sci-biology/lastz: Version BUmp; fix license; bump to EAPI=5; fix buildsystem

Package-Manager: portage-2.2.0_alpha179

5 files changed, 77 insertions, 19 deletions

diff --git a/sci-biology/lastz/ChangeLog b/sci-biology/lastz/ChangeLog
index 8c73100f2..97e871bc3 100644
--- a/sci-biology/lastz/ChangeLog
+++ b/sci-biology/lastz/ChangeLog
@@ -1,7 +1,17 @@
 # ChangeLog for sci-biology/lastz
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  12 Jun 2013; Justin Lecher <jlec@gentoo.org> -lastz-1.02.00.ebuild,
+  +lastz-1.03.34.ebuild, +files/lastz-1.03.34-build.patch, metadata.xml:
+  Version BUmp; fix license; bump to EAPI=5; fix buildsystem
+
+*lastz-1.03.34 (12 Jun 2013)
+
+  12 Jun 2013; Justin Lecher <jlec@gentoo.org> -lastz-1.02.00.ebuild,
+  +lastz-1.03.34.ebuild, +files/lastz-1.03.34-build.patch, metadata.xml:
+  Version BUmp; fix license; bump to EAPI=5; fix buildsystem
+
 *lastz-1.02.00 (16 Jan 2012)
 
   16 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/lastz/Manifest b/sci-biology/lastz/Manifest
index d9ecafa01..68cf4df31 100644
--- a/sci-biology/lastz/Manifest
+++ b/sci-biology/lastz/Manifest
@@ -1,2 +1 @@
-DIST lastz-1.02.00.tar.gz 1827527 SHA256 054515f27fdf9392f3d2e84ca421103b5e5575ba7a1979addf3c277212114a21 SHA512 5507f511b98ee3d90af08120c6a41b6606c1c71f458c043f4ee85e2ff8108fb2d02b31c347fd6f211b49fb97aeac0ff1ed5f96895644c7cd94918ac57073ee0c WHIRLPOOL 242a9fecaf57b71b2c3a50033a01e9f12083bc56e3c9945102d8a789f0d4476d0c66ea2b78ce870e914f095409bb1c3b7ac3a5fbee94c7a59a05e351786a22d5
-DIST lav_format.html 11901 SHA256 81949a94b4864481cd1c48c4fac413765ada74b6f5b8a9577684399af8472408 SHA512 93fc8d7b45f893beebb23ff2be10d4352691c6bd93b9ecc5750fdd37f10038f91a644f57e95653b9138e14a2344e124d3ca543e0beeabc5fa922194374659b96 WHIRLPOOL 403110222223787abaa0034a1496f63b5cf115a3abeb9609e77130545ff4d1fbf6193909a820b25e78e011bd5f0340171b82a11e928bc7a8900377674c49b3e2
+DIST lastz-1.03.34.tar.gz 716550 SHA256 b831cfb7dabf85e2f9bf33a76641481ede0d18a941c3a72d57d373b018232fbf SHA512 a29d27cd718c99762397f985ad9320e9cec9b288f94b766224f904abaa6793d4557cc253e82f568223c6a256c35e357c51d29ba89a0af3c915a82f27fadaaf1f WHIRLPOOL 4f3939005aaad44042ca219138355c02b95c6e7f182d4f11ad810a27625044a29075815efefb419aa8476be6cd9cf553d0e07f8a59a0a0fc74dd2bba77f1e9bd
diff --git a/sci-biology/lastz/files/lastz-1.03.34-build.patch b/sci-biology/lastz/files/lastz-1.03.34-build.patch
new file mode 100644
index 000000000..bc3a8c033
--- /dev/null
+++ b/sci-biology/lastz/files/lastz-1.03.34-build.patch
@@ -0,0 +1,43 @@
+ src/Makefile | 11 ++++++-----
+ 1 file changed, 6 insertions(+), 5 deletions(-)
+
+diff --git a/src/Makefile b/src/Makefile
+index f628f3c..5bb11bf 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,7 +1,7 @@
+ include ../make-include.mak
+ include version.mak
+ 
+-CC=gcc
++CC?=gcc
+ 
+ # default targets
+ 
+@@ -48,7 +48,8 @@ VERSION_FLAGS= \
+ 	-DSUBVERSION_REV="\"${SUBVERSION_REV}"\"
+ 
+ 
+-CFLAGS = -O3 ${definedForAll} ${VERSION_FLAGS}
++CFLAGS ?= -O3 ${definedForAll}
++CFLAGS += ${VERSION_FLAGS}
+ 
+ 
+ srcFiles = lastz infer_scores \
+@@ -78,13 +79,13 @@ incFiles = lastz.h infer_scores.h \
+ 
+ 
+ lastz: $(foreach part,${srcFiles},${part}.o)
+-	$(CC) $(foreach part,${srcFiles},${part}.o) -lm -o $@
++	$(CC) $(LDFLAGS) $(foreach part,${srcFiles},${part}.o) -lm -o $@
+ 
+ lastz_D: $(foreach part,${srcFiles},${part}_D.o)
+-	$(CC) $(foreach part,${srcFiles},${part}_D.o) -lm -o $@
++	$(CC) $(LDFLAGS) $(foreach part,${srcFiles},${part}_D.o) -lm -o $@
+ 
+ lastz_32: $(foreach part,${srcFiles},${part}_32.o)
+-	$(CC) $(foreach part,${srcFiles},${part}_32.o) -lm -o $@
++	$(CC) $(LDFLAGS) $(foreach part,${srcFiles},${part}_32.o) -lm -o $@
+ 
+ # cleanup
+ 
diff --git a/sci-biology/lastz/lastz-1.02.00.ebuild b/sci-biology/lastz/lastz-1.03.34.ebuild
index 233691f6d..7fd8e4ed2 100644
--- a/sci-biology/lastz/lastz-1.02.00.ebuild
+++ b/sci-biology/lastz/lastz-1.03.34.ebuild
@@ -1,27 +1,33 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-EAPI=3
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
 
 DESCRIPTION="A pairwise DNA sequence aligner (also chromosome to chromosome), a BLASTZ replacement"
 HOMEPAGE="http://www.bx.psu.edu/~rsharris/lastz/"
-SRC_URI="http://www.bx.psu.edu/miller_lab/dist/lastz-"${PV}".tar.gz
-		http://www.bx.psu.edu/miller_lab/dist/lav_format.html"
+SRC_URI="http://www.bx.psu.edu/~rsharris/lastz/newer/${P}.tar.gz"
 
-LICENSE=""
 SLOT="0"
-#KEYWORDS="~amd64 ~x86"
-KEYWORDS=""
+LICENSE="all-rights-reserved"
+KEYWORDS="~amd64 ~x86"
 IUSE=""
 
-DEPEND=""
-RDEPEND="${DEPEND}"
-
 S="${WORKDIR}"/lastz-distrib-"${PV}"
 
+RESTRICT="mirror"
+
+src_prepare() {
+	append-lfs-flags
+	epatch "${FILESDIR}"/${P}-build.patch
+
+	tc-export CC
+}
+
 src_install(){
 	dobin src/lastz src/lastz_D
 	dodoc README.lastz.html
-	dodoc "${DISTDIR}"/lav_format.html
+	dohtml lav_format.html
 }
diff --git a/sci-biology/lastz/metadata.xml b/sci-biology/lastz/metadata.xml
index 07b525505..2bc893037 100644
--- a/sci-biology/lastz/metadata.xml
+++ b/sci-biology/lastz/metadata.xml
@@ -1,9 +1,9 @@
 <?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@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
 </pkgmetadata>