Re: [fix] biology/p5-Bio-ASN1-EntrezGene: fix unescaped left braces

Ping.

On Wed, 17 Jul 2019 19:11:59 +0200
Charlene Wendling wrote:

>
> This version of this module contains unescaped left braces that, while
> not fatal until Perl 5.32, mark the tests as failing when it should
> not.
>
>
> I'm proposing a patch to fix that. There are no consumers. Indeed now
> 'make test' passes.
>
> OK?
>
> Charlène.

Index: Makefile
===================================================================
RCS file: /cvs/ports/biology/p5-Bio-ASN1-EntrezGene/Makefile,v
retrieving revision 1.12
diff -u -p -u -p -r1.12 Makefile
--- Makefile 12 Jul 2019 20:43:44 -0000 1.12
+++ Makefile 17 Jul 2019 17:08:19 -0000
@@ -5,7 +5,7 @@ COMMENT = regular expression-based pars
M = 1.10-withoutworldwriteables
DISTNAME = Bio-ASN1-EntrezGene-${M}
PKGNAME = p5-Bio-ASN1-EntrezGene-${M:S/-withoutworldwriteables//}
-REVISION = 2
+REVISION = 3
EPOCH = 0
CATEGORIES = biology

Index: patches/patch-lib_Bio_ASN1_EntrezGene_pm
===================================================================
RCS file: patches/patch-lib_Bio_ASN1_EntrezGene_pm
diff -N patches/patch-lib_Bio_ASN1_EntrezGene_pm
--- /dev/null 1 Jan 1970 00:00:00 -0000
+++ patches/patch-lib_Bio_ASN1_EntrezGene_pm 17 Jul 2019 17:08:19 -0000
@@ -0,0 +1,25 @@
+$OpenBSD$
+
+Fix unescaped left braces so it does not generate warnings with Perl 5.28
+
+Index: lib/Bio/ASN1/EntrezGene.pm
+--- lib/Bio/ASN1/EntrezGene.pm.orig
++++ lib/Bio/ASN1/EntrezGene.pm
+@@ -270,7 +270,7 @@ sub next_seq
+ {
+ chomp;
+ next unless /\S/;
+- my $tmp = (/^\s*Entrezgene ::= ({.*)/si)? $1 : "{" . $_; # get rid of the 'Entrezgene ::= ' at the beginning of Entrez Gene record
++ my $tmp = (/^\s*Entrezgene ::= (\{.*)/si)? $1 : "{" . $_; # get rid of the 'Entrezgene ::= ' at the beginning of Entrez Gene record
+ return $self->parse($tmp, $compact, 1); # 1 species no resetting line number
+ }
+ }
+@@ -324,7 +324,7 @@ sub _parse
+ elsif($data->{$id}) { $data->{$id} = [$data->{$id}, $value] } # hash value has a second terminal value now!
+ else { $data->{$id} = $value } # the first terminal value
+ }
+- elsif($self->{input} =~ /\G{/cg)
++ elsif($self->{input} =~ /\G\{/cg)
+ {
+ $self->{depth}++;
+ push(@{$data->{$id}}, $self->_parse());
Index: patches/patch-lib_Bio_ASN1_Sequence_pm
===================================================================
RCS file: patches/patch-lib_Bio_ASN1_Sequence_pm
diff -N patches/patch-lib_Bio_ASN1_Sequence_pm
--- /dev/null 1 Jan 1970 00:00:00 -0000
+++ patches/patch-lib_Bio_ASN1_Sequence_pm 17 Jul 2019 17:08:19 -0000
@@ -0,0 +1,25 @@
+$OpenBSD$
+
+Fix unescaped braces as it triggers a warning with Perl 5.28
+
+Index: lib/Bio/ASN1/Sequence.pm
+--- lib/Bio/ASN1/Sequence.pm.orig
++++ lib/Bio/ASN1/Sequence.pm
+@@ -256,7 +256,7 @@ sub next_seq
+ {
+ chomp;
+ next unless /\S/;
+- my $tmp = (/^\s*Seq-entry ::= set ({.*)/si)? $1 : "{" . $_; # get rid of the 'Seq-entry ::= set ' at the beginning of Sequence record
++ my $tmp = (/^\s*Seq-entry ::= set (\{.*)/si)? $1 : "{" . $_; # get rid of the 'Seq-entry ::= set ' at the beginning of Sequence record
+ return $self->parse($tmp, $compact, 1); # 1 species no resetting line number
+ }
+ }
+@@ -317,7 +317,7 @@ sub _parse
+ elsif($data->{$id}) { $data->{$id} = [$data->{$id}, $value] } # hash value has a second terminal value now!
+ else { $data->{$id} = $value } # the first terminal value
+ }
+- elsif($self->{input} =~ /\G{/cg)
++ elsif($self->{input} =~ /\G\{/cg)
+ {
+ $self->{depth}++;
+ push(@{$data->{$id}}, $self->_parse());