Rewrite, commit split 1.6.0 packages and live ebuilds for packages in 1.6.0 release. Bug 179110.

Package-Manager: portage-2.2_rc20/cvs/Linux 2.6.26-gentoo-r4 x86_64

5 files changed, 112 insertions, 43 deletions

diff --git a/sci-biology/bioperl/ChangeLog b/sci-biology/bioperl/ChangeLog
index 8866e83267e3..5ca66c5ff89d 100644
--- a/sci-biology/bioperl/ChangeLog
+++ b/sci-biology/bioperl/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/bioperl
 # Copyright 2002-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/ChangeLog,v 1.33 2009/03/13 00:41:34 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/ChangeLog,v 1.34 2009/03/16 23:37:10 weaver Exp $
+
+*bioperl-9999 (16 Mar 2009)
+*bioperl-1.6.0-r1 (16 Mar 2009)
+
+  16 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> -bioperl-1.6.0.ebuild,
+  +bioperl-1.6.0-r1.ebuild, +bioperl-9999.ebuild:
+  Rewrite, commit split 1.6.0 packages and live ebuilds for packages in 1.6.0
+  release. Bug 179110.
 
 *bioperl-1.6.0 (12 Mar 2009)
 
diff --git a/sci-biology/bioperl/Manifest b/sci-biology/bioperl/Manifest
index 1abac3d3601c..b8e4ee17c6eb 100644
--- a/sci-biology/bioperl/Manifest
+++ b/sci-biology/bioperl/Manifest
@@ -3,6 +3,7 @@ DIST bioperl-1.4.tar.bz2 4224508 RMD160 657170cc17655f2ab9ed5f6509cac5ae7eedd2c3
 DIST bioperl-1.5.1.tar.bz2 5538613 RMD160 422bdd0dc17dd246ec1fc3ae6fe020705111892d SHA1 9841a458fd928eb9715f14eb686c7b1af3a379e7 SHA256 696c8bd162bc79fa3c75eeb63bb42f8cbcbb4b72de4dcb3bec7ea7a293506f6c
 EBUILD bioperl-1.4.ebuild 1144 RMD160 7e3108360f973a5199cfe5d89471980fdf475813 SHA1 da03c6457bb8feefd939ec532c0292a31eeb3c57 SHA256 1f9f7fba2480c392b99e860af10910a881e39af8123540bc8e7e6ccf206cf741
 EBUILD bioperl-1.5.1-r1.ebuild 1191 RMD160 1ad0bd41869118ce4482427e7de56829f7fe22ce SHA1 c50b157d571897c896b678d6456f0f7bbed3b60b SHA256 bdee9659d5d464c2339678c1854bac42cf83e900d20380d6c4c3f1ff1606d504
-EBUILD bioperl-1.6.0.ebuild 1955 RMD160 5249a93a59e82cc8c1ee6bc710f2db3321b3cecd SHA1 f0af78d90550ed62fb468583f4b6a3a0fd86f8dc SHA256 6390540fa0672a0e8fc28e2af8ed20e5d502e44bf9d6d4f3393bc027ede2b020
-MISC ChangeLog 6698 RMD160 1fb84e6405b34293bbc81ebfec5eb9c4267f1586 SHA1 a23bf4dcaf1bf21195ab6e473c9899addc1809cc SHA256 e378b74e55a8bc6e14c1a8b76815e5903ae4b776d5f0664d3f4d66ee60fa0c47
-MISC metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 SHA1 3c024ca60a2b93ed0e0311f6b05ef5ef117bee31 SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f
+EBUILD bioperl-1.6.0-r1.ebuild 1774 RMD160 0ce87f940879f68a3785fa4bb072617f4bcc975c SHA1 2fa752362a7d85d9957247a35e8cb8a4c9f7bc08 SHA256 f35308db34016cc432ec577b9c867452b02df7c420d0c92a89b95877a7e6ddef
+EBUILD bioperl-9999.ebuild 1788 RMD160 a01f24e3d7e925336fa2d1f68d946eb48cac2256 SHA1 b559e156fb69af8db02481fa3e8780a055e3682d SHA256 6e7cde6379e4f9bf61ec935617b77cca6835ea7ce1cff57c7958b98f97e830f3
+MISC ChangeLog 6984 RMD160 1d7d1afa9f8397fca979da391e47a3f89c7fa68f SHA1 1a346bfa783f97d9909085fcfb4c77cdf47203fa SHA256 be3b28c78227e6e4df0fd20d0eeabebc87eb9a209f26ca133ffd620ad7054b7f
+MISC metadata.xml 454 RMD160 485a08e13f3bf1480491462eb2b9d59ee322cf00 SHA1 3295b47fd6f38269207dd823048886db7d31deb4 SHA256 1ca40160613fa3e9cd4f685dc512959033aea6db29ba8da960ddd26def4b9ef4
diff --git a/sci-biology/bioperl/bioperl-1.6.0.ebuild b/sci-biology/bioperl/bioperl-1.6.0-r1.ebuild
index a4241a881230..bb96818b20e1 100644
--- a/sci-biology/bioperl/bioperl-1.6.0.ebuild
+++ b/sci-biology/bioperl/bioperl-1.6.0-r1.ebuild
@@ -1,10 +1,12 @@
 # Copyright 1999-2009 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.6.0.ebuild,v 1.1 2009/03/13 00:41:34 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-1.6.0-r1.ebuild,v 1.1 2009/03/16 23:37:10 weaver Exp $
 
