-MD5 9508ce4a5708e17dd4aaa8f5d86decc7 bioperl-pipeline-0.1.ebuild 1954
+MD5 e777f1747bc324266de6a74508572a35 bioperl-pipeline-0.1.ebuild 1958
MD5 bda4eecce29fd270dedec6fd130d2d49 ChangeLog 703
MD5 e8b4df3df76800c376905734d8043cfa metadata.xml 216
MD5 cea8881ae00a651493915c7732732233 files/digest-bioperl-pipeline-0.1 72
+++ /dev/null
-# ChangeLog for app-sci/bioperl
-# Copyright 2002-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/bioperl/ChangeLog,v 1.17 2004/10/30 15:28:15 ribosome Exp $
-
- 30 Oct 2004; Olivier Fisette <ribosome@gentoo.org> bioperl-1.4.ebuild,
- bioperl-1.0.2.ebuild:
- Q.A.: Fixed RDEPEND=$DEPEND, fixed LICENSE.
-
- 03 Aug 2004; David Holm <dholm@gentoo.org> bioperl-1.4.ebuild:
- Added to ~ppc.
-
- 03 Jul 2004; Bryan Østergaard <kloeri@gentoo.org> bioperl-1.4.ebuild:
- Stable on alpha.
-
- 02 Jun 2004; Aron Griffis <agriffis@gentoo.org> bioperl-1.2.2.ebuild,
- bioperl-1.2.3.ebuild:
- Fix use invocation
-
- 05 May 2004; Stephen Diener <sediener@gentoo.org> bioperl-1.4.ebuild:
- bumped 1.4 to stable
-
- 05 May 2004; Bryan Østergaard <kloeri@gentoo.org> bioperl-1.2.ebuild:
- Stable on alpha.
-
- 20 Apr 2004; Bryan Østergaard <kloeri@gentoo.org> bioperl-1.4.ebuild:
- Added ~alpha to keywords.
-
- 14 Jan 2004; Stephen Diener <sediener@gentoo.org> bioperl-1.4.ebuild:
- removed src_test; fixes bug #38169, or at least works around it
-
-*bioperl-1.4 (08 Jan 2004)
-
- 08 Jan 2004; Stephen Diener <sediener@gentoo.org> bioperl-1.4.ebuild:
- version bump
-
- 24 Nov 2003; Stephen Diener <sediener@gentoo.org> bioperl-1.2.3.ebuild:
- bump to stable.
-
-*bioperl-1.2.3 (24 Oct 2003)
-
- 24 Oct 2003; <sediener@gentoo.org> bioperl-1.2.3.ebuild:
- new release added.
-
-*bioperl-1.2.2 (28 Aug 2003)
-
- 28 Aug 2003; Stephen Diener <sediener@gentoo.org> bioperl-1.2.2.ebuild:
- Bumped to stable x86
-
-*bioperl-1.2.2 (02 Aug 2003)
-
- 02 Aug 2003; Stephen Diener <sediener@gentoo.org> bioperl-1.2.2.ebuild,
- files/biodbgff-enable-1.2.2.patch, files/domanpages-1.2.2.patch:
- New Version thanks to Gontran Zepeda <gontran@gontran.net> in bug# 24467 :
- Also fixes bug# 25079
-
-*bioperl-1.2 (24 Apr 2003)
-
- 24 Apr 2003; Jon Portnoy <avenj@gentoo.org> bioperl-1.2.ebuild :
- Version bump, ebuild submitted by Gontran Zepeda <gontran@gontran.net>
- in bug #13826
-
-*bioperl-1.0.2 (21 Dec 2002)
-
- 21 Dec 2002; Michael Cummings <mcummings@gentoo.org>
- bioperl-1.0.2.ebuild:
-
- Initial import. Ebuild submitted by Gontran Zepeda <gontran@gontran.net>
- Bug 11498
+++ /dev/null
-MD5 7e363b2d0a741eca3070d31384dc79f4 bioperl-1.0.2.ebuild 1485
-MD5 78e0ffe0dc39547ccd257274720c5dae bioperl-1.2.3.ebuild 2063
-MD5 489552b0291b2c365cba1d314f8d9554 bioperl-1.2.ebuild 1514
-MD5 f2b9c1b81698a61d2783d18afd33b317 bioperl-1.2.2.ebuild 2178
-MD5 e90784817c0d42b6301d11661bfff929 bioperl-1.4.ebuild 1152
