sci-biology/mrfast: Version BUmp; punt base.eclass

Package-Manager: portage-2.2.8

5 files changed, 27 insertions, 69 deletions

diff --git a/sci-biology/mrfast/ChangeLog b/sci-biology/mrfast/ChangeLog
new file mode 100644
index 000000000..5db17a31b
--- /dev/null
+++ b/sci-biology/mrfast/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/mrfast
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mrfast-2.1.0.3.ebuild,
+  +mrfast-2.6.0.1.ebuild, -files/mrfast-2.1.0.3-disc_buffer_overflow.patch,
+  metadata.xml:
+  Version BUmp; punt base.eclass
+
diff --git a/sci-biology/mrfast/Manifest b/sci-biology/mrfast/Manifest
index a3da4999d..091754d4d 100644
--- a/sci-biology/mrfast/Manifest
+++ b/sci-biology/mrfast/Manifest
@@ -1 +1 @@
-DIST mrfast-2.1.0.3.tar.gz 42853 SHA256 2e96e908819ef4b982dd749444fe7b7a5198a0d8df1e4edb475394091c398f4a
+DIST mrfast-2.6.0.1.tar.gz 51200 SHA256 8635a217a91dcc1d16a21d4ad34898bd4e9a0080cc101f9cf7c28b172db31e8b SHA512 9bb3395f0d51cea9f2a7d85831913847cdf67c1995062593ccab25de2dc0a9c2cc7631c090f7c6c3e87a71244cee6882b342b3816e359f982838695240bebb76 WHIRLPOOL 45db8d343453c6fd24b3d7fe1eb6286991157e8bed93bfb0e678c220165b7f1a3784998a73f1e4fb94914858062262031869dc2ed9feff1c58ffcd57b55b5a51
diff --git a/sci-biology/mrfast/files/mrfast-2.1.0.3-disc_buffer_overflow.patch b/sci-biology/mrfast/files/mrfast-2.1.0.3-disc_buffer_overflow.patch
deleted file mode 100644
index bdf5cbb91..000000000
--- a/sci-biology/mrfast/files/mrfast-2.1.0.3-disc_buffer_overflow.patch
+++ /dev/null
@@ -1,52 +0,0 @@
-diff -durr mrfast-2.1.0.3.orig/MrFAST.c mrfast-2.1.0.3/MrFAST.c
---- mrfast-2.1.0.3.orig/MrFAST.c	2011-12-18 17:48:16.431973604 -0500
-+++ mrfast-2.1.0.3/MrFAST.c	2011-12-18 17:55:11.400723582 -0500
-@@ -7358,6 +7358,7 @@
- 	char fname1[FILE_NAME_LENGTH];
- 	char fname2[FILE_NAME_LENGTH];
- 	char l;
-+	int l_int;
- 	int loc1, loc2;
- 	int err1, err2;
- 	char dir1, dir2;
-@@ -7399,28 +7400,28 @@
- 
- 		//tmp = fwrite (&(mi2[k].cigarSize), sizeof(int), 1, out);
- 		
--		tmp = fread(&l, sizeof(int), 1, in);
--		tmp = fread(cigar1, sizeof(char), l, in);
--		cigar1[(int)l]='\0';
-+		tmp = fread(&l_int, sizeof(int), 1, in);
-+		tmp = fread(cigar1, sizeof(char), l_int, in);
-+		cigar1[l_int]='\0';
- 		//tmp = fwrite ((mi2[k].cigar), sizeof(char), mi2[k].cigarSize, out);
- 
- 		//tmp = fwrite (&(mi2[k].mdSize), sizeof(int), 1, out);
--		tmp = fread(&l, sizeof(int), 1, in);
--		tmp = fread(editString1, sizeof(char), l, in);
--		editString1[(int)l]='\0';
-+		tmp = fread(&l_int, sizeof(int), 1, in);
-+		tmp = fread(editString1, sizeof(char), l_int, in);
-+		editString1[l_int]='\0';
- 		//tmp = fwrite ((mi2[k].md), sizeof(char), mi2[k].mdSize, out);
- 
- 		tmp = fread(&loc2, sizeof(int), 1, in);
- 		tmp = fread(&err2, sizeof(int), 1, in);
- 		tmp = fread(&sc2, sizeof(float), 1, in);
- 
--		tmp = fread(&l, sizeof(int), 1, in);
--		tmp = fread(cigar2, sizeof(char), l, in);
--		cigar2[(int)l]='\0';
-+		tmp = fread(&l_int, sizeof(int), 1, in);
-+		tmp = fread(cigar2, sizeof(char), l_int, in);
-+		cigar2[l_int]='\0';
- 		/* FARHAD:  l is of type char; and you fread into it with sizeof(char) above; but as sizeof(int) here; are you sure? 1 byte vs. 4 bytes */
--		tmp = fread(&l, sizeof(int), 1, in);
--		tmp = fread(editString2, sizeof(char), l, in);
--		editString2[(int)l]='\0';
-+		tmp = fread(&l_int, sizeof(int), 1, in);
-+		tmp = fread(editString2, sizeof(char), l_int, in);
-+		editString2[l_int]='\0';
- 	
- 		convertMDCigarToMatrix(cigar1, strlen(cigar1), editString1, strlen(editString1), tmp_matrix1);
- 		convertMDCigarToMatrix(cigar2, strlen(cigar2), editString2, strlen(editString2), tmp_matrix2);
diff --git a/sci-biology/mrfast/metadata.xml b/sci-biology/mrfast/metadata.xml
index 3302123e5..fc7c76942 100644
--- a/sci-biology/mrfast/metadata.xml
+++ b/sci-biology/mrfast/metadata.xml
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<maintainer>
-		<email>weaver@gentoo.org</email>
-		<name>Andrey Kislyuk</name>
-	</maintainer>
-	<herd>sci-biology</herd>
+  <maintainer>
+    <email>weaver@gentoo.org</email>
+    <name>Andrey Kislyuk</name>
+  </maintainer>
+  <herd>sci-biology</herd>
 </pkgmetadata>
diff --git a/sci-biology/mrfast/mrfast-2.1.0.3.ebuild b/sci-biology/mrfast/mrfast-2.6.0.1.ebuild
index b04437fdf..896fbeaa6 100644
--- a/sci-biology/mrfast/mrfast-2.1.0.3.ebuild
+++ b/sci-biology/mrfast/mrfast-2.6.0.1.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2014 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=4
+EAPI=5
 
-inherit base
+inherit eutils toolchain-funcs
 
 DESCRIPTION="Micro Read Fast Alignment Search Tool"
 HOMEPAGE="http://mrfast.sourceforge.net/"
@@ -15,16 +15,17 @@ SLOT="0"
 IUSE=""
 KEYWORDS="~amd64"
 
-DEPEND=""
-RDEPEND=""
-
-PATCHES=("${FILESDIR}"/${P}-*.patch)
-
 src_prepare() {
-	base_src_prepare
-	sed -i -e 's/CFLAGS =/CFLAGS +=/' -e 's/LDFLAGS =/LDFLAGS +=/' Makefile
+	sed \
+		-e '/^CC/s:=:?=:g' \
+		-e 's/CFLAGS =/CFLAGS +=/' \
+		-e 's/LDFLAGS/LIBS/g' \
+		-e 's:-O3.*::g' \
+		-e 's:$(CC) $(OBJECTS):$(CC) $(LDFLAGS) $(OBJECTS):g' \
+		-i Makefile || die
+	tc-export CC
 }
 
 src_install() {
-	dobin mrfast
+	dobin ${PN}
 }