From b7d59953f363a041b704c2ae110ddaa5505aecc2 Mon Sep 17 00:00:00 2001 From: Olivier Fisette Date: Thu, 23 Dec 2004 22:07:40 +0000 Subject: [PATCH] Moving to sci-biology/bioperl-run --- app-sci/bioperl-run/ChangeLog | 28 ---------- app-sci/bioperl-run/Manifest | 7 --- app-sci/bioperl-run/bioperl-run-1.2.2.ebuild | 55 ------------------- app-sci/bioperl-run/bioperl-run-1.4.ebuild | 47 ---------------- .../files/bioperl-run-Pise-test-patch.diff | 22 -------- .../files/digest-bioperl-run-1.2.2 | 1 - .../bioperl-run/files/digest-bioperl-run-1.4 | 1 - app-sci/bioperl-run/metadata.xml | 6 -- 8 files changed, 167 deletions(-) delete mode 100644 app-sci/bioperl-run/ChangeLog delete mode 100644 app-sci/bioperl-run/Manifest delete mode 100644 app-sci/bioperl-run/bioperl-run-1.2.2.ebuild delete mode 100644 app-sci/bioperl-run/bioperl-run-1.4.ebuild delete mode 100644 app-sci/bioperl-run/files/bioperl-run-Pise-test-patch.diff delete mode 100644 app-sci/bioperl-run/files/digest-bioperl-run-1.2.2 delete mode 100644 app-sci/bioperl-run/files/digest-bioperl-run-1.4 delete mode 100644 app-sci/bioperl-run/metadata.xml diff --git a/app-sci/bioperl-run/ChangeLog b/app-sci/bioperl-run/ChangeLog deleted file mode 100644 index 317f54a7e304..000000000000 --- a/app-sci/bioperl-run/ChangeLog +++ /dev/null @@ -1,28 +0,0 @@ -# ChangeLog for app-sci/bioperl-run -# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/app-sci/bioperl-run/ChangeLog,v 1.7 2004/09/23 19:48:15 sediener Exp $ - - 23 Sep 2004; Stephen Diener bioperl-run-1.4.ebuild: - Bumped 1.4 to stable on x86 - - 03 Aug 2004; David Holm bioperl-run-1.4.ebuild: - Added to ~ppc. - - 22 Mar 2004; Patrick Kursawe bioperl-run-1.2.2.ebuild, - bioperl-run-1.4.ebuild: - removing DEPEND="${RDEPEND}" - -*bioperl-run-1.4 (08 Jan 2004) - - 08 Jan 2004; Stephen Diener bioperl-run-1.4.ebuild: - version bump to 1.4 - - 14 Dec 2003; Stephen Diener bioperl-run-1.2.2.ebuild: - Bump to stable - -*bioperl-run-1.2.2 (29 Sep 2003) - - 29 Sep 2003; bioperl-run-1.2.2.ebuild, metadata.xml, - files/bioperl-run-Pise-test-patch.diff: - Initial Import. Built of of the bioperl ebuild from Gontran Zepeda. - diff --git a/app-sci/bioperl-run/Manifest b/app-sci/bioperl-run/Manifest deleted file mode 100644 index 20d30ca0abaf..000000000000 --- a/app-sci/bioperl-run/Manifest +++ /dev/null @@ -1,7 +0,0 @@ -MD5 4cd3241aa707d6a6d276fd13d119e7d6 bioperl-run-1.4.ebuild 1306 -MD5 5c2ee510b374b6726d8b226c24662a5c bioperl-run-1.2.2.ebuild 1456 -MD5 81eb9eddaa9c418106d796b152b14ed0 ChangeLog 995 -MD5 e8b4df3df76800c376905734d8043cfa metadata.xml 216 -MD5 47db6a1f839dd45f8c891b5f6ab2ff2a files/digest-bioperl-run-1.4 67 -MD5 21ad123058f1e670f289ee1a87de4e82 files/bioperl-run-Pise-test-patch.diff 722 -MD5 b23d441d6d3f1d4ed3dead4c3dc2799b files/digest-bioperl-run-1.2.2 69 diff --git a/app-sci/bioperl-run/bioperl-run-1.2.2.ebuild b/app-sci/bioperl-run/bioperl-run-1.2.2.ebuild deleted file mode 100644 index e229d3dfe702..000000000000 --- a/app-sci/bioperl-run/bioperl-run-1.2.2.ebuild +++ /dev/null @@ -1,55 +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-run/bioperl-run-1.2.2.ebuild,v 1.4 2004/06/24 21:52:54 agriffis Exp $ - -inherit perl-module eutils -CATEGORY="app-sci" - -DESCRIPTION="collection of tools for bioinformatics, genomics and life science research : subset required to run