commit: b4583e60fe9db0b9407413d01a36c4b72d2fe6e4 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Mon Sep 21 12:33:54 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Mon Sep 21 12:33:54 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b4583e60
Drop obsolete package Sources unavailable Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> sci-biology/amos-short/ChangeLog | 12 --- sci-biology/amos-short/amos-short-0.9.3.ebuild | 32 ------ .../amos-short/files/amos-2.0.8-gcc44.patch | 117 --------------------- sci-biology/amos-short/metadata.xml | 9 -- 4 files changed, 170 deletions(-) diff --git a/sci-biology/amos-short/ChangeLog b/sci-biology/amos-short/ChangeLog deleted file mode 100644 index 9d643a4..0000000 --- a/sci-biology/amos-short/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-biology/amos-short -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Id$ - - 06 Sep 2015; Martin Mokrejs <[email protected]> - amos-short-0.9.3.ebuild: - sci-biology/amos-short: simplify package description - - 03 Apr 2015; Marius Brehler <[email protected]> - amos-short-0.9.3.ebuild: - Bump to EAPI=5, but drop KEYWORDS as SRC is - unavailable diff --git a/sci-biology/amos-short/amos-short-0.9.3.ebuild b/sci-biology/amos-short/amos-short-0.9.3.ebuild deleted file mode 100644 index 2493899..0000000 --- a/sci-biology/amos-short/amos-short-0.9.3.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit eutils - -DESCRIPTION="Whole genome assembler with defaults for short reads" -HOMEPAGE="http://amos.sourceforge.net/"; -SRC_URI="http://sourceforge.net/projects/amos/files/short_read_assembly/${PV}/AMOS-short.tgz"; - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="" - -DEPEND="" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/AMOS - -src_prepare() { - epatch "${FILESDIR}"/amos-2.0.8-gcc44.patch -} - -src_compile() { - emake -j1 -} - -src_install() { - emake DESTDIR="${D}" install -} diff --git a/sci-biology/amos-short/files/amos-2.0.8-gcc44.patch b/sci-biology/amos-short/files/amos-2.0.8-gcc44.patch deleted file mode 100644 index 00a37be..0000000 --- a/sci-biology/amos-short/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-short/metadata.xml b/sci-biology/amos-short/metadata.xml deleted file mode 100644 index 07b5255..0000000 --- a/sci-biology/amos-short/metadata.xml +++ /dev/null @@ -1,9 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> -</pkgmetadata>