-MD5 043fd61f9f8bcb61afca590109dbf371 ChangeLog 2175
-MD5 e8b4df3df76800c376905734d8043cfa metadata.xml 216
-MD5 8f6c3beb108aaa2b78b0b4f8d218187a files/biodbgff-enable-1.2.2.patch 3355
-MD5 1828ff2ba6225e17a98d27bfbad5c7c9 files/bioperl-1.2-manpage.diff 712
-MD5 8f6c3beb108aaa2b78b0b4f8d218187a files/biodbgff-enable-1.2.3.patch 3355
-MD5 14b9e16331895fe40e231065f7dda942 files/digest-bioperl-1.2 64
-MD5 d5d0bc711fb345c9b91086c5d47e1442 files/digest-bioperl-1.4 65
-MD5 08539f1d1fed6d673140cdc221ae13e6 files/domanpages-1.2.2.patch 412
-MD5 dfdb9921cbef92f60e9746a9531d8de7 files/digest-bioperl-1.0.2 66
-MD5 d8df3477f72bba80de83cfdb5416ecbf files/digest-bioperl-1.2.2 66
-MD5 a67f149bd10684a4b584bcd23282d5bf files/digest-bioperl-1.2.3 67
+++ /dev/null
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/bioperl/bioperl-1.0.2.ebuild,v 1.9 2004/10/30 15:28:15 ribosome Exp $
-
-inherit perl-module
-CATEGORY="app-sci"
-
-DESCRIPTION="collection of tools for bioinformatics, genomics and life science research"
-HOMEPAGE="http://www.bioperl.org/"
-SRC_URI="http://bioperl.org/DIST/${P}.tar.gz"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS="x86 ~ppc ~sparc ~alpha"
-IUSE="mysql gd"
-
-DEPEND="dev-perl/File-Temp
- dev-perl/HTML-Parser
- dev-perl/IO-String
- dev-perl/IO-stringy
- dev-perl/SOAP-Lite
- dev-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/Text-Shellwords
- gd? ( >=dev-perl/GD-1.32-r1 )
- mysql? ( >=dev-perl/DBD-mysql-2.1004-r3 )"
-
-src_compile() {
- # there's a test to run for BioGFFDB if using mysql
- # note: these echo's are for the default values for testing. Not that we're
- # testing.
- use mysql && (
- echo y
- echo test
- echo localhost
- echo undef
- echo undef
- ) | perl-module_src_compile || perl-module_src_compile || die "compile failed"
-
- # Sadly, it's not advisable to run make test for this installation, as the
- # tests are used by the bioperl developers as a sort of todo list. :) IOW,
- # it's OK if some fail.
- #perl-module_src_test || die "test failed"
-}
-
-src_install() {
- mydoc="AUTHORS BUGS FAQ"
- perl-module_src_install
-}
+++ /dev/null
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/bioperl/bioperl-1.2.2.ebuild,v 1.7 2004/06/24 21:52:29 agriffis Exp $
-
-inherit perl-module eutils
-CATEGORY="app-sci"
-
-DESCRIPTION="collection of tools for bioinformatics, genomics and life science research"
-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"
-IUSE="mysql gd"
-
-DEPEND="${DEPEND}
- dev-perl/File-Temp
- dev-perl/HTML-Parser
- dev-perl/IO-String
- dev-perl/IO-stringy
- dev-perl/SOAP-Lite
- dev-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 )
- mysql? ( >=dev-perl/DBD-mysql-2.1004-r3 )"
-
-src_unpack() {
- unpack ${A}
- cd ${S}
- # remove interactiveness
- use mysql && epatch ${FILESDIR}/biodbgff-enable-${PV}.patch
- # want man pages in addition to perldoc documentation??