analyses" -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="" - -RDEPEND=" - dev-perl/Algorithm-Diff - dev-perl/File-Temp - dev-perl/IO-String - dev-perl/XML-Parser" - -DEPEND="" - -src_unpack() { - unpack ${A} - cd ${S} - # remove interactiveness - epatch ${FILESDIR}/bioperl-run-Pise-test-patch.diff -} - -src_compile() { - # there's a test to run for BioGFFDB if using mysql - perl-module_src_compile || die "compile failed" - # make test -## perl-module_src_test || die "src test failed" -} - -src_install() { - mydoc="AUTHORS BUGS FAQ" - perl-module_src_install - - # bioperl scripts and examples - einfo 'Adding bioperl examples and scripts to /usr/share/...' - dodir /usr/share/${PF}/scripts - #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/app-sci/bioperl-run/bioperl-run-1.4.ebuild b/app-sci/bioperl-run/bioperl-run-1.4.ebuild deleted file mode 100644 index a0a217c88ad0..000000000000 --- a/app-sci/bioperl-run/bioperl-run-1.4.ebuild +++ /dev/null @@ -1,47 +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-run/bioperl-run-1.4.ebuild,v 1.5 2004/09/23 19:48:15 sediener Exp $ - -inherit perl-module eutils -CATEGORY="app-sci" - -DESCRIPTION="collection of tools for bioinformatics, genomics and life science research : subset required to run analyses" -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 - dev-perl/File-Temp - dev-perl/IO-String - dev-perl/XML-Parser" - -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/app-sci/bioperl-run/files/bioperl-run-Pise-test-patch.diff b/app-sci/bioperl-run/files/bioperl-run-Pise-test-patch.diff deleted file mode 100644 index 5683347a6b52..000000000000 --- a/app-sci/bioperl-run/files/bioperl-run-Pise-test-patch.diff +++ /dev/null @@ -1,22 +0,0 @@ ---- Makefile.PL.original 2003-09-28 23:33:16.000000000 -0400 -+++ Makefile.PL 2003-09-28 23:33:50.000000000 -0400 -@@ -73,19 +73,6 @@ - my $DISTNAME = "bioperl-run"; - my $VERSION = "1.2.2"; - --my $proceed = prompt("Do you want to run the Pise tests (requires a network connection) y/n",'n'); --if( $proceed =~ /^[yY]/) { -- my $address = prompt("Enter your email address (no default)",''); -- -- if (open T,">t/pise-email.test") { --print T "$address\n"; --close T; -- } else { warn("Cannot open file t/pise-email.test for writing - no Pise tests will be run"); } --} else { -- if( -e "t/pise-email.test" ) { --unlink "t/pise-email.test"; -- } --} - #$do_autoload_finesse = 0; - #$NAME = 'Bio'; - #$DISTNAME = "GFD"; diff --git a/app-sci/bioperl-run/files/digest-bioperl-run-1.2.2 b/app-sci/bioperl-run/files/digest-bioperl-run-1.2.2 deleted file mode 100644 index cf92f27aa20d..000000000000 --- a/app-sci/bioperl-run/files/digest-bioperl-run-1.2.2 +++ /dev/null @@ -1 +0,0 @@ -MD5 2ffbaa69e713f102f86c7b7462ccff52 bioperl-run-1.2.2.tar.gz 811989 diff --git a/app-sci/bioperl-run/files/digest-bioperl-run-1.4 b/app-sci/bioperl-run/files/digest-bioperl-run-1.4 deleted file mode 100644 index 5c20eceaee32..000000000000 --- a/app-sci/bioperl-run/files/digest-bioperl-run-1.4 +++ /dev/null @@ -1 +0,0 @@ -MD5 25914ab48d1ab0393ebb067a8f68a821 bioperl-run-1.4.tar.gz 830774 diff --git a/app-sci/bioperl-run/metadata.xml b/app-sci/bioperl-run/metadata.xml deleted file mode 100644 index 8a4bcd47220d..000000000000 --- a/app-sci/bioperl-run/metadata.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - -sci -sediener@gentoo.org - -- 2.26.2