[med-svn] [Git][med-team/gff2aplot][master] 2 commits: Add patch fixing some perlcritic issues, refresh perl_5.28.patch
Alexandre Mestiashvili
gitlab at salsa.debian.org
Wed Jan 30 10:20:46 GMT 2019
Alexandre Mestiashvili pushed to branch master at Debian Med / gff2aplot
Commits:
2892e5c5 by Alexandre Mestiashvili at 2019-01-30T09:40:03Z
Add patch fixing some perlcritic issues, refresh perl_5.28.patch
- - - - -
fff5d5ab by Alexandre Mestiashvili at 2019-01-30T10:20:09Z
Update perl_5.28.patch implement a better check for nested data structure
- - - - -
3 changed files:
- + debian/patches/non_lexical_loop_iterator.patch
- debian/patches/perl_5.28.patch
- debian/patches/series
Changes:
=====================================
debian/patches/non_lexical_loop_iterator.patch
=====================================
@@ -0,0 +1,87 @@
+Description: Make sure that iterator variable is explicitely decalred as
+ a lexcical using my keyword. See PBP, page 108. Add perl shebang.
+From: Alex Mestiashvili <amestia at rsh2.donotuse.de>
+--- gff2aplot.orig/src/gff2aplot.pl
++++ gff2aplot/src/gff2aplot.pl
+@@ -1,3 +1,4 @@
++#!/usr/bin/perl
+ #
+ # %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ # % GFF2APLOT %
+@@ -1663,7 +1664,7 @@
+ &report( 'NO_CUSTOM_FOUND', $file );
+ last MAIN;
+ };
+- LOAD: foreach $file (@custom_files) {
++ LOAD: foreach my $file (@custom_files) {
+ open( THIS, "< $file" )
+ || ( &warn( 'FILE_NO_OPEN', $T, $file ), next LOAD );
+ &report( 'READ_CUSTOM_FILE', $file );
+@@ -1934,7 +1935,7 @@
+
+ sub parse_GFF_files() {
+ &header("PARSING INPUT GFF RECORDS");
+- LOAD: foreach $file (@data_files) {
++ LOAD: foreach my $file (@data_files) {
+ open( THIS, "< $file" )
+ || ( &warn( 'FILE_NO_OPEN', $T, $file ), next LOAD );
+ $file eq '-' && ( $file = 'STANDARD INPUT' );
+@@ -2665,13 +2666,13 @@
+ my ( $out, $v );
+ $out = 0; #
+ # print STDERR ("#"x40)."\n";
+- foreach $v (qw/ FEATURE GROUP STRAND SOURCE SEQUENCE /) {
++ foreach my $v (qw/ FEATURE GROUP STRAND SOURCE SEQUENCE /) {
+
+ # print STDERR "### GET LAYER: $v ($name) : ".
+ # (defined($Defaults{$v}{$name})?$Defaults{$v}{$name}:"undef")."\n";
+ defined( $Defaults{$v}{$name} ) && ( $out = $Defaults{$v}{$name} );
+ }; # foreach
+- foreach $v (@refs) {
++ foreach my $v (@refs) {
+
+ # print STDERR "### GET LAYER: $v ($name) : ".
