Version bump

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

diff --git a/sci-biology/eugene/ChangeLog b/sci-biology/eugene/ChangeLog
index 2e8c04b8fd9e5069da47dafb77e55ccece25fa63..87f2b44aaaf43d0ac72be9bd98efbe34f055532a 100644 (file)
--- a/sci-biology/eugene/ChangeLog
+++ b/sci-biology/eugene/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/eugene
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/ChangeLog,v 1.4 2009/10/31 17:58:24 maekke Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/ChangeLog,v 1.5 2010/05/07 19:31:27 weaver Exp $
+
+*eugene-3.6 (07 May 2010)
+
+  07 May 2010; Andrey Kislyuk <weaver@gentoo.org> -eugene-3.5d.ebuild,
+  +eugene-3.6.ebuild:
+  Version bump
 
   31 Oct 2009; Markus Meier <maekke@gentoo.org> eugene-3.5g.ebuild:
   amd64/x86 stable, bug #290937

diff --git a/sci-biology/eugene/eugene-3.5d.ebuild b/sci-biology/eugene/eugene-3.6.ebuild
similarity index 64%
rename from sci-biology/eugene/eugene-3.5d.ebuild
rename to sci-biology/eugene/eugene-3.6.ebuild
index 6cb3ba3f02df335a451d58b7088392f541debdfd..95144de428a17852a3d3adc2f8ea8233e39e07d2 100644 (file)
--- a/sci-biology/eugene/eugene-3.5d.ebuild
+++ b/sci-biology/eugene/eugene-3.6.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/eugene-3.5d.ebuild,v 1.4 2009/09/09 21:58:14 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/eugene/eugene-3.6.ebuild,v 1.1 2010/05/07 19:31:27 weaver Exp $
 
 EAPI=2
 
@@ -8,12 +8,14 @@ inherit autotools
 
 DESCRIPTION="Eukaryotic gene predictor"
 HOMEPAGE="http://www.inra.fr/mia/T/EuGene/"
-SRC_URI="http://mulcyber.toulouse.inra.fr/gf/download/frsrelease/220/3675/${P}-1.tar.gz"
+# self-signed https SRC_URI
+#SRC_URI="http://mulcyber.toulouse.inra.fr/gf/download/frsrelease/220/3675/${P}-1.tar.gz"
+SRC_URI="mirror://gentoo/${P}.tar.gz"
 
 LICENSE="Artistic"
 SLOT="0"
 IUSE="doc"
-KEYWORDS="amd64 x86"
+KEYWORDS="~amd64 ~x86"
 
 RESTRICT="test"
 
@@ -26,11 +28,7 @@ DEPEND="media-libs/gd[png]
                )"
 RDEPEND="${DEPEND}"
 
-S="${WORKDIR}/${P}-1"
-
-src_unpack() {
-       unpack ${A}
-       cd "${S}"
+src_prepare() {
        if ( ! use doc ); then
                sed -i -e '/SUBDIRS/ s/doc//' \
                        -e '/INSTALL.*doc/ s/\(.*\)//' \

diff --git a/sci-biology/last/ChangeLog b/sci-biology/last/ChangeLog
index c5690010469e368fb0c909d68523f6c3e9f35c87..fe4f969d1ee49d8f3ca31b2f6b0a0d9bb6a89f87 100644 (file)
--- a/sci-biology/last/ChangeLog
+++ b/sci-biology/last/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/last
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/last/ChangeLog,v 1.4 2010/04/05 12:10:02 phajdan.jr Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/last/ChangeLog,v 1.5 2010/05/07 19:35:18 weaver Exp $
+
+*last-103 (07 May 2010)
+
+  07 May 2010; Andrey Kislyuk <weaver@gentoo.org> +last-103.ebuild:
+  Version bump
 
   05 Apr 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org> last-96.ebuild:
   x86 stable wrt bug #311831

diff --git a/sci-biology/last/last-103.ebuild b/sci-biology/last/last-103.ebuild
new file mode 100644 (file)
index 0000000..ede712f
--- /dev/null
+++ b/sci-biology/last/last-103.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/last/last-103.ebuild,v 1.1 2010/05/07 19:35:18 weaver Exp $
+
+EAPI="2"
+
+DESCRIPTION="Genome-scale comparison of biological sequences"
+HOMEPAGE="http://last.cbrc.jp/"
+SRC_URI="http://last.cbrc.jp/archive/${P}.zip"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="app-arch/unzip"
+RDEPEND=""
+
+src_prepare() {
+       sed -i -e 's/CXXFLAGS =/CXXFLAGS +=/' -e 's/CCFLAGS =/CCFLAGS = ${CFLAGS}/' \
+               src/makefile || die
+}
+
+src_compile() {
+       emake -C src || die
+}
+
+src_install() {
+       dobin src/last{al,db} || die
+       exeinto /usr/share/${PN}/scripts
+       doexe scripts/* || die
+       insinto /usr/share/doc/${PF}
+       doins -r doc ChangeLog.txt README.txt
+}

diff --git a/sci-biology/meme/ChangeLog b/sci-biology/meme/ChangeLog
index e136263f832122ab6e45486456beb3aa9d18a3f9..990b4987db5eaa8a99573e243b37b698d7a63eba 100644 (file)
--- a/sci-biology/meme/ChangeLog
+++ b/sci-biology/meme/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/meme
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.14 2010/03/07 20:56:03 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.15 2010/05/07 19:40:14 weaver Exp $
+
+*meme-4.4.0 (07 May 2010)
+
+  07 May 2010; Andrey Kislyuk <weaver@gentoo.org> -meme-4.2.0.ebuild,
+  +meme-4.4.0.ebuild:
+  Version bump
 
 *meme-4.3.0-r1 (07 Mar 2010)
 

diff --git a/sci-biology/meme/meme-4.2.0.ebuild b/sci-biology/meme/meme-4.4.0.ebuild
similarity index 85%
rename from sci-biology/meme/meme-4.2.0.ebuild
rename to sci-biology/meme/meme-4.4.0.ebuild
index 373cbbf7c0a121546a9eb4f0f97c2dfc01d1b560..bfde3f36c95dfe13023300978e9eae5fa5bf8a36 100644 (file)
--- a/sci-biology/meme/meme-4.2.0.ebuild
+++ b/sci-biology/meme/meme-4.4.0.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-4.2.0.ebuild,v 1.1 2009/09/19 00:00:39 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-4.4.0.ebuild,v 1.1 2010/05/07 19:40:14 weaver Exp $
 
 EAPI="2"
 
@@ -12,7 +12,7 @@ SRC_URI="http://meme.nbcr.net/downloads/${PN}_${PV}.tar.gz"
 LICENSE="meme"
 
 SLOT="0"
-KEYWORDS="~x86 ~amd64"
+KEYWORDS="~amd64 ~x86"
 
 IUSE="mpi"
 
@@ -59,5 +59,6 @@ src_install() {
 #}
 
 src_test() {
-       make test || die "Regression tests failed."
+       # bug #297070
+       emake -j1 test || die "Regression tests failed."
 }