- #epatch ${FILESDIR}/domanpages-${PV}.patch
-}
-
-src_compile() {
- # there's a test to run for BioGFFDB if using mysql
- perl-module_src_compile || die "compile failed"
- # make test
-## perl-module_src_test || die "src test failed"
-}
-
-src_install() {
- mydoc="AUTHORS BUGS FAQ"
- perl-module_src_install
- # get the bptutorial installed and executeable
- dodir /usr/bin
- dosym /usr/lib/perl5/site_perl/5.8.0/bptutorial.pl /usr/bin/bptutorial.pl
- fperms +x /usr/lib/perl5/site_perl/5.8.0/bptutorial.pl
-
- # 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 ${S}
-
- # some pods in maindir
- eval `perl '-V:installsitelib'`
- MY_SITE_LIB=${installsitelib}
- insinto ${MY_SITE_LIB}
- doins biodatabases.pod biodesign.pod bioperl.pod bioscripts.pod
-}
+++ /dev/null
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/bioperl/bioperl-1.2.3.ebuild,v 1.7 2004/06/24 21:52:29 agriffis Exp $
-
-inherit perl-module eutils
-
-CATEGORY="app-sci"
-
-DESCRIPTION="collection of tools for bioinformatics, genomics and life science research"
-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.bz2"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS="x86"
-IUSE="mysql gd"
-
-DEPEND="${DEPEND}
- dev-perl/File-Temp
- dev-perl/HTML-Parser
- dev-perl/IO-String
- dev-perl/IO-stringy
- dev-perl/SOAP-Lite
- dev-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 )
- mysql? ( >=dev-perl/DBD-mysql-2.1004-r3 )"
-
-src_unpack() {
- unpack ${A}
- cd ${S}
- # remove interactiveness
- use mysql && epatch ${FILESDIR}/biodbgff-enable-${PV}.patch
- # want man pages in addition to perldoc documentation??
- #epatch ${FILESDIR}/domanpages-${PV}.patch
-}
-
-src_compile() {
- # there's a test to run for BioGFFDB if using mysql
- perl-module_src_compile || die "compile failed"
- # make test
-## perl-module_src_test || die "src test failed"
-}
-
-src_install() {
- mydoc="AUTHORS BUGS FAQ"
- perl-module_src_install
-
- # bioperl scripts and examples
- einfo 'Adding bioperl examples and scripts to /usr/share/...'
- dodir /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 -)
- dodir /usr/share/doc/${P}
- cd ${S}
- tar cf - ./ | ( cd ${D}/usr/share/doc/${P}; tar xf -)
-
- # some pods in maindir
- eval `perl '-V:installvendorlib'`
- MY_SITE_LIB=${installvendorlib}/Bio
- insinto ${MY_SITE_LIB}
- doins biodatabases.pod biodesign.pod bioperl.pod bioscripts.pod
-
- dobin bptutorial.pl
-
-}
+++ /dev/null
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/bioperl/bioperl-1.2.ebuild,v 1.7 2004/06/24 21:52:29 agriffis Exp $
-
-inherit perl-module debug
-
-DESCRIPTION="collection of tools for bioinformatics, genomics and life science research"
-HOMEPAGE="http://www.bioperl.org/"
-SRC_URI="http://bioperl.org/ftp/DIST/${P}.tar.gz"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS="x86 ~ppc ~sparc alpha"
-IUSE="mysql gd"
-
-DEPEND="dev-perl/File-Temp
- dev-perl/Graph
- dev-perl/HTML-Parser
- dev-perl/IO-String
- dev-perl/IO-stringy
- dev-perl/Parse-RecDescent
- dev-perl/SOAP-Lite
- dev-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/Text-Shellwords
- gd? ( >=dev-perl/GD-1.32-r1 )
- mysql? ( >=dev-perl/DBD-mysql-2.1004-r3 )"
-
-# uncomment this if you'd like to access bioperl docs via man in addition to
-# perldoc.
-#src_unpack() {
-# unpack ${A}
-# cd ${S}
-# echo
-# einfo " Patching to build manified pods..."
-# echo
-# patch < ${FILESDIR}/${P}-manpage.diff
-#}
-
-src_compile() {
- # note: these echo's give the default values for testing.
