[gentoo-commits] proj/sci:master commit in: sci-biology/amos-short/files/, sci-biology/amos-short/

[Justin Lecher]

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 <mmokrejs@×××××××××××××××.cz>
-  amos-short-0.9.3.ebuild:
-  sci-biology/amos-short: simplify package description
-
-  03 Apr 2015; Marius Brehler <marbre@××××××××××××××.de>
-  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>mmokrejs@×××××××××××××××.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-</pkgmetadata>