diff options
| -rw-r--r-- | sci-biology/amos/ChangeLog | 9 | ||||
| -rw-r--r-- | sci-biology/amos/amos-2.0.8-r1.ebuild | 36 | ||||
| -rw-r--r-- | sci-biology/amos/amos-3.0.0.ebuild | 30 | ||||
| -rw-r--r-- | sci-biology/amos/amos-3.0.1.ebuild | 30 | ||||
| -rw-r--r-- | sci-biology/amos/amos-3.1.0.ebuild | 13 | ||||
| -rw-r--r-- | sci-biology/amos/files/amos-2.0.8-gcc44.patch | 117 | ||||
| -rw-r--r-- | sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch | 15 |
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; |