From e2b9177a1b3b7b4dece69db0355e6b282cfd4788 Mon Sep 17 00:00:00 2001 From: Wen Heping Date: Fri, 4 Dec 2009 11:50:10 +0000 Subject: - Update to 1.6.1 Approved by: maintainer (via Email) --- biology/p5-bioperl/files/patch-Bio-Root-Build.pm | 73 ++++++++++++++++++++++++ biology/p5-bioperl/files/patch-Build.PL | 19 +++--- biology/p5-bioperl/files/patch-Build.pm | 73 ------------------------ 3 files changed, 84 insertions(+), 81 deletions(-) create mode 100644 biology/p5-bioperl/files/patch-Bio-Root-Build.pm delete mode 100644 biology/p5-bioperl/files/patch-Build.pm (limited to 'biology/p5-bioperl/files') diff --git a/biology/p5-bioperl/files/patch-Bio-Root-Build.pm b/biology/p5-bioperl/files/patch-Bio-Root-Build.pm new file mode 100644 index 000000000000..0b1369eb05eb --- /dev/null +++ b/biology/p5-bioperl/files/patch-Bio-Root-Build.pm @@ -0,0 +1,73 @@ +--- Bio/Root/Build.pm.orig 2009-09-30 00:33:53.000000000 +0800 ++++ Bio/Root/Build.pm 2009-12-01 10:31:39.000000000 +0800 +@@ -124,48 +124,8 @@ + } + } + closedir($scripts_dir); +- my $question = $int_ok ? "Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively?" : "Install [a]ll BioPerl scripts or [n]one?"; +- +- my $prompt = $accept ? 'a' : $self->prompt($question, 'a'); +- +- if ($prompt =~ /^[aA]/) { +- $self->log_info(" - will install all scripts\n"); +- $self->notes(chosen_scripts => 'all'); +- } +- elsif ($prompt =~ /^[iI]/) { +- $self->log_info(" - will install interactively:\n"); +- +- my @chosen_scripts; +- foreach my $group_dir (@group_dirs) { +- my $group = File::Basename::basename($group_dir); +- print " * group '$group' has:\n"; +- +- my @script_files = @{$self->rscan_dir($group_dir, qr/\.PLS$|\.pl$/)}; +- foreach my $script_file (@script_files) { +- my $script = File::Basename::basename($script_file); +- print " $script\n"; +- } +- +- my $result = $self->prompt(" Install scripts for group '$group'? [y]es [n]o [q]uit", 'n'); +- die if $result =~ /^[qQ]/; +- if ($result =~ /^[yY]/) { +- $self->log_info(" + will install group '$group'\n"); +- push(@chosen_scripts, @script_files); +- } +- else { +- $self->log_info(" - will not install group '$group'\n"); +- } +- } +- +- my $chosen_scripts = @chosen_scripts ? join("|", @chosen_scripts) : 'none'; +- +- $self->notes(chosen_scripts => $chosen_scripts); +- } +- else { +- $self->log_info(" - won't install any scripts\n"); +- $self->notes(chosen_scripts => 'none'); +- } +- ++ $self->log_info(" - will install all scripts\n"); ++ $self->notes(chosen_scripts => 'all'); + print "\n"; + } + +@@ -1205,16 +1165,9 @@ + sub prompt_for_network { + my ($self, $accept) = @_; + +- my $proceed = $accept ? 0 : $self->y_n("Do you want to run tests that require connection to servers across the internet\n(likely to cause some failures)? y/n", 'n'); +- +- if ($proceed) { +- $self->notes(network => 1); +- $self->log_info(" - will run internet-requiring tests\n"); +- } +- else { +- $self->notes(network => 0); +- $self->log_info(" - will not run internet-requiring tests\n"); +- } ++ my $proceed = 0; ++ $self->notes(network => 0); ++ $self->log_info(" - will not run internet-requiring tests\n"); + } + + 1; diff --git a/biology/p5-bioperl/files/patch-Build.PL b/biology/p5-bioperl/files/patch-Build.PL index b6f498ff7505..5e617cc16be0 100644 --- a/biology/p5-bioperl/files/patch-Build.PL +++ b/biology/p5-bioperl/files/patch-Build.PL @@ -1,6 +1,6 @@ ---- Build.PL.orig 2009-01-25 02:19:13.000000000 -0300 -+++ Build.PL 2009-02-22 02:21:33.000000000 -0300 -@@ -36,7 +36,7 @@ +--- Build.PL.orig 2009-09-30 00:33:45.000000000 +0800 ++++ Build.PL 2009-12-01 10:25:51.000000000 +0800 +@@ -37,7 +37,7 @@ 'Test::More' => 0, 'Module::Build' => 0.2805, 'Test::Harness' => 2.62, @@ -9,7 +9,7 @@ }, recommends => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml 'Ace' => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace', -@@ -214,83 +214,8 @@ +@@ -234,86 +234,9 @@ sub prompt_for_biodb { my $accept = shift; @@ -19,7 +19,7 @@ - - if ($proceed) { - my @driver_choices; -- foreach my $poss ('mysql', 'Pg', 'Oracle') { +- foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') { - if (grep {/$poss/i} @drivers) { - my $choice = $poss; - $choice =~ s/^(.)