sci-biology/repeatmasker: Version BUmp; cleaned old

Package-Manager: portage-2.2.0_alpha166/cvs/Linux x86_64
Manifest-Sign-Key: 0x70EB7916

6 files changed, 34 insertions, 136 deletions

diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog
index 350da2366896..a6c5baf3f6e9 100644
--- a/sci-biology/repeatmasker/ChangeLog
+++ b/sci-biology/repeatmasker/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/repeatmasker
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker/ChangeLog,v 1.5 2011/02/03 01:34:28 weaver Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker/ChangeLog,v 1.6 2013/03/07 14:53:28 jlec Exp $
+
+*repeatmasker-4.0.1 (07 Mar 2013)
+
+  07 Mar 2013; Justin Lecher <jlec@gentoo.org> -repeatmasker-3.2.7.ebuild,
+  -repeatmasker-3.2.8.ebuild, -repeatmasker-3.2.9.ebuild,
+  +repeatmasker-4.0.1.ebuild, metadata.xml:
+  Version BUmp; cleaned old
 
 *repeatmasker-3.2.9 (03 Feb 2011)
 
diff --git a/sci-biology/repeatmasker/Manifest b/sci-biology/repeatmasker/Manifest
index 783ffd119e36..374510324fbd 100644
--- a/sci-biology/repeatmasker/Manifest
+++ b/sci-biology/repeatmasker/Manifest
@@ -1,8 +1,14 @@
-DIST RepeatMasker-open-3-2-7.tar.gz 11398018 RMD160 63a79ea9146805cc1e7f4cca8b94903136bf2a0c SHA1 22ca2ea2369e1543d58c82954870e114e25c80b9 SHA256 3ceb21658f23780c345d27bb603ef407b953c59dce5b97436a578d28dcb7e477
-DIST RepeatMasker-open-3-2-8.tar.gz 14096137 RMD160 0f8b463bc9d0d8ac71c0d9261ed7161bcaac63f9 SHA1 76684c1fa85049c5c124df718a08d4d21ab684fe SHA256 644c705db9ec239e9a372d0a262548a4a84b58738775f1427021bdbef90a21c1
-DIST RepeatMasker-open-3-2-9.tar.gz 14123559 RMD160 219cb2c2668346d51ddc7c03f63e24064e84968a SHA1 a8df75da847ea64afec2c2f5fcab915d383c7e45 SHA256 60597ac511f2ad37200b80a69c29a4bccfbc7fe697a6400ce19cb6af83dc71d2
-EBUILD repeatmasker-3.2.7.ebuild 1655 RMD160 f36843903117759852420d27c3b75918846df3ff SHA1 a10f55d589c0abf4f106a346623a8565da44752e SHA256 aa304e8c744fb8f875a0804b8b2ca5d492ffb140a100f1bade7e6da42b6c0c09
-EBUILD repeatmasker-3.2.8.ebuild 1655 RMD160 d08c4b1f921bf8026d04af062227c99fbd9c4bc5 SHA1 3995ebad225693aa83f6744ee346555f25c4f950 SHA256 73bc60d01f51809b2bc5ad3186a434b711ccf19bb7fe1a10b73767152873c185
-EBUILD repeatmasker-3.2.9.ebuild 1665 RMD160 2eecf7a2e1e08cc91102620c457d54f41d75446f SHA1 d9243084592bdcce6656febee2f4fe1328514d28 SHA256 a7ca538a466a473444f0f9f180760d4317a3f259d653e8608294823883c21e91
-MISC ChangeLog 1285 RMD160 41cc016eda4f3900dc369eb9ea993ea77455cab2 SHA1 05602ae50f63e50b3efae96ecbb1ccf79403fbff SHA256 590374ed56ca5f2d87606fa383e17acb428230b8e3efde4497e8a10cb9d51a47
-MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
+DIST RepeatMasker-open-4-0-1.tar.gz 84077910 SHA256 638ed02d970052ecb7dac6c71d2cb9625b0a0713df88d46ae78865aa4fd3fc92 SHA512 6b710a02b2964bca6acb25cc918bd56f7caba7b80b3b683972f0584180bf0fd3704f657d7ee341187a4ac86d9883e62eb4f09da237fa8ef1b481137d1a89963e WHIRLPOOL f2d67ea6e97a0667ac9ce89f8ed8c590b911d9cd4fc4482bdc48c0ea7ca07161a8bec267ed3e2a950f6d8c501f992ceadc62e1211a80b6bc1c90d293cbf45e77
