Fix building with GCC 4.4 and GLIBC 2.10+ wrt #279572.

Package-Manager: portage-2.2_rc33/cvs/Linux x86_64

4 files changed, 133 insertions, 19 deletions

diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog
index fc5eae2fe31c..cd63f255d364 100644
--- a/sci-biology/amos/ChangeLog
+++ b/sci-biology/amos/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-biology/amos
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/ChangeLog,v 1.4 2009/03/15 17:58:50 maekke Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/ChangeLog,v 1.5 2009/07/30 16:49:34 ssuominen Exp $
+
+  30 Jul 2009; Samuli Suominen <ssuominen@gentoo.org> amos-2.0.8.ebuild,
+  +files/amos-2.0.8-gcc44.patch:
+  Fix building with GCC 4.4 and GLIBC 2.10+ wrt #279572.
 
   15 Mar 2009; Markus Meier <maekke@gentoo.org> amos-2.0.8.ebuild:
   amd64/x86 stable, bug #261786
diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest
index 7ec506a7c5e7..347b3e689cb7 100644
--- a/sci-biology/amos/Manifest
+++ b/sci-biology/amos/Manifest
@@ -1,14 +1,5 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
+AUX amos-2.0.8-gcc44.patch 3555 RMD160 8bf9d9f6290b573b373542d180f8f788d8042334 SHA1 0d5b92c9203ce4a0ba4681b301ee419984d9b3ba SHA256 e07bd2b40ee21db39d096db5367ef7c12baa78ba776101919945f60b8507d5b1
 DIST amos-2.0.8.tar.gz 1757124 RMD160 98cfa30081e849a36285e159010ab85b3a116eeb SHA1 3b59c07325b108df9683a57dc168cdf60714cedc SHA256 5c8adf33816278411ead7ad2f6509ebfee2388f9cb89d2196d8e5ad9b0c8ffd1
-EBUILD amos-2.0.8.ebuild 734 RMD160 a9e78fd7cbb6419ed790b109b001fdc8e52bb495 SHA1 5263c1aedc1f53dfdce3fe03b8ddca3ccd03cbb2 SHA256 d9ccee46b58b9c7ca0859007514b901cca131fb6b65411b0a96cdbd05b96ea5f
-MISC ChangeLog 711 RMD160 f7992c322b5425e01baa283c74af56bd64603f0d SHA1 11f2702ea9579d8c869c20ad7acda2e0e2c38b84 SHA256 5ed05003c754d57f496eb761a8fd9e9736b7dad2b8a22555f2ae7390444126c9
+EBUILD amos-2.0.8.ebuild 724 RMD160 5985c531cbabe7981337167718ba64b8c19a5595 SHA1 713ac5cde3161601a765ac5e3efc09389b57b612 SHA256 44825bd27932ef61df1fc193d62203e6e8bcad98237fbce1ffa79f9d88179d31
+MISC ChangeLog 878 RMD160 9ed889cdb955ff1e38f65579ae8ec599770e5e50 SHA1 3cdc2e92b7ebad3cd8d4ded5a4cdb5f2f18e6719 SHA256 2fccc2405f9428fd8ffdb15612608f867db479bbbc97db0aa8b7a211c893fef0
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
------BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.9 (GNU/Linux)
-
-iEYEARECAAYFAkm9QeQACgkQkKaRLQcq0GKp2gCfeerPVsSvpgAxpKigsWLhADqF
-yKEAn2SM8vLVhBhRb7q5sJH6KZyFlaMY
-=JZQC
------END PGP SIGNATURE-----
diff --git a/sci-biology/amos/amos-2.0.8.ebuild b/sci-biology/amos/amos-2.0.8.ebuild
index 18236ac5f113..867df2b0fb68 100644
--- a/sci-biology/amos/amos-2.0.8.ebuild
+++ b/sci-biology/amos/amos-2.0.8.ebuild
@@ -1,9 +1,9 @@
 # Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/amos-2.0.8.ebuild,v 1.2 2009/03/15 17:58:50 maekke Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/amos-2.0.8.ebuild,v 1.3 2009/07/30 16:49:34 ssuominen Exp $
 
-EAPI="1"
-inherit qt3 eutils
+EAPI=2
+inherit eutils qt3
 
 DESCRIPTION="A Modular, Open-Source whole genome assembler"
 HOMEPAGE="http://amos.sourceforge.net/"
@@ -19,12 +19,14 @@ RDEPEND="${DEPEND}
 	dev-perl/DBI
 	sci-biology/mummer"
 
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-gcc44.patch
+}
+
 src_compile() {
-	econf || die "econf failed"
-	# TODO: fix parallel make. Notified upstream
 	emake -j1 || die "emake failed"
 }
 
