From 27ab87f6ed9f5f90cc4c592e5417d2d810779e79 Mon Sep 17 00:00:00 2001 From: Olivier Fisette Date: Thu, 23 Dec 2004 22:04:07 +0000 Subject: [PATCH] Moving to sci-biology/bioperl --- app-sci/bioperl-pipeline/Manifest | 2 +- app-sci/bioperl/ChangeLog | 68 ------------- app-sci/bioperl/Manifest | 16 --- app-sci/bioperl/bioperl-1.0.2.ebuild | 54 ---------- app-sci/bioperl/bioperl-1.2.2.ebuild | 76 -------------- app-sci/bioperl/bioperl-1.2.3.ebuild | 77 --------------- app-sci/bioperl/bioperl-1.2.ebuild | 62 ------------ app-sci/bioperl/bioperl-1.4.ebuild | 49 ---------- .../bioperl/files/biodbgff-enable-1.2.2.patch | 98 ------------------- .../bioperl/files/biodbgff-enable-1.2.3.patch | 98 ------------------- .../bioperl/files/bioperl-1.2-manpage.diff | 28 ------ app-sci/bioperl/files/digest-bioperl-1.0.2 | 1 - app-sci/bioperl/files/digest-bioperl-1.2 | 1 - app-sci/bioperl/files/digest-bioperl-1.2.2 | 1 - app-sci/bioperl/files/digest-bioperl-1.2.3 | 1 - app-sci/bioperl/files/digest-bioperl-1.4 | 1 - app-sci/bioperl/files/domanpages-1.2.2.patch | 19 ---- app-sci/bioperl/metadata.xml | 6 -- 18 files changed, 1 insertion(+), 657 deletions(-) delete mode 100644 app-sci/bioperl/ChangeLog delete mode 100644 app-sci/bioperl/Manifest delete mode 100644 app-sci/bioperl/bioperl-1.0.2.ebuild delete mode 100644 app-sci/bioperl/bioperl-1.2.2.ebuild delete mode 100644 app-sci/bioperl/bioperl-1.2.3.ebuild delete mode 100644 app-sci/bioperl/bioperl-1.2.ebuild delete mode 100644 app-sci/bioperl/bioperl-1.4.ebuild delete mode 100644 app-sci/bioperl/files/biodbgff-enable-1.2.2.patch delete mode 100644 app-sci/bioperl/files/biodbgff-enable-1.2.3.patch delete mode 100644 app-sci/bioperl/files/bioperl-1.2-manpage.diff delete mode 100644 app-sci/bioperl/files/digest-bioperl-1.0.2 delete mode 100644 app-sci/bioperl/files/digest-bioperl-1.2 delete mode 100644 app-sci/bioperl/files/digest-bioperl-1.2.2 delete mode 100644 app-sci/bioperl/files/digest-bioperl-1.2.3 delete mode 100644 app-sci/bioperl/files/digest-bioperl-1.4 delete mode 100644 app-sci/bioperl/files/domanpages-1.2.2.patch delete mode 100644 app-sci/bioperl/metadata.xml diff --git a/app-sci/bioperl-pipeline/Manifest b/app-sci/bioperl-pipeline/Manifest index f84324bd710d..460acd752f66 100644 --- a/app-sci/bioperl-pipeline/Manifest +++ b/app-sci/bioperl-pipeline/Manifest @@ -1,4 +1,4 @@ -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 diff --git a/app-sci/bioperl/ChangeLog b/app-sci/bioperl/ChangeLog deleted file mode 100644 index ad5c836060b9..000000000000 --- a/app-sci/bioperl/ChangeLog +++ /dev/null @@ -1,68 +0,0 @@ -# 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 bioperl-1.4.ebuild, - bioperl-1.0.2.ebuild: - Q.A.: Fixed RDEPEND=$DEPEND, fixed LICENSE. - - 03 Aug 2004; David Holm bioperl-1.4.ebuild: - Added to ~ppc. - - 03 Jul 2004; Bryan Østergaard bioperl-1.4.ebuild: - Stable on alpha. - - 02 Jun 2004; Aron Griffis bioperl-1.2.2.ebuild, - bioperl-1.2.3.ebuild: - Fix use invocation - - 05 May 2004; Stephen Diener bioperl-1.4.ebuild: - bumped 1.4 to stable - - 05 May 2004; Bryan Østergaard bioperl-1.2.ebuild: - Stable on alpha. - - 20 Apr 2004; Bryan Østergaard bioperl-1.4.ebuild: - Added ~alpha to keywords. - - 14 Jan 2004; Stephen Diener 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 bioperl-1.4.ebuild: - version bump - - 24 Nov 2003; Stephen Diener bioperl-1.2.3.ebuild: - bump to stable. - -*bioperl-1.2.3 (24 Oct 2003) - - 24 Oct 2003; bioperl-1.2.3.ebuild: - new release added. - -*bioperl-1.2.2 (28 Aug 2003) - - 28 Aug 2003; Stephen Diener bioperl-1.2.2.ebuild: - Bumped to stable x86 - -*bioperl-1.2.2 (02 Aug 2003) - - 02 Aug 2003; Stephen Diener bioperl-1.2.2.ebuild, - files/biodbgff-enable-1.2.2.patch, files/domanpages-1.2.2.patch: - New Version thanks to Gontran Zepeda in bug# 24467 : - Also fixes bug# 25079 - -*bioperl-1.2 (24 Apr 2003) - - 24 Apr 2003; Jon Portnoy bioperl-1.2.ebuild : - Version bump, ebuild submitted by Gontran Zepeda - in bug #13826 - -*bioperl-1.0.2 (21 Dec 2002) - - 21 Dec 2002; Michael Cummings - bioperl-1.0.2.ebuild: - - Initial import. Ebuild submitted by Gontran Zepeda - Bug 11498 diff --git a/app-sci/bioperl/Manifest b/app-sci/bioperl/Manifest deleted file mode 100644 index 31fbc55140a2..000000000000 --- a/app-sci/bioperl/Manifest +++ /dev/null @@ -1,16 +0,0 @@ -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 diff --git a/app-sci/bioperl/bioperl-1.0.2.ebuild b/app-sci/bioperl/bioperl-1.0.2.ebuild deleted file mode 100644 index d347db4a316f..000000000000 --- a/app-sci/bioperl/bioperl-1.0.2.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# 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 -} diff --git a/app-sci/bioperl/bioperl-1.2.2.ebuild b/app-sci/bioperl/bioperl-1.2.2.ebuild deleted file mode 100644 index a2ef029f0b56..000000000000 --- a/app-sci/bioperl/bioperl-1.2.2.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# 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 -} diff --git a/app-sci/bioperl/bioperl-1.2.3.ebuild b/app-sci/bioperl/bioperl-1.2.3.ebuild deleted file mode 100644 index bc80d2f46889..000000000000 --- a/app-sci/bioperl/bioperl-1.2.3.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# 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 - -} diff --git a/app-sci/bioperl/bioperl-1.2.ebuild b/app-sci/bioperl/bioperl-1.2.ebuild deleted file mode 100644 index da704620818a..000000000000 --- a/app-sci/bioperl/bioperl-1.2.ebuild +++ /dev/null @@ -1,62 +0,0 @@ -# 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 -} diff --git a/app-sci/bioperl/bioperl-1.4.ebuild b/app-sci/bioperl/bioperl-1.4.ebuild deleted file mode 100644 index 64e65b2c66bf..000000000000 --- a/app-sci/bioperl/bioperl-1.4.ebuild +++ /dev/null @@ -1,49 +0,0 @@ -# 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 -} diff --git a/app-sci/bioperl/files/biodbgff-enable-1.2.2.patch b/app-sci/bioperl/files/biodbgff-enable-1.2.2.patch