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

Package-Manager: portage-2.2.0_alpha116/cvs/Linux x86_64

8 files changed, 43 insertions, 234 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/Manifest b/sci-biology/amos/Manifest
index 75dc50e57a8a..95bf9ee74268 100644
--- a/sci-biology/amos/Manifest
+++ b/sci-biology/amos/Manifest
@@ -1,21 +1,16 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
+Hash: SHA256
 
-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
-DIST amos-3.0.0.tar.gz 1940705 RMD160 3c2f2819696b01a5e7fc293e0f76f5ee591c7b57 SHA1 7ffc685ae9bb354b163916609189d3cb3c6775b5 SHA256 6426ca20dd98b7f9329c016a8b61b98f7d71bf1527e32441efca8beaf55792af
-DIST amos-3.0.1.tar.gz 1876671 RMD160 857c9703ba11391a1fbe1bea1b950c8bf81dc21e SHA1 977b66f24565d29e01b6c30c1b44636f4d6527f8 SHA256 3c6638c8c012b2a8457d1d1f15ac207e42db662a68da9d90f6d08a81462a6b63
-DIST amos-3.1.0.tar.gz 2094268 RMD160 2ee8cb46c18d2807878feed5a9df94230db180e2 SHA1 28e799e37713594ba7147d300ecae6574beb14a4 SHA256 2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b
-EBUILD amos-2.0.8-r1.ebuild 843 RMD160 56cb133c15ee3edb74eab731990465e9a5d38ad4 SHA1 b7880ccf266a5779a22acd80c436c8953d01540a SHA256 f40d1a766830bddc1dca3ab715e7a85270acd5871343815b304ab4f55a053475
-EBUILD amos-3.0.0.ebuild 680 RMD160 6edbbf991063fc2230718a01110d1bfe37399cbf SHA1 f9b95020529356574772849409ed9f3740889723 SHA256 d6da11cfbf41cedc32ace765ab4cfacd0b7c246c94452412e273d4fed21452a9
-EBUILD amos-3.0.1.ebuild 678 RMD160 634708e69761a33376cd058b77b79885eeb50105 SHA1 0c2b430fb94351b46d6f58a435bc5b5563a06abf SHA256 b0b9319e52b6cdac7fbeacf6170242941686d928892afd0347432621d99f1594
-EBUILD amos-3.1.0.ebuild 574 RMD160 ae9ff7b01945b30b90a2703b606d5f3ec8ca333f SHA1 0c9d0879d2d08857ea046cd4049873f1ef0f4055 SHA256 95a908721e7b8425c9add18ce2aa0c86cbf31d6817a020427ead8b9f9c39fe95
-MISC ChangeLog 1993 RMD160 ae3d2981e4d6b98d8b5c0b7cba27200029d674ae SHA1 fa906429fed701ad9e3e7005856a47cd755059ac SHA256 aa9beb145886862d146ba779548a5c2224fae38e523947adb72bb40d71fb75fc
-MISC metadata.xml 335 RMD160 8f6e0c2e26e665d562b6edbeb1b1a91f675ae61f SHA1 7be7c42d23bebc0a4db48d78bd1aff6fe053c99a SHA256 99f66a3cf796736d0197e764898ccea7fc460b348576b4bfb1e864381d44e625
+AUX amos-3.1.0-gcc-4.7.patch 400 SHA256 59be7e1fa3c4125f463e666f304f2194fc73026c71005ac16891e950e75b8af6 SHA512 3777885d5cd5edcb881abfbe1580092e073311797bd4776cd3ec9d27b634339718238be7f452f1ea1a0aea5fb9f6059d6b6f6a47bc2a0fb6d1811a2ec51a0835 WHIRLPOOL 5c446c940eed42a5d8b47c102e97a4fc3c9818aa40f6049ab6b4e78ee8cf445665afbc78b9c2742e3de3adccb087e8f61ba3ebe567140d2e26d2a6167fe13b65
+DIST amos-3.1.0.tar.gz 2094268 SHA256 2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 WHIRLPOOL df9b547fcc0b7bf0149641fd8df9e4558f61bb6c17ded0facfeecde25d3a6307b40414e7cb8b2f021fa8cc192ee956672c26e0fc287981f4733a393739e80b61
+EBUILD amos-3.1.0.ebuild 654 SHA256 7622e12b1dc1df57c514aba93145c1eb7b7f756baef442592fd27511d6bc9388 SHA512 19d9586cc8ab94168f6d40f2d4d4987968f7fca26e1f87301b8f7659782535d2dec358caecec5ff2f24938277339f3a374a9225e9dcb39d85663db6af611f4cf WHIRLPOOL 62d4f0b2af61340092c02839e8aa01b79bce1362b4d73a0ef7f855b79aa6632ae368dba2a45870b7c56bb4f2188e37bd4d9db352bcc0f6ec851234dbbb0e2b05
+MISC ChangeLog 2235 SHA256 b081bc4837a114d3a418b4e672d9401a40e16437aef0459a6ddd34eb192babde SHA512 6c56f8518d5ef113a033a648d54826aef5b1f7be82b9ae97b47cafd5af89768570e8757604c0ba1f34427615961dcfae0c1343e76395bc3b5bcbb545ba16f2b0 WHIRLPOOL 538aefb7363ffac362cb38f12d2e7fe7a4ea113d792474463889181bc0b290baec33d8387b3778dc031771f49796032a104e39cb2ced82b5e4d069c6bba5a9e9
+MISC metadata.xml 335 SHA256 99f66a3cf796736d0197e764898ccea7fc460b348576b4bfb1e864381d44e625 SHA512 06d5da78b39e73a68a145afad016df7389f8a6d7079b3e1740852700a994220a05e9e883584fa6b925bb05a13cc834d82821abb4502d108a5875eb2c46ab5669 WHIRLPOOL 99d627d5704f4000005b5ba6c4f5bbbb12f9ac52d496adf1320bfac86b6f8b505ff22bc725ee9c81c83adcfd170adb911d1b99c28ddecf16c76423fefea64d35
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.18 (GNU/Linux)
+Version: GnuPG v2.0.19 (GNU/Linux)
+Comment: GPGTools - http://gpgtools.org
 
-iEYEAREKAAYFAk6MtUAACgkQgAnW8HDreRZbHQCdF1an9eDFYY59Xz4Er+EPFB5L
-ySsAnRZl7vOaZI2X+sTtIvQ48zRlAsRK
-=qr/2
+iEYEAREIAAYFAk/5w1gACgkQgAnW8HDreRYC9QCfQcXKDSNup0c7SxdSyBWB7kWk
+880AoKYxQjp3ce+8wc4WOOk1LDx8MBZ1
+=x37J
 -----END PGP SIGNATURE-----
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;