+EBUILD repeatmasker-4.0.1.ebuild 1652 SHA256 1a901a3e599eb5651fd95045c2e2674b2aba70db365b0fbc1910789e23978fbf SHA512 6ae68d0d0e82770981bbdc45dc4f296732f18fa2b5306f76a4726042c52b79571ebca64088938f2b205e474bf4c9ee3dd0b7a01e753595dc1385d90ef38b98e7 WHIRLPOOL e4e6619f777f94573349664555eed35706f5138db569928176d6dfdbad90fc32274ae76926033da8af56f614857562e27527147484a1108d216f479b5d5283af
+MISC ChangeLog 1524 SHA256 bfb4ece008080da4dfb20e836e28a7780097116e61372918d5d3e79ffff9dbb2 SHA512 cb5d5242572991f4ef6112c27670d733ec9fd002d7e3f5fdc2cf8fd3e984e4131c35fb4fb825e3215aa994692745f269d839bb04fb83da65b8dffa16406ba04f WHIRLPOOL 2ae75f380f64b224f55af44b21fc1590f8377c50093a1910cd5c9cb831d991aa73452cc06a0ddd8aee279d1dd05781e889e21c4f55d9f1a46344ae02025766fa
+MISC metadata.xml 266 SHA256 98c7d1da8a728a1f1d796a79d51f25e4164e24048ec1aacbbf0ae2ffb171ff35 SHA512 879cdcca092d4c82b8c63672c91e08e7b01e81419d2c7c7b766de96ba2a32dd1e21c18968ed7172eec8604f52c92b19a31773f428bce9461d9b8190384680194 WHIRLPOOL 0f46288ab7090ad3da5b31816792427e4ad1a950e39a503bb406ebe8789cffedd9c85b46bfbf040fffb8aad443f512c28716a0a6436d0c06309155277060cdcd
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.19 (GNU/Linux)
+
+iEYEAREIAAYFAlE4qekACgkQgAnW8HDreRY1BQCgnt0eVyYZnOybr65VY2zlbh+c
+ztsAoJEukVIbHSUxi2RxbQrfcObRc9sC
+=vlhl
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/repeatmasker/metadata.xml b/sci-biology/repeatmasker/metadata.xml
index 3302123e5718..fc7c76942a10 100644
--- a/sci-biology/repeatmasker/metadata.xml
+++ b/sci-biology/repeatmasker/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/repeatmasker/repeatmasker-3.2.7.ebuild b/sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild
deleted file mode 100644
index 9ae733e288f8..000000000000
--- a/sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker/repeatmasker-3.2.7.ebuild,v 1.2 2009/08/17 19:41:31 weaver Exp $
-
-inherit versionator
-
-MY_PV=$(replace_all_version_separators '-')
-
-DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA"
-HOMEPAGE="http://repeatmasker.org/"
-SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz"
-
-LICENSE="OSL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="sci-biology/phrap
-	sci-biology/trf
-	>=sci-biology/repeatmasker-libraries-20090120"
-
-S="${WORKDIR}/RepeatMasker"
-
-src_compile() {
-	sed -i -e 's/system( "clear" );//' \
-		-e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' "${S}/configure" || die
-	echo "
-env
-/usr/share/${PN}
-/usr/bin
-1
-/usr/bin
-Y
-4" | "${S}/configure" || die "configure failed"
-	sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \
-		-e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/\1"|' \
-		-e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \
-		"${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die
-}
-
-src_install() {
