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 <[email protected]> +--- 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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
