Version bump, drop old

Package-Manager: portage-2.2_rc86/cvs/Linux x86_64

10 files changed, 204 insertions, 103 deletions

diff --git a/sci-biology/bioperl-db/ChangeLog b/sci-biology/bioperl-db/ChangeLog
index 3396f4911eb6..e46952f72394 100644
--- a/sci-biology/bioperl-db/ChangeLog
+++ b/sci-biology/bioperl-db/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/bioperl-db
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-db/ChangeLog,v 1.5 2010/10/17 22:13:33 weaver Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-db/ChangeLog,v 1.6 2011/07/18 06:30:29 weaver Exp $
+
+*bioperl-db-1.6.9 (18 Jul 2011)
+
+  18 Jul 2011; Andrey Kislyuk <weaver@gentoo.org> +bioperl-db-1.6.9.ebuild:
+  Version bump, drop old
 
 *bioperl-db-9999-r1 (17 Oct 2010)
 
diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild
new file mode 100644
index 000000000000..879089a661dd
--- /dev/null
+++ b/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-db/bioperl-db-1.6.9.ebuild,v 1.1 2011/07/18 06:30:29 weaver Exp $
+
+EAPI="2"
+
+BIOPERL_RELEASE=1.6.9
+
+MY_PN=BioPerl-DB
+MODULE_AUTHOR=CJFIELDS
+MODULE_VERSION=1.006900
+inherit perl-module
+
+DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema"
+HOMEPAGE="http://www.bioperl.org/"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+SRC_TEST="do"
+
+CDEPEND=">=sci-biology/bioperl-${PV}
+	dev-perl/DBI
+	sci-biology/biosql"
+DEPEND="virtual/perl-Module-Build
+	${CDEPEND}"
+RDEPEND="${CDEPEND}"
+
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+}
diff --git a/sci-biology/bioperl-network/ChangeLog b/sci-biology/bioperl-network/ChangeLog
index 15318032d607..41c79755c356 100644
--- a/sci-biology/bioperl-network/ChangeLog
+++ b/sci-biology/bioperl-network/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/bioperl-network
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-network/ChangeLog,v 1.5 2010/10/17 22:15:30 weaver Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-network/ChangeLog,v 1.6 2011/07/18 06:30:02 weaver Exp $
+
+*bioperl-network-1.6.9 (18 Jul 2011)
+
+  18 Jul 2011; Andrey Kislyuk <weaver@gentoo.org>
+  +bioperl-network-1.6.9.ebuild:
+  Version bump, drop old
 
 *bioperl-network-9999-r1 (17 Oct 2010)
 
diff --git a/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild
new file mode 100644
index 000000000000..0789f79852e7
--- /dev/null
+++ b/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-network/bioperl-network-1.6.9.ebuild,v 1.1 2011/07/18 06:30:02 weaver Exp $
+
+EAPI="2"
+
+BIOPERL_RELEASE=1.6.9
+
+MY_PN=BioPerl-Network
+MODULE_AUTHOR=CJFIELDS
+MODULE_VERSION=1.006900
+inherit perl-module
+
+DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interaction networks"
+HOMEPAGE="http://www.bioperl.org/"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+SRC_TEST="do"
+
+CDEPEND=">=sci-biology/bioperl-${PV}
+	>=dev-perl/Graph-0.86"
+DEPEND="virtual/perl-Module-Build
+	${CDEPEND}"
+RDEPEND="${CDEPEND}"
+
+src_install() {
+	mydoc="AUTHORS BUGS"
+	perl-module_src_install
+}
diff --git a/sci-biology/bioperl-run/ChangeLog b/sci-biology/bioperl-run/ChangeLog
index 0b7ebd7c5de7..07f848f889bc 100644
--- a/sci-biology/bioperl-run/ChangeLog
+++ b/sci-biology/bioperl-run/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/bioperl-run
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/ChangeLog,v 1.20 2010/10/17 22:18:33 weaver Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/ChangeLog,v 1.21 2011/07/18 06:30:59 weaver Exp $
+
+*bioperl-run-1.6.9 (18 Jul 2011)
+
+  18 Jul 2011; Andrey Kislyuk <weaver@gentoo.org> -bioperl-run-1.4.ebuild,
+  +bioperl-run-1.6.9.ebuild:
+  Version bump, drop old
 
