commit: f71d2fd07f0ec1a96b6772fa4412e6ece900c6e2 Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> AuthorDate: Sun Apr 17 20:26:33 2022 +0000 Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> CommitDate: Sun Apr 17 20:26:33 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f71d2fd0
sci-biology/GBrowse: treeclean Closes: https://bugs.gentoo.org/828702 Closes: https://bugs.gentoo.org/690042 Closes: https://bugs.gentoo.org/513594 Closes: https://bugs.gentoo.org/402849 Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org> profiles/package.mask | 6 -- sci-biology/GBrowse/GBrowse-2.48-r1.ebuild | 71 --------------------- sci-biology/GBrowse/Manifest | 1 - .../GBrowse/files/GBrowseInstall.pm-2.39.patch | 72 ---------------------- sci-biology/GBrowse/metadata.xml | 11 ---- 5 files changed, 161 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index b46a90885dfb..494aede6f438 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -276,12 +276,6 @@ sys-cluster/lustre # to a fresher gcc branch. <sys-devel/gcc-9 -# David Seifert <s...@gentoo.org> (2022-03-19) -# Unmaintained, no revdeps in tree, not even on latest version, EAPI 5, -# typical 'webapp' smell, last upstream release more than 9 years ago. -# Bug #402849, #513594, #690042, #828702, removal on 2022-04-18. -sci-biology/GBrowse - # Michał Górny <mgo...@gentoo.org> (2022-03-18) # The new version breaks building docs w/o Internet access (because it # tries to fetch and install all dependencies locally). diff --git a/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild deleted file mode 100644 index 2fcef3b41aff..000000000000 --- a/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -MODULE_AUTHOR=LDS -inherit perl-module webapp - -DESCRIPTION="Generic Model Organism Database Project - The Generic Genome Browser" -HOMEPAGE="http://gmod.org/wiki/GBrowse"; -KEYWORDS="~amd64 ~x86" -IUSE="minimal mysql postgres +sqlite" - -SLOT="0" -WEBAPP_MANUAL_SLOT="yes" - -CDEPEND="!<sci-biology/GBrowse-2.44-r1 - >=sci-biology/bioperl-1.6.9 - >=dev-perl/Bio-Graphics-2.09 - >=dev-perl/GD-2.07 - >=dev-perl/CGI-Session-4.02 - dev-perl/IO-String - dev-perl/JSON - dev-perl/libwww-perl - dev-perl/Statistics-Descriptive - !minimal? ( - dev-perl/Bio-Das - >=dev-perl/Bio-SamTools-1.20 - dev-perl/Crypt-SSLeay - dev-perl/DB_File-Lock - dev-perl/DBI - mysql? ( dev-perl/DBD-mysql ) - postgres? ( dev-perl/DBD-Pg ) - sqlite? ( dev-perl/DBD-SQLite ) - dev-perl/FCGI - dev-perl/File-NFSLock - dev-perl/GD-SVG - dev-perl/Net-OpenID-Consumer - dev-perl/Net-SMTP-SSL - )" -# >=dev-perl/Bio-DB-BigFile-1.00 - requires jklib to compile -DEPEND="dev-perl/Module-Build - dev-perl/Capture-Tiny - ${CDEPEND}" -RDEPEND="${CDEPEND}" - -PATCHES=( "${FILESDIR}"/GBrowseInstall.pm-2.39.patch ) - -src_configure() { - webapp_src_preinst - -# myconf="--install_base=${D}/usr" or "--install_base=/opt/gbrowse" - myconf="--conf=/etc/gbrowse2" - myconf="${myconf} --htdocs=${MY_HTDOCSDIR}" - myconf="${myconf} --cgibin=${MY_CGIBINDIR}" - myconf="${myconf} --tmp=/var/tmp/gbrowse2" - myconf="${myconf} --persistent=/var/db/gbrowse2" - myconf="${myconf} --databases=/var/db/gbrowse2/databases" - myconf="${myconf} --installconf=no" - myconf="${myconf} --installetc=no" - perl-module_src_configure -} - -src_install() { - dodir /var/tmp/gbrowse2 - dodir /var/db/gbrowse2/sessions - dodir /var/db/gbrowse2/userdata - webapp_serverowned -R /var/tmp/gbrowse2 /var/db/gbrowse2 - perl-module_src_install - webapp_src_install -} diff --git a/sci-biology/GBrowse/Manifest b/sci-biology/GBrowse/Manifest deleted file mode 100644 index 47384b63de9a..000000000000 --- a/sci-biology/GBrowse/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST GBrowse-2.48.tar.gz 11958127 BLAKE2B e9527eb47302775d62e37990c42154b677284fff0f0f9624e9173e30e46c5aebbc8a02ee8dec0a1e98761812ef2363e0183008087bce4d283528b7935b4d5f91 SHA512 d5a07caf1517fb15741e8e6056669763eb04678a42637a9e90788c91e74fb34515b5f86aac10a00f29d8848aceb19d6f5f7258d2dda0e281feee550e9e2fb3db diff --git a/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch b/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch deleted file mode 100644 index 5aa0be9df918..000000000000 --- a/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch +++ /dev/null @@ -1,72 +0,0 @@ -diff -durr GBrowse-2.39-orig/install_util/GBrowseInstall.pm GBrowse-2.39/install_util/GBrowseInstall.pm ---- GBrowse-2.39-orig/install_util/GBrowseInstall.pm 2011-07-19 20:14:52.434608020 +0000 -+++ GBrowse-2.39/install_util/GBrowseInstall.pm 2011-07-19 21:02:13.685107753 +0000 -@@ -454,33 +454,33 @@ - $gid =~ /^(\d+)$/; - $gid = $1; - -- unless (chown $uid,$gid,$tmp) { -- $self->ownership_warning($tmp,$user); -- } -+# unless (chown $uid,$gid,$tmp) { -+# $self->ownership_warning($tmp,$user); -+# } - - my $htdocs_i = File::Spec->catfile($self->install_path->{htdocs},'i'); - my $images = File::Spec->catfile($tmp,'images'); - my $htdocs = $self->install_path->{htdocs}; -- chown $uid,-1,$htdocs; -+# chown $uid,-1,$htdocs; - { - local $> = $uid; -- symlink($images,$htdocs_i); # so symlinkifowner match works! -+# symlink($images,$htdocs_i); # so symlinkifowner match works! - } -- chown $>,-1,$self->install_path->{htdocs}; -+# chown $>,-1,$self->install_path->{htdocs}; - - my $persistent = $self->install_path->{'persistent'}; - my $sessions = File::Spec->catfile($persistent,'sessions'); - my $userdata = File::Spec->catfile($persistent,'userdata'); -- mkpath([$sessions,$userdata],0711); -+# mkpath([$sessions,$userdata],0711); - - my $databases = $self->install_path->{'databases'}; - -- unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { -- $self->ownership_warning($databases,$user); -- } -+# unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) { -+# $self->ownership_warning($databases,$user); -+# } - -- chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); -- $self->fix_selinux; -+ # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave'); -+ # $self->fix_selinux; - - my $base = basename($self->install_path->{htdocs}); - -@@ -489,14 +489,14 @@ - my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl"); - my $perl = $self->perl; - my @inc = map{"-I$_"} split ':',$self->added_to_INC; -- system $perl,@inc,$metadb_script; -- system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata; -+# system $perl,@inc,$metadb_script; -+# system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata; - -- if (Module::Build->y_n( -- "It is recommended that you restart Apache. Shall I try this for you?",'y' -- )) { -- system "sudo /etc/init.d/apache2 restart"; -- } -+# if (Module::Build->y_n( -+# "It is recommended that you restart Apache. Shall I try this for you?",'y' -+# )) { -+# system "sudo /etc/init.d/apache2 restart"; -+# } - - print STDERR "\n***INSTALLATION COMPLETE***\n"; - print STDERR "Load http://localhost/$base for demo and documentation.\n"; -Only in GBrowse-2.39/install_util: GBrowseInstall.pm~ diff --git a/sci-biology/GBrowse/metadata.xml b/sci-biology/GBrowse/metadata.xml deleted file mode 100644 index 08238dd44f7a..000000000000 --- a/sci-biology/GBrowse/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> -<maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> -</maintainer> -<upstream> - <remote-id type="cpan">GBrowse</remote-id> -</upstream> -</pkgmetadata>