- use mysql && (
- echo y
- echo test
- echo localhost
- echo undef
- echo undef
- ) | perl-module_src_compile || perl-module_src_compile || die "compile failed"
-
- # This dies at RootIO.t:
- # perl-module_src_test || die "test failed"
-}
-
-src_install() {
- mydoc="AUTHORS BUGS FAQ"
- perl-module_src_install
-}
+++ /dev/null
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/bioperl/bioperl-1.4.ebuild,v 1.8 2004/10/30 15:28:15 ribosome Exp $
-
-inherit perl-module eutils
-
-CATEGORY="app-sci"
-
-DESCRIPTION="collection of tools for bioinformatics, genomics and life science research"
-HOMEPAGE="http://www.bioperl.org/"
-SRC_URI="http://www.bioperl.org/ftp/DIST/${P}.tar.bz2"
-
-LICENSE="Artistic GPL-2"
-SLOT="0"
-KEYWORDS="x86 alpha ~ppc"
-IUSE="mysql gd"
-
-DEPEND="
- dev-perl/File-Temp
- dev-perl/HTML-Parser
- dev-perl/IO-String
- dev-perl/IO-stringy
- dev-perl/SOAP-Lite
- dev-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
- #perl-module_src_test || die "Test Failed"
-}
-
-src_install() {
- mydoc="AUTHORS BUGS FAQ"
- perl-module_src_install
-}
+++ /dev/null
---- Makefile.PL.orig 2003-07-14 16:09:49.000000000 +0100
-+++ Makefile.PL 2003-07-14 16:15:56.000000000 +0100
-@@ -83,9 +83,6 @@
- # Prompt user for BioDBGFF stuff
- #
-
--if( eval { require DBI } && grep {/mysql/} DBI->available_drivers) {
-- my $proceed = prompt("Do you want to run the BioDBGFF tests (requires a mysql database) y/n",'n');
-- if( $proceed =~ /^[yY]/) {
- my $cfg = {dbd_driver => 'mysql'};
- GFFQueryDb($cfg,{'prompt'=>1,'verbose'=>1});
- if (open T,">t/do_biodbgff.tests") {
-@@ -94,13 +91,6 @@
- }
- close T;
- }
-- } else {
-- if( -e "t/do_biodbgff.tests" ) {
-- unlink "t/do_biodbgff.tests";
-- }
-- }
--}
--
-
- ############################################################################
- #
-@@ -124,55 +114,27 @@
- my $d = lc $driver;
- my $prompt = $options->{'prompt'};
-
-- my $test_db = exists($options->{"$d-test-db"}) ?
-- $options->{"$d-test-db"} : ($cfg->{'test_db'} || 'test');
-- $test_db = prompt
-- ("Which database should I use for testing the $db drivers?",
-- $test_db) if $prompt;
--
-- my $test_host = exists($options->{"$d-test-host"}) ?
-- $options->{"$d-test-host"} : ($cfg->{'test_host'} || 'localhost');
-- $test_host = prompt
-- ("On which host is database $test_db running (hostname, ip address or host:port)", $test_host) if $prompt;
--
-- my($test_user, $test_pass);
--
-- $test_user = exists($options->{"$d-test-user"}) ?
-- $options->{"$d-test-user"} : ($cfg->{'test_user'} || "undef");
-- $test_user = prompt
-- ("User name for connecting to database $test_db?", $test_user)
-- if $prompt;
-- $test_user = undef if $test_user eq 'undef';
--
-- $test_pass = exists($options->{"$d-test-pass"}) ?
