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p5-Bio-ASN1-EntrezGene: fix unescaped left braces in regexes that

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generated warnings that made tests failing.

OK sthen@
This commit is contained in:
cwen 2019-08-09 16:03:10 +00:00
parent 6855453486
commit 9bf3f6048c
3 changed files with 52 additions and 2 deletions
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4
biology/p5-Bio-ASN1-EntrezGene/Makefile
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@ -1,11 +1,11 @@
# $OpenBSD: Makefile,v 1.12 2019/07/12 20:43:44 sthen Exp $
# $OpenBSD: Makefile,v 1.13 2019/08/09 16:03:10 cwen Exp $
COMMENT = regular expression-based parser for NCBI Entrez Gene
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

25
biology/p5-Bio-ASN1-EntrezGene/patches/patch-lib_Bio_ASN1_EntrezGene_pm Normal file
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@ -0,0 +1,25 @@
$OpenBSD: patch-lib_Bio_ASN1_EntrezGene_pm,v 1.1 2019/08/09 16:03:10 cwen Exp $
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());

25
biology/p5-Bio-ASN1-EntrezGene/patches/patch-lib_Bio_ASN1_Sequence_pm Normal file
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@ -0,0 +1,25 @@
$OpenBSD: patch-lib_Bio_ASN1_Sequence_pm,v 1.1 2019/08/09 16:03:10 cwen Exp $
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());