[med-svn] [gbrowse] 04/04: Refresh patches

Andreas Tille tille at debian.org
Mon Jan 16 04:36:36 UTC 2017 

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository gbrowse.

commit cb5e7fc2964c988c52402155a71078a7a3f35fdb
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jan 16 05:24:37 2017 +0100

    Refresh patches
---
 debian/patches/debian-packaging-patch           | 31 ++++++++++++-------------
 debian/patches/fix_perl_deprecation             |  4 ++--
 debian/patches/fix_pop_url                      |  8 +++----
 debian/patches/gbrowse-slave-fix_defaults_path  |  6 ++---
 debian/patches/manpages.patch                   | 28 +++++++++++-----------
 debian/patches/series                           |  1 -
 debian/patches/skipRenderFarmTest_UpstreamBug12 |  4 ++++
 debian/patches/skip_check_installed_test.patch  |  8 +++----
 debian/patches/source_init_functions            |  6 ++---
 debian/tests/pkg-perl/smoke-skip                |  3 +++
 10 files changed, 52 insertions(+), 47 deletions(-)

diff --git a/debian/patches/debian-packaging-patch b/debian/patches/debian-packaging-patch
index d1b2368..6bea611 100644
--- a/debian/patches/debian-packaging-patch
+++ b/debian/patches/debian-packaging-patch
@@ -21,7 +21,7 @@ Forwarded: not-needed
  # Short-Description: Start/Stop the gbrowse_slave rendering server.
  ### END INIT INFO
  
-@@ -13,7 +13,7 @@
+@@ -13,7 +13,7 @@ DAEMON=$INSTALLSCRIPT/gbrowse_slave
  NAME="gbrowse-slave"
  DESC="GBrowse slave track rendering server"
  
@@ -32,8 +32,7 @@ Forwarded: not-needed
  USER=$WWWUSER
 --- a/etc/default/gbrowse-slave
 +++ b/etc/default/gbrowse-slave
-@@ -1,10 +1,9 @@
--#!/bin/sh
+@@ -2,9 +2,9 @@
  
  export PERL5LIB=$PERL5LIB
  
@@ -43,12 +42,12 @@ Forwarded: not-needed
 +DAEMON=/usr/bin/gbrowse_slave
 +USER=www-data
 +PRELOAD=/etc/gbrowse/slave_preload.conf
- RUNDIR=/var/run/gbrowse
- LOGDIR=/var/log/gbrowse
+ RUNDIR=/var/run/gbrowse2
+ LOGDIR=/var/log/gbrowse2
  PREFORK=3
 --- a/bin/gbrowse_metadb_config.pl
 +++ b/bin/gbrowse_metadb_config.pl
-@@ -21,7 +21,10 @@
+@@ -21,7 +21,10 @@ use constant SCHEMA_VERSION => 4;
  my @argv = @ARGV;
  
  my ($dsn, $admin);
@@ -59,7 +58,7 @@ Forwarded: not-needed
             'admin=s'       => \$admin) or die <<EOF;
  Usage: $0 [options] <optional path to GBrowse.conf>
  
-@@ -169,10 +172,12 @@
+@@ -169,10 +172,12 @@ check_table("openid_users",     $openid_
  check_table("uploads",          $uploads_columns);
  check_table("sharing",          $sharing_columns);
  
@@ -74,7 +73,7 @@ Forwarded: not-needed
  
 --- a/htdocs/index.html
 +++ b/htdocs/index.html
-@@ -24,7 +24,7 @@
+@@ -24,7 +24,7 @@ Welcome to the Generic Genome Browser!
    <dd><a href="example_scripts">/var/www/gbrowse2/example_scripts</a></dd>
  </dl>
  
@@ -83,7 +82,7 @@ Forwarded: not-needed
  
  <p>
  
-@@ -32,9 +32,9 @@
+@@ -32,9 +32,9 @@ Example in-memory databases from yeast c
  installed for you.  Try them at these URL:
  
