sci-biology/amos: Add fix for gcc-4.7, #425264; cleaned old

(Portage version: 2.2.0_alpha116/cvs/Linux x86_64)

7 files changed, 32 insertions, 218 deletions

diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog
index 1cdcc0bc2f01..c19b0d3f120a 100644
--- a/sci-biology/amos/ChangeLog
+++ b/sci-biology/amos/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/amos
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/ChangeLog,v 1.14 2011/10/05 19:51:18 jlec Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/ChangeLog,v 1.15 2012/07/08 17:28:51 jlec Exp $
+
+  08 Jul 2012; Justin Lecher <jlec@gentoo.org> -amos-2.0.8-r1.ebuild,
+  -files/amos-2.0.8-gcc44.patch, -amos-3.0.0.ebuild, -amos-3.0.1.ebuild,
+  amos-3.1.0.ebuild, +files/amos-3.1.0-gcc-4.7.patch:
+  Add fix for gcc-4.7, #425264; cleaned old
 
   05 Oct 2011; Justin Lecher <jlec@gentoo.org> amos-3.1.0.ebuild, metadata.xml:
   Another simplification
diff --git a/sci-biology/amos/amos-2.0.8-r1.ebuild b/sci-biology/amos/amos-2.0.8-r1.ebuild
deleted file mode 100644
index 835b20b8bda8..000000000000
--- a/sci-biology/amos/amos-2.0.8-r1.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2010 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-r1.ebuild,v 1.1 2010/02/11 16:47:31 weaver Exp $
-
-EAPI="2"
-
-# qt3 is scheduled for removal, so don't depend on it - package compiles fine either way
-#inherit eutils qt3
-inherit eutils
-
-DESCRIPTION="A Modular, Open-Source whole genome assembler"
-HOMEPAGE="http://amos.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-#DEPEND=">=x11-libs/qt-3.3:3"
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-perl/DBI
-	sci-biology/mummer"
-
-src_prepare() {
-	epatch "${FILESDIR}"/${P}-gcc44.patch
-}
-
-src_compile() {
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	emake DESTDIR="${D}" install || die "emake install failed"
-}
diff --git a/sci-biology/amos/amos-3.0.0.ebuild b/sci-biology/amos/amos-3.0.0.ebuild
deleted file mode 100644
index dd704b984592..000000000000
--- a/sci-biology/amos/amos-3.0.0.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/amos-3.0.0.ebuild,v 1.3 2011/05/28 19:26:40 phajdan.jr Exp $
-
-EAPI="3"
-
-inherit eutils
-
-DESCRIPTION="A Modular, Open-Source whole genome assembler"
-HOMEPAGE="http://amos.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-#DEPEND=">=x11-libs/qt-3.3:3"
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-perl/DBI
-	sci-biology/mummer"
-
-src_compile() {
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	emake DESTDIR="${D}" install || die "emake install failed"
-}
diff --git a/sci-biology/amos/amos-3.0.1.ebuild b/sci-biology/amos/amos-3.0.1.ebuild
deleted file mode 100644
index fe8bd7bda324..000000000000
--- a/sci-biology/amos/amos-3.0.1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2011 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/amos-3.0.1.ebuild,v 1.1 2011/08/12 15:48:21 weaver Exp $
-
-EAPI="3"
-
-inherit eutils
-
-DESCRIPTION="A Modular, Open-Source whole genome assembler"
-HOMEPAGE="http://amos.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-#DEPEND=">=x11-libs/qt-3.3:3"
-DEPEND=""
-RDEPEND="${DEPEND}
-	dev-perl/DBI
-	sci-biology/mummer"
-
-src_compile() {
-	emake -j1 || die "emake failed"
-}
-
-src_install() {
-	emake DESTDIR="${D}" install || die "emake install failed"
-}
diff --git a/sci-biology/amos/amos-3.1.0.ebuild b/sci-biology/amos/amos-3.1.0.ebuild
index 893793a80ec4..af4f9b42d5f3 100644
--- a/sci-biology/amos/amos-3.1.0.ebuild
+++ b/sci-biology/amos/amos-3.1.0.ebuild
@@ -1,17 +1,19 @@
-# 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/amos/amos-3.1.0.ebuild,v 1.5 2011/10/05 19:51:18 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/amos-3.1.0.ebuild,v 1.6 2012/07/08 17:28:51 jlec Exp $
 
 EAPI=4
 
+inherit eutils
+
 DESCRIPTION="A Modular, Open-Source whole genome assembler"
 HOMEPAGE="http://amos.sourceforge.net/"
 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
 
 LICENSE="Artistic"
 SLOT="0"
-IUSE="qt"
 KEYWORDS="amd64 x86"
+IUSE="qt"
 
 DEPEND="qt? ( x11-libs/qt-core:4 )"
 RDEPEND="${DEPEND}
@@ -20,3 +22,8 @@ RDEPEND="${DEPEND}
 	sci-biology/mummer"
 
 MAKEOPTS+=" -j1"
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${P}-gcc-4.7.patch
+}
diff --git a/sci-biology/amos/files/amos-2.0.8-gcc44.patch b/sci-biology/amos/files/amos-2.0.8-gcc44.patch
deleted file mode 100644
index 00a37be1d18c..000000000000
--- a/sci-biology/amos/files/amos-2.0.8-gcc44.patch
+++ /dev/null
@@ -1,117 +0,0 @@
-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
diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
new file mode 100644
index 000000000000..de2a41184c52
--- /dev/null
+++ b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ src/Align/find-tandem.cc |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc
+index ddf1cab..a29e21e 100644
+--- a/src/Align/find-tandem.cc
++++ b/src/Align/find-tandem.cc
+@@ -7,6 +7,7 @@
+ #include <vector>
+ #include <ctime>
+ #include <sys/time.h>
++#include <unistd.h>
+ using namespace std;
+ 
+ const int OFFSET_TABLE_SIZE = 100;