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 <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