+ # (defined($v->{$name})?$v->{$name}:"undef")."\n";
+@@ -3002,7 +3003,7 @@
+
+ #
+ ( $sq_a, $sq_b ) = @$_ra;
+- foreach $naln (@$_ro) {
++ foreach my $naln (@$_ro) {
+ ( $nm_a, $nm_b ) = split /:/o, $naln->[0], 2;
+ ( "$nm_a" eq "$sq_a" && "$nm_b" eq "$sq_b" ) && do {
+ @$_ra = ( $nm_a, $nm_b );
+@@ -3010,7 +3011,7 @@
+ };
+ }; # foreach $naln
+ # swapping
+- foreach $naln (@$_ro) {
++ foreach my $naln (@$_ro) {
+ ( $nm_a, $nm_b ) = split /:/o, $naln->[0], 2;
+ ( "$nm_a" eq "$sq_b" && "$nm_b" eq "$sq_a" ) && do {
+ @$_ra = ( $nm_a, $nm_b );
+@@ -3024,7 +3025,7 @@
+ sub search_seqname() {
+ my ( $sq_a, $sq_b, $_ro ) = @_;
+ my ( $a_found, $naln );
+- foreach $naln (@$_ro) {
++ foreach my $naln (@$_ro) {
+ ( $sq_a eq '.+' && defined($sq_b) && "$naln->[0]" eq "$sq_b" ) && next;
+ ( $sq_a eq '.+' || "$naln->[0]" eq "$sq_a" ) && do {
+ $sq_a = $naln->[0];
+@@ -4279,13 +4280,13 @@
+ my ( $out, $v );
+
+ # print STDERR ("#"x40)."\n";
+- foreach $v (qw/ FEATURE GROUP STRAND SOURCE SEQUENCE /) {
++ foreach my $v (qw/ FEATURE GROUP STRAND SOURCE SEQUENCE /) {
+ defined( $Defaults{$v}{$name} ) && ( $out = $Defaults{$v}{$name} );
+
+ # print STDERR "### GET VAR VALUE: $v ($name) : ".
+ # (defined($Defaults{$v}{$name})?$Defaults{$v}{$name}:"undef")."\n";
+ }; # foreach
+- foreach $v (@$refs) {
++ foreach my $v (@$refs) {
+ defined( $v->[$_prop]{$name} ) && ( $out = $v->[$_prop]{$name} );
+
+ # print STDERR "### GET VAR VALUE: $v ($name) : ".
=====================================
debian/patches/perl_5.28.patch
=====================================
@@ -2,18 +2,20 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Mon, 10 Dec 2018 07:36:57 +0100
Description: Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/bin/gff2aplot line 1737.
---- a/src/gff2aplot.pl
-+++ b/src/gff2aplot.pl
-@@ -1733,7 +1734,7 @@ sub varscheck() {
+--- gff2aplot.orig/src/gff2aplot.pl
++++ gff2aplot/src/gff2aplot.pl
+@@ -1734,8 +1734,8 @@
|| return $F;
$flag && do {
my @tmpary = ();
- defined( @{ $varec->{$class}{ $$rec[1] } } ) || do {
-+ @{ $varec->{$class}{ $$rec[1] } } || do {
- @{ $varec->{$class}{ $$rec[1] } } = ();
+- @{ $varec->{$class}{ $$rec[1] } } = ();
++ eval {exists $varec->{$class}{ $$rec[1] }} || do {
++ @{ $varec->{$class}{ $$rec[1] } } = ();
};
@tmpary = &find_regexp( $$rec[0] );
-@@ -2930,7 +2931,8 @@ sub set_page_axes() {
+ $tmpary[3] = lc( $tmpary[3] ) if ( $class eq 'FEATURE' );
+@@ -2931,7 +2931,8 @@
( $vrf->{_x_sequence_name}, $vrf->{_y_sequence_name} ) = split /:/o,
$vrf->{alignment_name}, 2;
}
@@ -23,7 +25,7 @@ Description: Can't use 'defined(@array)' (Maybe you should just omit the defined
( $vrf->{_x_sequence_name}, $vrf->{_y_sequence_name} ) = split /:/o,
$Order{ALN}[0][0], 2;
}
-@@ -3730,7 +3732,11 @@ sub fill_mid() {
+@@ -3731,7 +3732,11 @@
sub counter { # $_[0]~current_pos++ $_[1]~char
my $str;
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+non_lexical_loop_iterator.patch
02-blat2gff.diff
03-parseblast.diff
use-dpkg-buildflags.patch
View it on GitLab: https://salsa.debian.org/med-team/gff2aplot/compare/7eaea1fe1e0becc8047ceae2e8ec764507e388b9...fff5d5ab38c06272b476e9a4620f4460eacb0c7a
--
View it on GitLab: https://salsa.debian.org/med-team/gff2aplot/compare/7eaea1fe1e0becc8047ceae2e8ec764507e388b9...fff5d5ab38c06272b476e9a4620f4460eacb0c7a
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