  <ul>
@@ -96,7 +95,7 @@ Forwarded: not-needed
  </ul>
  
  <p>
-@@ -56,13 +56,13 @@
+@@ -56,13 +56,13 @@ configuration, you can use the alias /gb
  <li><a href="/gb2/gbrowse/yeast">http://your.host/gb2/gbrowse/yeast</a></li>
  <li><a href="/gb2/gbrowse/yeast_advanced">http://your.host/gb2/gbrowse/yeast_advanced</a></li>
  <li><a href="/gb2/gbrowse/yeast_renderfarm">http://your.host/gb2/gbrowse/yeast_renderfarm</a></li>
@@ -105,17 +104,17 @@ Forwarded: not-needed
  
  <h3>Accelerated Demos</h3>
  
--If you have FastCGI and/or ModPerl installed, you will have access to
+-If you have mod_fcgid, mod_fastcgi and/or ModPerl installed, you will have access to
 -an accelerated version of gbrowse at these URLs:
 +By default, FastCGI and ModPerl are not set by gbrowse installation,
 +However, if you have FastCGI and/or ModPerl installed, you will have access to
 + accelerated versions of gbrowse a these URLs:
  
  <ul>
-   <li>FastCGI
+   <li>mod_fcgid
 --- a/install_util/GBrowseInstall.pm
 +++ b/install_util/GBrowseInstall.pm
-@@ -33,6 +33,7 @@
+@@ -33,6 +33,7 @@ my @OK_PROPS = (conf          => 'Direct
  		wwwuser       => 'User account under which Apache daemon runs?',
  		installconf   => 'Automatically update Apache config files to run GBrowse?',
  		installetc    => 'Automatically update system config files to run gbrowse-slave?',
@@ -123,7 +122,7 @@ Forwarded: not-needed
      );
  my %OK_PROPS = @OK_PROPS;
  
-@@ -422,6 +423,82 @@
+@@ -447,6 +448,82 @@ ScriptAlias  "/gb2"      "$cgibin"
  END
  }
  
@@ -206,7 +205,7 @@ Forwarded: not-needed
  sub ACTION_install {
      my $self = shift;
      my $prefix = $self->install_base || $self->prefix || '';
-@@ -776,8 +853,9 @@
+@@ -826,8 +903,9 @@ sub has_openid {
  sub guess_user_account_db {
      my $self = shift;
      if (eval "require DBD::SQLite; 1") {
@@ -220,7 +219,7 @@ Forwarded: not-needed
      } else {
 --- a/conf/GBrowse.conf
 +++ b/conf/GBrowse.conf
-@@ -163,9 +163,9 @@
+@@ -166,9 +166,9 @@ max keyword results    = 1000
  # "user_accounts" is true, then GBrowse
  # will attempt to use its internal user accounts database
  # to authenticate and/or register users.
diff --git a/debian/patches/fix_perl_deprecation b/debian/patches/fix_perl_deprecation
index 6b64768..42c1f31 100644
--- a/debian/patches/fix_perl_deprecation
+++ b/debian/patches/fix_perl_deprecation
@@ -7,11 +7,11 @@ Bug-Debian: https://bugs.debian.org/826458
 Forwarded: no
 --- a/lib/Bio/Graphics/Browser2/DataSource.pm
 +++ b/lib/Bio/Graphics/Browser2/DataSource.pm
-@@ -960,7 +960,7 @@
+@@ -960,7 +960,7 @@ sub db_settings {
  