 *bioperl-run-9999-r1 (17 Oct 2010)
 
diff --git a/sci-biology/bioperl-run/bioperl-run-1.4.ebuild b/sci-biology/bioperl-run/bioperl-run-1.4.ebuild
deleted file mode 100644
index 6285d4198e47..000000000000
--- a/sci-biology/bioperl-run/bioperl-run-1.4.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/bioperl-run-1.4.ebuild,v 1.10 2006/10/22 17:38:22 ribosome Exp $
-
-inherit perl-app eutils
-
-DESCRIPTION="Perl tools for bioinformatics - Analysis run modules"
-HOMEPAGE="http://www.bioperl.org/"
-#SRC_URI="http://www.cpan.org/modules/by-module/Bio/${P}.tar.gz"
-SRC_URI="http://www.bioperl.org/ftp/DIST/${P}.tar.gz"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS="x86 ~ppc"
-IUSE=""
-
-RDEPEND="
-	dev-perl/Algorithm-Diff
-	virtual/perl-File-Temp
-	dev-perl/IO-String
-	dev-perl/XML-Parser
-	=sci-biology/bioperl-1.4*"
-
-DEPEND=""
-
-src_compile() {
-	perl-module_src_compile || die "compile failed"
-	# make test
-	#perl-module_src_test || die "src test failed"
-}
-
-src_install() {
-	mydoc="AUTHORS BUGS INSTALL.PROGRAMS README"
-	perl-module_src_install
-
-	# bioperl scripts and examples
-	einfo 'Adding bioperl examples and scripts to /usr/share/...'
-	dodir /usr/share/${PF}/scripts
-	#insinto /usr/share/${PF}/scripts
-	cd "${S}"/scripts/
-	tar cf - ./ | ( cd "${D}"/usr/share/${PF}/scripts; tar xf -)
-	dodir /usr/share/${PF}/examples
-	cd "${S}"/examples/
-	tar cf - ./ | ( cd "${D}"/usr/share/${PF}/examples; tar xf -)
-	cd "${S}"
-}
diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
new file mode 100644
index 000000000000..03269a36d870
--- /dev/null
+++ b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild,v 1.1 2011/07/18 06:30:59 weaver Exp $
+
+EAPI="2"
+
+BIOPERL_RELEASE=1.6.9
+
+MY_PN=BioPerl-Run
+MODULE_AUTHOR=CJFIELDS
+MODULE_VERSION=1.006900
+inherit perl-module
+
+DESCRIPTION="Perl tools for bioinformatics - Wrapper modules around key bioinformatics applications"
+HOMEPAGE="http://www.bioperl.org/"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="-minimal test"
+#SRC_TEST="do"
+
+RESTRICT="test"
+
+CDEPEND=">=sci-biology/bioperl-${BIOPERL_RELEASE}
+	!minimal? (
+		dev-perl/Algorithm-Diff
+		dev-perl/XML-Twig
+		dev-perl/IO-String
+		dev-perl/IPC-Run
+		dev-perl/File-Sort
+	)"
+DEPEND="virtual/perl-Module-Build
+	${CDEPEND}"
+RDEPEND="${CDEPEND}"
+
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+	# TODO: File collision in Bio/ConfigData.pm (a Module::Build internal file)
+	# with sci-biology/bioperl. Workaround: the "nuke it from orbit" solution :D
+	#find "${D}" -name '*ConfigData*' -print -delete
+}
diff --git a/sci-biology/bioperl/ChangeLog b/sci-biology/bioperl/ChangeLog
index 7a71184f13a8..c501c9d360ab 100644
--- a/sci-biology/bioperl/ChangeLog
+++ b/sci-biology/bioperl/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/bioperl
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/ChangeLog,v 1.47 2010/10/17 22:06:04 weaver Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/ChangeLog,v 1.48 2011/07/18 06:31:35 weaver Exp $
+
+*bioperl-1.6.9 (18 Jul 2011)
+
+  18 Jul 2011; Andrey Kislyuk <weaver@gentoo.org> -bioperl-1.4.ebuild,
+  +bioperl-1.6.9.ebuild:
+  Version bump, drop old
 