/[$1]/; @@ -44,6 +44,9 @@ - elsif ($driver =~ /^[oO]/) { - $driver = 'Oracle'; - } +- elsif ($driver =~ /^[sS]/) { +- $driver = 'SQLite'; +- } - - my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n". - "This database should already be present but doesn't have to ". @@ -58,7 +61,7 @@ - } - - my $test_dsn; -- if ($driver eq 'Pg') { +- if ($driver eq 'Pg' || $driver eq 'SQLite') { - $test_dsn = "dbi:$driver:dbname=$test_db"; - $mysql_ok = 0; - } @@ -84,12 +87,12 @@ - " User $test_user\n", - " Password $test_pass\n"); - $build->log_info(" - will not run the BioDBSeqFeature live ". -- "database tests (requires MySQL driver)\n") unless ($driver eq 'mysql'); +- "database tests (requires MySQL or Pg driver)\n") unless ($driver eq 'mysql' or $driver eq 'Pg'); - } - else { - $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"); - } -- + + my $proceed = 0; + $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"); $build->log_info("\n"); diff --git a/biology/p5-bioperl/files/patch-Build.pm b/biology/p5-bioperl/files/patch-Build.pm deleted file mode 100644 index bdca7e89404b..000000000000 --- a/biology/p5-bioperl/files/patch-Build.pm +++ /dev/null @@ -1,73 +0,0 @@ ---- Bio/Root/Build.pm.orig 2009-01-25 02:19:26.000000000 -0300 -+++ Bio/Root/Build.pm 2009-02-22 02:24:05.000000000 -0300 -@@ -141,48 +141,8 @@ - } - } - closedir($scripts_dir); -- my $question = $int_ok ? "Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively?" : "Install [a]ll Bioperl scripts or [n]one?"; -- -- my $prompt = $accept ? 'a' : $self->prompt($question, 'a'); -- -- if ($prompt =~ /^[aA]/) { -- $self->log_info(" - will install all scripts\n"); -- $self->notes(chosen_scripts => 'all'); -- } -- elsif ($prompt =~ /^[iI]/) { -- $self->log_info(" - will install interactively:\n"); -- -- my @chosen_scripts; -- foreach my $group_dir (@group_dirs) { -- my $group = File::Basename::basename($group_dir); -- print " * group '$group' has:\n"; -- -- my @script_files = @{$self->rscan_dir($group_dir, qr/\.PLS$|\.pl$/)}; -- foreach my $script_file (@script_files) { -- my $script = File::Basename::basename($script_file); -- print " $script\n"; -- } -- -- my $result = $self->prompt(" Install scripts for group '$group'? [y]es [n]o [q]uit", 'n'); -- die if $result =~ /^[qQ]/; -- if ($result =~ /^[yY]/) { -- $self->log_info(" + will install group '$group'\n"); -- push(@chosen_scripts, @script_files); -- } -- else { -- $self->log_info(" - will not install group '$group'\n"); -- } -- } -- -- my $chosen_scripts = @chosen_scripts ? join("|", @chosen_scripts) : 'none'; -- -- $self->notes(chosen_scripts => $chosen_scripts); -- } -- else { -- $self->log_info(" - won't install any scripts\n"); -- $self->notes(chosen_scripts => 'none'); -- } -- -+ $self->log_info(" - will install all scripts\n"); -+ $self->notes(chosen_scripts => 'all'); - print "\n"; - } - -@@ -1177,16 +1137,9 @@ - sub prompt_for_network { - my ($self, $accept) = @_; - -- my $proceed = $accept ? 0 : $self->y_n("Do you want to run tests that require connection to servers across the internet\n(likely to cause some failures)? y/n", 'n'); -- -- if ($proceed) { -- $self->notes(network => 1); -- $self->log_info(" - will run internet-requiring tests\n"); -- } -- else { -- $self->notes(network => 0); -- $self->log_info(" - will not run internet-requiring tests\n"); -- } -+ my $proceed = 0; -+ $self->notes(network => 0); -+ $self->log_info(" - will not run internet-requiring tests\n"); - } - - 1; -- cgit v1.2.3