    # Do environment substitutions in the args. Assume that the environment is safe.
    foreach (@argv) {
--      s/\$ENV{(\w+)}/$ENV{$1}||''/ge;
+-      s/\$ENV\{(\w+)\}/$ENV{$1}||''/ge;
 +      s/\$ENV\{(\w+)\}/$ENV\{$1\}||''/ge;
        s/\$HTDOCS/Bio::Graphics::Browser2->htdocs_base/ge;
        s/\$DB/Bio::Graphics::Browser2->db_base/ge;
diff --git a/debian/patches/fix_pop_url b/debian/patches/fix_pop_url
index b8779eb..2e71421 100644
--- a/debian/patches/fix_pop_url
+++ b/debian/patches/fix_pop_url
@@ -5,18 +5,18 @@ Description: update URL for details in example conf files to match /gb2 instead
 Forwarded: not-needed
 --- a/conf/yeast_chr1+2.conf
 +++ b/conf/yeast_chr1+2.conf
-@@ -158,7 +158,7 @@
+@@ -158,7 +158,7 @@ balloon click = <table>
        This gene brought to you by <a href="http://www.yeastgenome.org">SGD</a>.</th>
            <th bgcolor="cyan">Gene $name</th>
        </tr>
--      <tr align='left'><th><a href="/cgi-bin/gb2/gbrowse_details/yeast?name=$name" target="_new">See gene details</a></th></tr>
-+      <tr align='left'><th><a href="/gb2/gbrowse_details/yeast?name=$name" target="_new">See gene details</a></th></tr>
+-      <tr align='left'><th><a href="/cgi-bin/gb2/gbrowse_details/yeast_advanced?feature_id=$id" target="_new">See gene details</a></th></tr>
++      <tr align='left'><th><a href="/gb2/gbrowse_details/yeast_advanced?feature_id=$id" target="_new">See gene details</a></th></tr>
        <tr align='left'><th><a href="http://db.yeastgenome.org/cgi-bin/locus.pl?locus=$name" target="_new">Ask SGD about $name</a></th></tr>
        <tr align='left'><th><a href="http://en.wikipedia.org/wiki/Special:Search?search=$name" target="_new">Ask Wikipedia about $name</a></th></tr>
        <tr align='left'><th><a href="http://www.google.com/search?q=$name" target="_new">Ask Google about $name</a></th></tr>
 --- a/conf/yeast_renderfarm.conf
 +++ b/conf/yeast_renderfarm.conf
-@@ -153,7 +153,7 @@
+@@ -153,7 +153,7 @@ balloon click = <table>
        This gene brought to you by <a href="http://www.yeastgenome.org">SGD</a>.</th>
            <th bgcolor="cyan">Gene $name</th>
        </tr>
diff --git a/debian/patches/gbrowse-slave-fix_defaults_path b/debian/patches/gbrowse-slave-fix_defaults_path
index 64f53ba..2b5ad72 100644
--- a/debian/patches/gbrowse-slave-fix_defaults_path
+++ b/debian/patches/gbrowse-slave-fix_defaults_path
@@ -18,9 +18,9 @@ Last-Updated: 2012-02-19
  ### END INIT INFO
  
  PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin
-@@ -24,8 +25,8 @@
- VERBOSITY=1
- NICE=0
+@@ -31,8 +32,8 @@ if [ "$*" != "" ]; then
+     PORT=$*
+ fi
  
 -if [ -f $ETC/default/gbrowse-slave ]; then
 -  . $ETC/default/gbrowse-slave
diff --git a/debian/patches/manpages.patch b/debian/patches/manpages.patch
index 70f7e4a..23e8526 100644
--- a/debian/patches/manpages.patch
+++ b/debian/patches/manpages.patch
@@ -8,7 +8,7 @@ Bug-Debian: https://bugs.debian.org/645861
 
 --- a/bin/gtf2gff3.pl
 +++ b/bin/gtf2gff3.pl
-@@ -1320,7 +1320,7 @@
+@@ -1320,7 +1320,7 @@ sub max_feature {
  
  =head1 NAME
  
@@ -17,7 +17,7 @@ Bug-Debian: https://bugs.debian.org/645861
  
  =head1 VERSION
  
-@@ -1496,7 +1496,7 @@
+@@ -1496,7 +1496,7 @@ indicates a software bug.  Please contac
  =item C<< FATAL: Invalid value passed to strand: strand.  >>
  
  This may indicate that your GTF file does not indicate the strand for
@@ -39,7 +39,7 @@ Bug-Debian: https://bugs.debian.org/645861
  
 --- a/lib/Bio/DB/GFF/Aggregator/match_gap.pm
 +++ b/lib/Bio/DB/GFF/Aggregator/match_gap.pm
-@@ -34,7 +34,6 @@
+@@ -34,7 +34,6 @@ This module only recognizes the M and D
  should be sufficient for simple nucleotide to nucleotide
  alignments.
  
@@ -59,7 +59,7 @@ Bug-Debian: https://bugs.debian.org/645861
  
 --- a/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
 +++ b/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
-@@ -23,7 +23,6 @@
+@@ -23,7 +23,6 @@ GBrowse internal module.
  