-- $options->{"$d-test-pass"} : ($cfg->{'test_pass'} || "undef");
-- $test_pass = prompt
-- ("Password for connecting to database $test_db?", $test_pass)
-- if $prompt;
-- $test_pass = undef if $test_pass eq 'undef';
--
-- $cfg->{'test_db'} = $test_db;
-- $cfg->{'test_host'} = $test_host;
-- $cfg->{'test_user'} = $test_user;
-- $cfg->{'test_pass'} = $test_pass;
-- if ($test_host eq 'undef' || $test_host eq 'localhost') {
-- $test_host = '';
-- }
-- my $test_dsn = "DBI:$driver:database=$test_db";
-- $cfg->{test_dsn} = $test_dsn;
-- if ($test_host) {
-- $cfg->{'test_dsn'} .= ";host=$test_host";
-- }
-+ $options->{"$d-test-db"} = 'test';
-+ $options->{"$d-test-host"} = 'localhost';
-+ $options->{"$d-test-user"} = n0b0dy;
-+ $options->{"$d-test-pass"} = undef;
-+
-+ $cfg->{'test_db'} = $options->{"$d-test-db"};
-+ $cfg->{'test_host'} = $options->{"$d-test-host"};
-+ $cfg->{'test_user'} = $options->{"$d-test-user"};
-+ $cfg->{'test_pass'} = $options->{"$d-test-pass"};
-
-+ my $test_dsn = "DBI:$driver:database=" . $cfg->{test_db};
-+ $cfg->{'test_dsn'} = $test_dsn;
-
- if ($options->{'verbose'}) {
- local $^W=0; # some uninitialized variable warning coming through
- print("Driver $driver is using the following settings for tests:\n",
-- " Database $test_db\n",
-- " Host $test_host\n",
-- " DSN $test_dsn\n",
-- " User $test_user\n",
-- " Password $test_pass\n");
-+ " Database ".$cfg->{test_db}. "\n",
-+ " Host ".$cfg->{test_host}."\n",
-+ " DSN ".$cfg->{test_dsn}. "\n",
-+ " User ".$cfg->{test_user}."\n",
-+ " Password ".$cfg->{test_pass}."\n");
- }
- }
-
+++ /dev/null
---- Makefile.PL.orig 2003-07-14 16:09:49.000000000 +0100
-+++ Makefile.PL 2003-07-14 16:15:56.000000000 +0100
-@@ -83,9 +83,6 @@
- # Prompt user for BioDBGFF stuff
- #
-
--if( eval { require DBI } && grep {/mysql/} DBI->available_drivers) {
-- my $proceed = prompt("Do you want to run the BioDBGFF tests (requires a mysql database) y/n",'n');
-- if( $proceed =~ /^[yY]/) {
- my $cfg = {dbd_driver => 'mysql'};
- GFFQueryDb($cfg,{'prompt'=>1,'verbose'=>1});
- if (open T,">t/do_biodbgff.tests") {
-@@ -94,13 +91,6 @@
- }
- close T;
- }
-- } else {
-- if( -e "t/do_biodbgff.tests" ) {
-- unlink "t/do_biodbgff.tests";
-- }
-- }
--}
--
-
- ############################################################################
- #
-@@ -124,55 +114,27 @@
- my $d = lc $driver;
- my $prompt = $options->{'prompt'};
-
-- my $test_db = exists($options->{"$d-test-db"}) ?
-- $options->{"$d-test-db"} : ($cfg->{'test_db'} || 'test');
-- $test_db = prompt
-- ("Which database should I use for testing the $db drivers?",
-- $test_db) if $prompt;
--
-- my $test_host = exists($options->{"$d-test-host"}) ?
-- $options->{"$d-test-host"} : ($cfg->{'test_host'} || 'localhost');
-- $test_host = prompt
-- ("On which host is database $test_db running (hostname, ip address or host:port)", $test_host) if $prompt;
--
-- my($test_user, $test_pass);
--
-- $test_user = exists($options->{"$d-test-user"}) ?
-- $options->{"$d-test-user"} : ($cfg->{'test_user'} || "undef");
-- $test_user = prompt
-- ("User name for connecting to database $test_db?", $test_user)
-- if $prompt;
-- $test_user = undef if $test_user eq 'undef';
--
-- $test_pass = exists($options->{"$d-test-pass"}) ?