deleted file mode 100644 index 7bd66206a0b4..000000000000 --- a/app-sci/bioperl/files/biodbgff-enable-1.2.2.patch +++ /dev/null @@ -1,98 +0,0 @@ ---- 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"); - } - } - diff --git a/app-sci/bioperl/files/biodbgff-enable-1.2.3.patch b/app-sci/bioperl/files/biodbgff-enable-1.2.3.patch deleted file mode 100644 index 7bd66206a0b4..000000000000 --- a/app-sci/bioperl/files/biodbgff-enable-1.2.3.patch +++ /dev/null @@ -1,98 +0,0 @@ ---- 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"); - } - } - diff --git a/app-sci/bioperl/files/bioperl-1.2-manpage.diff b/app-sci/bioperl/files/bioperl-1.2-manpage.diff deleted file mode 100644 index 54ba46aa680e..000000000000 --- a/app-sci/bioperl/files/bioperl-1.2-manpage.diff +++ /dev/null @@ -1,28 +0,0 @@ ---- 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(@_); -+# } -+# } diff --git a/app-sci/bioperl/files/digest-bioperl-1.0.2 b/app-sci/bioperl/files/digest-bioperl-1.0.2 deleted file mode 100644 index 226e52d402eb..000000000000 --- a/app-sci/bioperl/files/digest-bioperl-1.0.2 +++ /dev/null @@ -1 +0,0 @@ -MD5 1e4b14269a321aeb1d35d1bdb8c4d75e bioperl-1.0.2.tar.gz 2645781 diff --git a/app-sci/bioperl/files/digest-bioperl-1.2 b/app-sci/bioperl/files/digest-bioperl-1.2 deleted file mode 100644 index 183c203289e2..000000000000 --- a/app-sci/bioperl/files/digest-bioperl-1.2 +++ /dev/null @@ -1 +0,0 @@ -MD5 23c0de12d08c394b336331caf33d3e94 bioperl-1.2.tar.gz 3425575 diff --git a/app-sci/bioperl/files/digest-bioperl-1.2.2 b/app-sci/bioperl/files/digest-bioperl-1.2.2 deleted file mode 100644 index f9d1b2b95180..000000000000 --- a/app-sci/bioperl/files/digest-bioperl-1.2.2 +++ /dev/null @@ -1 +0,0 @@ -MD5 c630a5f13a452a65cfa1cbbed1d10378 bioperl-1.2.2.tar.gz 3585206 diff --git a/app-sci/bioperl/files/digest-bioperl-1.2.3 b/app-sci/bioperl/files/digest-bioperl-1.2.3 deleted file mode 100644 index 05b4fc161597..000000000000 --- a/app-sci/bioperl/files/digest-bioperl-1.2.3 +++ /dev/null @@ -1 +0,0 @@ -MD5 c64219b6540a722e781a53aea215ebc8 bioperl-1.2.3.tar.bz2 3086024 diff --git a/app-sci/bioperl/files/digest-bioperl-1.4 b/app-sci/bioperl/files/digest-bioperl-1.4 deleted file mode 100644 index 43354ceffe03..000000000000 --- a/app-sci/bioperl/files/digest-bioperl-1.4 +++ /dev/null @@ -1 +0,0 @@ -MD5 c49922bb58699cf42765056da8944f6e bioperl-1.4.tar.bz2 4224508 diff --git a/app-sci/bioperl/files/domanpages-1.2.2.patch b/app-sci/bioperl/files/domanpages-1.2.2.patch deleted file mode 100644 index 14cbe35de59a..000000000000 --- a/app-sci/bioperl/files/domanpages-1.2.2.patch +++ /dev/null @@ -1,19 +0,0 @@ ---- 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(@_); -- } -- } -- -- diff --git a/app-sci/bioperl/metadata.xml b/app-sci/bioperl/metadata.xml deleted file mode 100644 index 8a4bcd47220d..000000000000 --- a/app-sci/bioperl/metadata.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - -sci -sediener@gentoo.org - -- 2.26.2