  =head2 METHODS
  
@@ -69,7 +69,7 @@ Bug-Debian: https://bugs.debian.org/645861
  
 --- a/lib/Bio/Graphics/Browser2/DataBase.pm
 +++ b/lib/Bio/Graphics/Browser2/DataBase.pm
-@@ -66,12 +66,16 @@
+@@ -66,12 +66,16 @@ sub delete_database {
      $CACHE->delete($key);
  }
  
@@ -88,7 +88,7 @@ Bug-Debian: https://bugs.debian.org/645861
  sub clone_databases {
 --- a/lib/Bio/Graphics/Browser2/Plugin.pm
 +++ b/lib/Bio/Graphics/Browser2/Plugin.pm
-@@ -238,7 +238,7 @@
+@@ -238,7 +238,7 @@ if you do not want a descriptive verb fo
  
  The purpose of this methods is to suppress the 'Configure...'
  or 'Find...' title that is printed at the top of the page when the 
@@ -99,7 +99,7 @@ Bug-Debian: https://bugs.debian.org/645861
  =item $type = $self->type()
 --- a/lib/Bio/Graphics/Browser2/Region.pm
 +++ b/lib/Bio/Graphics/Browser2/Region.pm
-@@ -3,6 +3,12 @@
+@@ -3,6 +3,12 @@ package Bio::Graphics::Browser2::Region;
  # provide method for fetching and manipulating the current
  # region or regions.
  
@@ -114,7 +114,7 @@ Bug-Debian: https://bugs.debian.org/645861
  use Bio::Graphics::Browser2::Shellwords;
 --- a/lib/Bio/Graphics/Browser2/Render.pm
 +++ b/lib/Bio/Graphics/Browser2/Render.pm
-@@ -3,6 +3,12 @@
+@@ -3,6 +3,12 @@ package Bio::Graphics::Browser2::Render;
  use strict;	
  use warnings;
  
@@ -129,7 +129,7 @@ Bug-Debian: https://bugs.debian.org/645861
  use CGI qw(:standard param request_method header url iframe img span div br center url_param);
 --- a/lib/Bio/Graphics/Browser2/RenderPanels.pm
 +++ b/lib/Bio/Graphics/Browser2/RenderPanels.pm
-@@ -2,6 +2,13 @@
+@@ -2,6 +2,13 @@ package Bio::Graphics::Browser2::RenderP
  use strict;
  use warnings;
  
@@ -145,7 +145,7 @@ Bug-Debian: https://bugs.debian.org/645861
  use Bio::Graphics;
 --- a/lib/Legacy/Graphics/Browser.pm
 +++ b/lib/Legacy/Graphics/Browser.pm
-@@ -4,6 +4,12 @@
+@@ -4,6 +4,12 @@ package Legacy::Graphics::Browser;
  # This is an old version of Bio::Graphics::Browser retained for gbrowse_syn
  # It is on the path to deprecation
  
@@ -160,7 +160,7 @@ Bug-Debian: https://bugs.debian.org/645861
  The remainder of this document describes the methods available to the
 --- a/lib/Bio/Graphics/Browser2/DataSource.pm
 +++ b/lib/Bio/Graphics/Browser2/DataSource.pm
-@@ -32,6 +32,10 @@
+@@ -32,6 +32,10 @@ BEGIN {
      }
  }
  
@@ -171,7 +171,7 @@ Bug-Debian: https://bugs.debian.org/645861
  =head1 SYNOPSIS
  
  =head1 DESCRIPTION
-@@ -150,6 +154,8 @@
+@@ -150,6 +154,8 @@ sub clear_cached_config {
      delete $CONFIG_CACHE{$self->config_file};
  }
  
@@ -180,7 +180,7 @@ Bug-Debian: https://bugs.debian.org/645861
  =head2 userdata()
  
    $path = $source->userdata(@path_components)
-@@ -871,6 +877,8 @@
+@@ -871,6 +877,8 @@ sub make_link {
    croak "Do not call make_link() on the DataSource. Call it on the Render object";
  }
  
@@ -189,7 +189,7 @@ Bug-Debian: https://bugs.debian.org/645861
  =item $db = $dsn->databases
  