 *bioperl-9999-r1 (17 Oct 2010)
 
diff --git a/sci-biology/bioperl/bioperl-1.4.ebuild b/sci-biology/bioperl/bioperl-1.4.ebuild
deleted file mode 100644
index 05a4443352c3..000000000000
--- a/sci-biology/bioperl/bioperl-1.4.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2006 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.4.ebuild,v 1.15 2006/10/22 17:25:15 ribosome Exp $
-
-inherit perl-app eutils
-
-DESCRIPTION="Perl tools for bioinformatics - Core modules"
-HOMEPAGE="http://www.bioperl.org/"
-SRC_URI="http://www.${PN}.org/ftp/DIST/${P}.tar.bz2"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS="alpha amd64 ~ia64 ~ppc ~sparc x86"
-IUSE="mysql gd"
-
-DEPEND="virtual/perl-File-Temp
-	dev-perl/HTML-Parser
-	dev-perl/IO-String
-	dev-perl/IO-stringy
-	dev-perl/SOAP-Lite
-	virtual/perl-Storable
-	dev-perl/XML-DOM
-	dev-perl/XML-Parser
-	dev-perl/XML-Writer
-	dev-perl/XML-Twig
-	dev-perl/libxml-perl
-	dev-perl/libwww-perl
-	dev-perl/Graph
-	dev-perl/Text-Shellwords
-	gd? (
-			>=dev-perl/GD-1.32-r1
-			dev-perl/SVG
-			dev-perl/GD-SVG
-		)
-	mysql? ( >=dev-perl/DBD-mysql-2.1004-r3 )"
-
-src_compile() {
-	yes "" | perl Makefile.PL ${myconf} \
-	         PREFIX="${D}"/usr INSTALLDIRS=vendor
-}
-
-src_test() {
-	perl-module_src_test || die "Test failed"
-}
-
-src_install() {
-	mydoc="AUTHORS BUGS FAQ"
-	perl-module_src_install
-}
diff --git a/sci-biology/bioperl/bioperl-1.6.9.ebuild b/sci-biology/bioperl/bioperl-1.6.9.ebuild
new file mode 100644
index 000000000000..14990381aa04
--- /dev/null
+++ b/sci-biology/bioperl/bioperl-1.6.9.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.6.9.ebuild,v 1.1 2011/07/18 06:31:35 weaver Exp $
+
+EAPI="2"
+
+MY_PN=BioPerl
+MODULE_AUTHOR=CJFIELDS
+MODULE_VERSION=1.6.901
+inherit perl-module
+
+SUBPROJECTS="+db +network +run"
+MIN_PV=$PV
+
+DESCRIPTION="Perl tools for bioinformatics - Core modules"
+HOMEPAGE="http://www.bioperl.org/"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="-minimal graphviz sqlite ${SUBPROJECTS}"
+
+CDEPEND="dev-perl/libwww-perl
+	!minimal? (
+		dev-perl/Algorithm-Munkres
+		dev-perl/Array-Compare
+		dev-perl/yaml
+		dev-perl/Clone
+		dev-perl/Convert-Binary-C
+		dev-perl/GD
+		dev-perl/Graph
+		>=dev-perl/HTML-Parser-3.60
+		dev-perl/List-MoreUtils
+		dev-perl/Math-Random
+		dev-perl/PostScript
+		dev-perl/set-scalar
+		dev-perl/SOAP-Lite
+		dev-perl/Sort-Naturally
+		dev-perl/Spreadsheet-ParseExcel
+		>=perl-core/Storable-2.05
+		>=dev-perl/SVG-2.26
+		>=dev-perl/SVG-Graph-0.01
+		dev-perl/URI
+		>=dev-perl/XML-DOM-XPath-0.13
+		dev-perl/XML-Parser
+		>=dev-perl/XML-SAX-0.15
+		dev-perl/XML-Simple
+		dev-perl/XML-Twig
+		>=dev-perl/XML-Writer-0.4
+		dev-perl/XML-DOM
+		dev-perl/XML-XPath
+	)
+	graphviz? ( dev-perl/GraphViz )
+	sqlite? ( dev-perl/DBD-SQLite )"
+DEPEND="virtual/perl-Module-Build
+	${CDEPEND}"
+RDEPEND="${CDEPEND}"
+PDEPEND="db? ( >=sci-biology/bioperl-db-${MIN_PV} )
+	network? ( >=sci-biology/bioperl-network-${MIN_PV} )
+	run? ( >=sci-biology/bioperl-run-${MIN_PV} )"
+
+src_configure() {
+	if use minimal && use graphviz; then die "USE flags minimal and graphviz cannot be used together"; fi
+	perl-module_src_configure
+}
+
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+}