-EAPI="1"
+EAPI="2"
 
-inherit perl-module eutils
+inherit perl-module
+
+SUBPROJECTS="+db +network +run"
 
 DESCRIPTION="Perl tools for bioinformatics - Core modules"
 HOMEPAGE="http://www.bioperl.org/"
@@ -13,40 +15,24 @@ SRC_URI="http://www.bioperl.org/DIST/BioPerl-${PV}.tar.bz2"
 LICENSE="Artistic GPL-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="-minimal graphviz"
+IUSE="-minimal graphviz ${SUBPROJECTS}"
 
-# FIXME: Unhandled deps:
-# >=dev-lang/perl-5.10.0 (includes cpan >= 1.81)
-# dev-perl/SVG-Graph
-# dev-perl/Ace
-# dev-perl/Bio-ASN1-EntrezGene
-# dev-perl/XML-DOM-XPath
-# dev-perl/Convert-Binary-C
-# Deprecated/unrecognized deps from 1.5 series (to be verified):
-#virtual/perl-File-Temp
-#dev-perl/IO-String
-#dev-perl/IO-stringy
-#virtual/perl-Storable
-#dev-perl/libxml-perl
-#dev-perl/Text-Shellwords
-#~sci-libs/io_lib-1.8.12b
-#!>=sci-libs/io_lib-1.9
-#	gd? (
-#			>=dev-perl/GD-1.32-r1
-#			dev-perl/SVG
-#			dev-perl/GD-SVG
-#		)
-#	mysql? ( >=dev-perl/DBD-mysql-2.1004-r3 )"
+# TODO: SVG::Graph, Convert::Binary::C
 
 DEPEND="virtual/perl-Module-Build
 	dev-perl/Data-Stag
 	dev-perl/libwww-perl
 	!minimal? (
+		dev-perl/Ace
+		dev-perl/Bio-ASN1-EntrezGene
 		dev-perl/Spreadsheet-ParseExcel
+		dev-perl/Spreadsheet-WriteExcel
 		>=dev-perl/XML-SAX-0.15
 		dev-perl/Graph
 		dev-perl/SOAP-Lite
 		dev-perl/Array-Compare
+		dev-perl/SVG
+		dev-perl/XML-Simple
 		dev-perl/XML-Parser
 		dev-perl/XML-Twig
 		>=dev-perl/HTML-Parser-3.60
@@ -55,29 +41,27 @@ DEPEND="virtual/perl-Module-Build
 		dev-perl/XML-DOM
 		dev-perl/set-scalar
 		dev-perl/XML-XPath
+		dev-perl/XML-DOM-XPath
 		dev-perl/Algorithm-Munkres
 		dev-perl/Data-Stag
 		dev-perl/Math-Random
 		dev-perl/PostScript
-		)
+	)
 	graphviz? ( dev-perl/GraphViz )"
 
 RDEPEND="${DEPEND}"
+PDEPEND="
+	db? ( >=sci-biology/bioperl-db-${PV} )
+	network? ( >=sci-biology/bioperl-network-${PV} )
+	run? ( >=sci-biology/bioperl-run-${PV} )"
 