  Return all named databases from [name:database] tracks.
-@@ -1116,6 +1124,8 @@
+@@ -1115,6 +1123,8 @@ sub clear_cache {
      %DB_SETTINGS = ();
  }
  
diff --git a/debian/patches/series b/debian/patches/series
index 99a42a2..2651d71 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,7 +2,6 @@ debian-packaging-patch
 gbrowse-slave-fix_defaults_path
 manpages.patch
 fix_pop_url
-skipRenderFarmTest_UpstreamBug12
 skip_check_installed_test.patch
 source_init_functions
 fix_perl_deprecation
diff --git a/debian/patches/skipRenderFarmTest_UpstreamBug12 b/debian/patches/skipRenderFarmTest_UpstreamBug12
index 331fe16..435ca78 100644
--- a/debian/patches/skipRenderFarmTest_UpstreamBug12
+++ b/debian/patches/skipRenderFarmTest_UpstreamBug12
@@ -1,3 +1,7 @@
+This patch applied to version 2.54 but is skiped in favour of
+   debian/tests/pkg-perl/smoke-skip
+mentioning the 3 tests that are to be ignored
+
 Subject: remove renderfarm tests
 Description: there is an upstream bug with renderfarm involved
  tests. Upstream bug id 12 has been created witj instructions to
diff --git a/debian/patches/skip_check_installed_test.patch b/debian/patches/skip_check_installed_test.patch
index 14319bc..f80bbe3 100644
--- a/debian/patches/skip_check_installed_test.patch
+++ b/debian/patches/skip_check_installed_test.patch
@@ -6,7 +6,7 @@ Last-Updated: 2012-09-20
 Forwarded: not-needed
 --- a/install_util/GBrowseInstall.pm
 +++ b/install_util/GBrowseInstall.pm
-@@ -636,7 +636,7 @@
+@@ -677,7 +677,7 @@ sub process_conf_files {
  	my $copied = $self->copy_if_modified($_=>'blib');
  	if ($copied || !$self->up_to_date('_build/config_data',"blib/$_")) {
  	    $self->substitute_in_place("blib/$_");
@@ -15,7 +15,7 @@ Forwarded: not-needed
  	}
      }
  
-@@ -698,7 +698,7 @@
+@@ -739,7 +739,7 @@ sub process_htdocs_files {
  	my $copied = $self->copy_if_modified($base=>'blib');
  	if ($copied or !$self->up_to_date('_build/config_data',"blib/$base")) {
  	    $self->substitute_in_place("blib/$base");
@@ -23,8 +23,8 @@ Forwarded: not-needed
 +	    #$self->check_installed($install_path,$base) if $copied;
  	}
      }
- }
-@@ -736,7 +736,7 @@
+ 
+@@ -786,7 +786,7 @@ sub process_etc_files {
  	    my $copied = $self->copy_if_modified($_=>'blib');
  	    if ($copied or !$self->up_to_date('_build/config_data',"blib/$_")) {
  		$self->substitute_in_place("blib/$_");
diff --git a/debian/patches/source_init_functions b/debian/patches/source_init_functions
index 8094b85..d5b07be 100644
--- a/debian/patches/source_init_functions
+++ b/debian/patches/source_init_functions
@@ -5,9 +5,9 @@ Last-Updated: 2014-07-10
 Forwarded: no
 --- a/etc/init.d/gbrowse-slave
 +++ b/etc/init.d/gbrowse-slave
-@@ -25,6 +25,8 @@
- VERBOSITY=1
- NICE=0
+@@ -32,6 +32,8 @@ if [ "$*" != "" ]; then
+     PORT=$*
+ fi
  
 +. /lib/lsb/init-functions
 +
diff --git a/debian/tests/pkg-perl/smoke-skip b/debian/tests/pkg-perl/smoke-skip
new file mode 100644
index 0000000..2f82cd3
--- /dev/null
+++ b/debian/tests/pkg-perl/smoke-skip
@@ -0,0 +1,3 @@
+03.render.t
+04.remoteserver.t
+06.featuresearch.t

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gbrowse.git

More information about the debian-med-commit mailing list