 src_install() {
-	emake DESTDIR="${D}" install || die "install failed"
+	emake DESTDIR="${D}" install || die "emake install failed"
 }
diff --git a/sci-biology/amos/files/amos-2.0.8-gcc44.patch b/sci-biology/amos/files/amos-2.0.8-gcc44.patch
new file mode 100644
index 000000000000..00a37be1d18c
--- /dev/null
+++ b/sci-biology/amos/files/amos-2.0.8-gcc44.patch
@@ -0,0 +1,117 @@
+diff -ur amos-2.0.8.orig/src/Align/align.cc amos-2.0.8/src/Align/align.cc
+--- amos-2.0.8.orig/src/Align/align.cc	2008-03-19 16:07:24.000000000 +0200
++++ amos-2.0.8/src/Align/align.cc	2009-07-30 19:40:51.000000000 +0300
+@@ -247,7 +247,7 @@
+ //  Add  incr_val  to the  after  count in this  Vote_t  for  ch .
+ 
+   {
+-   char  * p;
++   const char  * p;
+ 
+    p = strchr (ALPHABET, tolower (ch));
+    if  (p == NULL)
+@@ -285,7 +285,7 @@
+ //  count for a blank.
+ 
+   {
+-   char  * p;
++   const char  * p;
+ 
+    p = strchr (ALPHABET, tolower (ch));
+    if  (p == NULL)
+@@ -357,7 +357,7 @@
+ 
+   {
+    int  i;
+-   char  * p;
++   const char  * p;
+ 
+    for  (i = 0;  i <= ALPHABET_SIZE;  i ++)
+      here [i] = after [i] = 0;
+diff -ur amos-2.0.8.orig/src/Align/align_poly.cc amos-2.0.8/src/Align/align_poly.cc
+--- amos-2.0.8.orig/src/Align/align_poly.cc	2006-03-30 05:03:12.000000000 +0300
++++ amos-2.0.8/src/Align/align_poly.cc	2009-07-30 19:43:44.000000000 +0300
+@@ -247,7 +247,7 @@
+ //  Add 1 to the  after  count in this  Vote_t  for  ch .
+ 
+   {
+-   char  * p;
++   const char  * p;
+ 
+    p = strchr (ALPHABET, tolower (ch));
+    if  (p == NULL)
+@@ -285,7 +285,7 @@
+ //  count for a blank.
+ 
+   {
+-   char  * p;
++   const char  * p;
+ 
+    p = strchr (ALPHABET, tolower (ch));
+    if  (p == NULL)
+@@ -357,7 +357,7 @@
+ 
+   {
+    int  i;
+-   char  * p;
++   const char  * p;
+ 
+    for  (i = 0;  i <= ALPHABET_SIZE;  i ++)
+      here [i] = after [i] = 0;
+diff -ur amos-2.0.8.orig/src/AMOS/IDMap_AMOS.cc amos-2.0.8/src/AMOS/IDMap_AMOS.cc
+--- amos-2.0.8.orig/src/AMOS/IDMap_AMOS.cc	2006-11-21 17:45:46.000000000 +0200
++++ amos-2.0.8/src/AMOS/IDMap_AMOS.cc	2009-07-30 19:30:03.000000000 +0300
+@@ -10,6 +10,7 @@
+ #include "IDMap_AMOS.hh"
+ #include <string>
+ #include <sstream>
++#include <cstdio>
+ #include <cstring>
+ using namespace AMOS;
+ using namespace std;
+diff -ur amos-2.0.8.orig/src/AMOS/Message_AMOS.cc amos-2.0.8/src/AMOS/Message_AMOS.cc
+--- amos-2.0.8.orig/src/AMOS/Message_AMOS.cc	2005-01-07 23:53:05.000000000 +0200
++++ amos-2.0.8/src/AMOS/Message_AMOS.cc	2009-07-30 19:32:21.000000000 +0300
+@@ -7,6 +7,8 @@
+ //!
+ ////////////////////////////////////////////////////////////////////////////////
+ 
++#include <cstdio>
++
+ #include "Message_AMOS.hh"
+ using namespace AMOS;
+ using namespace std;
+diff -ur amos-2.0.8.orig/src/Common/amp.cc amos-2.0.8/src/Common/amp.cc
+--- amos-2.0.8.orig/src/Common/amp.cc	2006-10-25 16:56:41.000000000 +0300
++++ amos-2.0.8/src/Common/amp.cc	2009-07-30 19:33:59.000000000 +0300
+@@ -1,6 +1,7 @@
+ #include "amp.hh"
+ #include <new>
+ #include <iostream>
++#include <cstdio>
+ #include <cstring>
+ #include <ctime>
+ using namespace std;
+diff -ur amos-2.0.8.orig/src/Foundation/FileSystem.cc amos-2.0.8/src/Foundation/FileSystem.cc
+--- amos-2.0.8.orig/src/Foundation/FileSystem.cc	2005-07-09 00:52:03.000000000 +0300
++++ amos-2.0.8/src/Foundation/FileSystem.cc	2009-07-30 19:35:48.000000000 +0300
+@@ -55,7 +55,7 @@
+   {
+     // Check to see if path was given
+ 
+-    char * end_of_path = strrchr(filename, PATH_DELIMINATOR);
++    const char * end_of_path = strrchr(filename, PATH_DELIMINATOR);
+     
+     if (end_of_path)
+     {
+diff -ur amos-2.0.8.orig/src/Foundation/Options.cc amos-2.0.8/src/Foundation/Options.cc
+--- amos-2.0.8.orig/src/Foundation/Options.cc	2008-06-22 18:19:07.000000000 +0300
++++ amos-2.0.8/src/Foundation/Options.cc	2009-07-30 19:37:40.000000000 +0300
+@@ -26,6 +26,7 @@
+  */
+ 
+ #include "Options.hh"
++#include <cstdio>
+ #include <cstring>
+ 
+ //! Constructor takes command line options in standard argc, argv format