 S="${WORKDIR}/BioPerl-${PV}"
 
-src_unpack() {
-	unpack ${A}
-	sed -i "/'CPAN' *=> *1.81/d" "${S}/Build.PL" || die
-}
-
-src_compile() {
-	yes "" | perl Makefile.PL ${myconf} \
-	         PREFIX=${D}/usr INSTALLDIRS=vendor || die
-}
-
-src_test() {
-	make test || die "Tests failed."
+src_configure() {
+	sed -i -e '/add_post_install_script.*symlink_script.pl/d' \
+		-e "/'CPAN' *=> *1.81/d" "${S}/Build.PL" || die
+	if use minimal && use graphviz; then die "USE flags minimal and graphviz cannot be used together"; fi
+	perl-module_src_configure
 }
 
 src_install() {
diff --git a/sci-biology/bioperl/bioperl-9999.ebuild b/sci-biology/bioperl/bioperl-9999.ebuild
new file mode 100644
index 000000000000..be107a8fbbdb
--- /dev/null
+++ b/sci-biology/bioperl/bioperl-9999.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/bioperl/bioperl-9999.ebuild,v 1.1 2009/03/16 23:37:10 weaver Exp $
+
+EAPI="2"
+
+inherit perl-module subversion
+
+SUBPROJECTS="+db +network +run"
+
+DESCRIPTION="Perl tools for bioinformatics - Core modules"
+HOMEPAGE="http://www.bioperl.org/"
+SRC_URI=""
+ESVN_REPO_URI="svn://code.open-bio.org/bioperl/bioperl-live/trunk"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE="-minimal graphviz ${SUBPROJECTS}"
+
+# TODO: SVG::Graph, Convert::Binary::C
+
+DEPEND="virtual/perl-Module-Build
+	dev-perl/Data-Stag
+	dev-perl/libwww-perl
+	!minimal? (
+		dev-perl/Ace
+		dev-perl/Bio-ASN1-EntrezGene
+		dev-perl/Spreadsheet-ParseExcel
+		dev-perl/Spreadsheet-WriteExcel
+		>=dev-perl/XML-SAX-0.15
+		dev-perl/Graph
+		dev-perl/SOAP-Lite
+		dev-perl/Array-Compare
+		dev-perl/SVG
+		dev-perl/XML-Simple
+		dev-perl/XML-Parser
+		dev-perl/XML-Twig
+		>=dev-perl/HTML-Parser-3.60
+		>=dev-perl/XML-Writer-0.4
+		dev-perl/Clone
+		dev-perl/XML-DOM
+		dev-perl/set-scalar
+		dev-perl/XML-XPath
+		dev-perl/XML-DOM-XPath
+		dev-perl/Algorithm-Munkres
+		dev-perl/Data-Stag
+		dev-perl/Math-Random
+		dev-perl/PostScript
+	)
+	graphviz? ( dev-perl/GraphViz )"
+
+RDEPEND="${DEPEND}"
+PDEPEND="
+	db? ( >=sci-biology/bioperl-db-${PV} )
+	network? ( >=sci-biology/bioperl-network-${PV} )
+	run? ( >=sci-biology/bioperl-run-${PV} )"
+
+S="${WORKDIR}/BioPerl-${PV}"
+
+src_configure() {
+	sed -i -e '/add_post_install_script.*symlink_script.pl/d' \
+		-e "/'CPAN' *=> *1.81/d" "${S}/Build.PL" || die
+	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
+}
diff --git a/sci-biology/bioperl/metadata.xml b/sci-biology/bioperl/metadata.xml
index ebbff811d3b4..30501da524e2 100644
--- a/sci-biology/bioperl/metadata.xml
+++ b/sci-biology/bioperl/metadata.xml
@@ -6,4 +6,9 @@
 		<name>Olivier Fisette</name>
 	</maintainer>
 	<herd>sci-biology</herd>
+	<use>
+		<flag name='run'>Install sci-biology/bioperl-run</flag>
+		<flag name='network'>Install sci-biology/bioperl-run</flag>
+		<flag name='db'>Install sci-biology/bioperl-run</flag>
+	</use>
 </pkgmetadata>