-	exeinto /usr/share/${PN}
-	for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do
-		doexe $i
-		dosym /usr/share/${PN}/$i /usr/bin/$i
-	done
-
-	dodir /usr/share/${PN}/lib
-	insinto /usr/share/${PN}/lib
-	doins "${S}"/*.pm
-
-	insinto /usr/share/${PN}
-	doins -r util Matrices Libraries taxonomy.dat
-	keepdir /usr/share/${PN}/Libraries
-
-	dodoc README INSTALL *.help
-}
diff --git a/sci-biology/repeatmasker/repeatmasker-3.2.8.ebuild b/sci-biology/repeatmasker/repeatmasker-3.2.8.ebuild
deleted file mode 100644
index e92b1e77e6b3..000000000000
--- a/sci-biology/repeatmasker/repeatmasker-3.2.8.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker/repeatmasker-3.2.8.ebuild,v 1.1 2009/08/20 13:41:10 weaver Exp $
-
-EAPI="2"
-
-MY_PV=${PV//\./-}
-
-DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity DNA"
-HOMEPAGE="http://repeatmasker.org/"
-SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz"
-
-LICENSE="OSL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="sci-biology/phrap
-	sci-biology/trf
-	>=sci-biology/repeatmasker-libraries-20090604"
-
-S="${WORKDIR}/RepeatMasker"
-
-src_configure() {
-	sed -i -e 's/system( "clear" );//' \
-		-e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|' "${S}/configure" || die
-	echo "
-env
-/usr/share/${PN}
-/usr/bin
-1
-/usr/bin
-Y
-4" | "${S}/configure" || die "configure failed"
-	sed -i -e 's|use lib $FindBin::RealBin;|use lib "/usr/share/'${PN}'/lib";|' \
-		-e 's|".*\(taxonomy.dat\)"|"/usr/share/'${PN}'/\1"|' \
-		-e '/$REPEATMASKER_DIR/ s|$FindBin::RealBin|/usr/share/'${PN}'|' \
-		"${S}"/{DateRepeats,ProcessRepeats,RepeatMasker,DupMasker,RepeatProteinMask,RepeatMaskerConfig.pm,Taxonomy.pm} || die
-}
-
-src_install() {
-	exeinto /usr/share/${PN}
-	for i in DateRepeats ProcessRepeats RepeatMasker DupMasker RepeatProteinMask; do
-		doexe $i || die
-		dosym /usr/share/${PN}/$i /usr/bin/$i || die
-	done
-
-	dodir /usr/share/${PN}/lib
-	insinto /usr/share/${PN}/lib
-	doins "${S}"/*.pm || die
-
-	insinto /usr/share/${PN}
-	doins -r util Matrices Libraries taxonomy.dat *.help || die
-	keepdir /usr/share/${PN}/Libraries
-
-	dodoc README INSTALL *.help
-}
diff --git a/sci-biology/repeatmasker/repeatmasker-3.2.9.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild
index 4b333576eced..7b65ee6fc74a 100644
--- a/sci-biology/repeatmasker/repeatmasker-3.2.9.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker/repeatmasker-3.2.9.ebuild,v 1.1 2011/02/03 01:34:28 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/repeatmasker/repeatmasker-4.0.1.ebuild,v 1.1 2013/03/07 14:53:28 jlec Exp $
 
-EAPI="2"
+EAPI=5
 
 MY_PV=${PV//\./-}
 
@@ -16,9 +16,10 @@ KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 DEPEND=""
-RDEPEND="sci-biology/rmblast
+RDEPEND="
+	sci-biology/rmblast
 	sci-biology/trf
-	>=sci-biology/repeatmasker-libraries-20090604"
+	sci-biology/repeatmasker-libraries"
 
 S="${WORKDIR}/RepeatMasker"