* [gentoo-commits] repo/gentoo:master commit in: sci-biology/GBrowse/files/, profiles/, sci-biology/GBrowse/
@ 2022-04-17 20:27 Jakov Smolić
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From: Jakov Smolić @ 2022-04-17 20:27 UTC (permalink / raw
To: gentoo-commits
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 <soap@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 <mgorny@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-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
-</maintainer>
-<upstream>
- <remote-id type="cpan">GBrowse</remote-id>
-</upstream>
-</pkgmetadata>
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