-- $options->{"$d-test-pass"} : ($cfg->{'test_pass'} || "undef");
-- $test_pass = prompt
-- ("Password for connecting to database $test_db?", $test_pass)
-- if $prompt;
-- $test_pass = undef if $test_pass eq 'undef';
--
-- $cfg->{'test_db'} = $test_db;
-- $cfg->{'test_host'} = $test_host;
-- $cfg->{'test_user'} = $test_user;
-- $cfg->{'test_pass'} = $test_pass;
-- if ($test_host eq 'undef' || $test_host eq 'localhost') {
-- $test_host = '';
-- }
-- my $test_dsn = "DBI:$driver:database=$test_db";
-- $cfg->{test_dsn} = $test_dsn;
-- if ($test_host) {
-- $cfg->{'test_dsn'} .= ";host=$test_host";
-- }
-+ $options->{"$d-test-db"} = 'test';
-+ $options->{"$d-test-host"} = 'localhost';
-+ $options->{"$d-test-user"} = n0b0dy;
-+ $options->{"$d-test-pass"} = undef;
-+
-+ $cfg->{'test_db'} = $options->{"$d-test-db"};
-+ $cfg->{'test_host'} = $options->{"$d-test-host"};
-+ $cfg->{'test_user'} = $options->{"$d-test-user"};
-+ $cfg->{'test_pass'} = $options->{"$d-test-pass"};
-
-+ my $test_dsn = "DBI:$driver:database=" . $cfg->{test_db};
-+ $cfg->{'test_dsn'} = $test_dsn;
-
- if ($options->{'verbose'}) {
- local $^W=0; # some uninitialized variable warning coming through
- print("Driver $driver is using the following settings for tests:\n",
-- " Database $test_db\n",
-- " Host $test_host\n",
-- " DSN $test_dsn\n",
-- " User $test_user\n",
-- " Password $test_pass\n");
-+ " Database ".$cfg->{test_db}. "\n",
-+ " Host ".$cfg->{test_host}."\n",
-+ " DSN ".$cfg->{test_dsn}. "\n",
-+ " User ".$cfg->{test_user}."\n",
-+ " Password ".$cfg->{test_pass}."\n");
- }
- }
-
+++ /dev/null
---- Makefile.PL.orig 2003-01-09 19:22:26.000000000 -0700
-+++ Makefile.PL 2003-01-09 19:23:06.000000000 -0700
-@@ -270,16 +270,16 @@
- },
- );
-
--
--sub MY::manifypods {
-- my $self = shift;
-- #print STDERR "In manifypods moment\n";
-- if( 1 ) {
-- return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n"
-- }
-- else {
-- return $self->SUPER::manifypods(@_);
-- }
-- }
-+# build pods by commenting out
-+#sub MY::manifypods {
-+# my $self = shift;
-+# #print STDERR "In manifypods moment\n";
-+# if( 1 ) {
-+# return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n"
-+# }
-+# else {
-+# return $self->SUPER::manifypods(@_);
-+# }
-+# }
+++ /dev/null
-MD5 1e4b14269a321aeb1d35d1bdb8c4d75e bioperl-1.0.2.tar.gz 2645781
+++ /dev/null
-MD5 23c0de12d08c394b336331caf33d3e94 bioperl-1.2.tar.gz 3425575
+++ /dev/null
-MD5 c630a5f13a452a65cfa1cbbed1d10378 bioperl-1.2.2.tar.gz 3585206
+++ /dev/null
-MD5 c64219b6540a722e781a53aea215ebc8 bioperl-1.2.3.tar.bz2 3086024
+++ /dev/null
-MD5 c49922bb58699cf42765056da8944f6e bioperl-1.4.tar.bz2 4224508
+++ /dev/null
---- Makefile.PL.orig 2003-07-14 17:31:03.000000000 +0100
-+++ Makefile.PL 2003-07-14 17:31:15.000000000 +0100
-@@ -270,16 +270,3 @@
- },
- );
-
--
--sub MY::manifypods {
-- my $self = shift;
-- #print STDERR "In manifypods moment\n";
-- if( 1 ) {
-- return "\nmanifypods : pure_all\n\t$self->{NOECHO}\$(NOOP)\n"
-- }
-- else {
-- return $self->SUPER::manifypods(@_);
-- }
-- }
--
--
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-<maintainer><email>sediener@gentoo.org</email></maintainer>
-</pkgmetadata>
projects / gentoo.git / commitdiff