2pqr/pdb2pqr-1.3.0.ebuild
index acc332c03593..425b8c037469 100644
--- a/sci-chemistry/pdb2pqr/pdb2pqr-1.3.0.ebuild
+++ b/sci-chemistry/pdb2pqr/pdb2pqr-1.3.0.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2008 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.3.0.ebuild,v 1.1 2008/02/06 15:14:10 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb2pqr/pdb2pqr-1.3.0.ebuild,v 1.2 2008/06/19 13:02:12 markusle Exp $
 
 inherit eutils fortran multilib flag-o-matic distutils
 
@@ -17,6 +17,12 @@ DEPEND="dev-lang/python"
 
 FORTRAN="g77 gfortran"
 
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${P}-gcc4.3.patch
+}
+
 src_compile() {
 	# we need to compile the *.so as pic
 	append-flags -fPIC