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