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bioperl: unbreak tests, fix runtime with Perl 5.28, move HOMEPAGE to https 

Thanks to afresh1@ for patches and hints!

OK afresh1@
This commit is contained in:
cwen 2019-02-21 10:25:48 +00:00
parent ab2abc9293
commit d00e4f9c95
4 changed files with 44 additions and 8 deletions
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12
biology/bioperl/Makefile
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@ -1,13 +1,13 @@
# $OpenBSD: Makefile,v 1.19 2016/04/05 12:21:41 sthen Exp $
# $OpenBSD: Makefile,v 1.20 2019/02/21 10:25:48 cwen Exp $
COMMENT= perl tools for bioinformatics
DISTNAME= BioPerl-1.6.924
REVISION= 0
REVISION= 1
PKGNAME= ${DISTNAME:L}# No p5-prefix here.
CATEGORIES= biology
HOMEPAGE= http://bioperl.org/
HOMEPAGE= https://bioperl.org/
# perl
PERMIT_PACKAGE_CDROM= Yes
@ -19,7 +19,7 @@ PKG_ARCH= *
MODCPAN_EXAMPLES= Yes
MODCPAN_EXAMPLES_DIR= ${PREFIX}/share/examples/bioperl/
CONFIGURE_STYLE=modbuild
CONFIGURE_STYLE= modbuild
BUILD_DEPENDS= ${RUN_DEPENDS}
RUN_DEPENDS= biology/AcePerl \
@ -55,6 +55,10 @@ RUN_DEPENDS= biology/AcePerl \
www/p5-SOAP-Lite \
www/p5-URI \
www/p5-libwww
TEST_DEPENDS= devel/p5-Test-Most \
www/p5-HTML-TableExtract
MAKE_ENV += TEST_POD=Yes
# Optional (not ported) dependencies:
# Postscript-TextBlock

15
biology/bioperl/patches/patch-Bio_Tools_Alignment_Consed_pm Normal file
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@ -0,0 +1,15 @@
$OpenBSD: patch-Bio_Tools_Alignment_Consed_pm,v 1.1 2019/02/21 10:25:48 cwen Exp $
Fix:
Error: Can't redeclare "my" in "my"
Index: Bio/Tools/Alignment/Consed.pm
--- Bio/Tools/Alignment/Consed.pm.orig
+++ Bio/Tools/Alignment/Consed.pm
@@ -1709,7 +1709,7 @@ Recursion is kewl, but this sub should likely be _reve
sub reverse_recurse($$) {
- my ($r_source,my $r_destination) = @_;
+ my ($r_source, $r_destination) = @_;
if (!@$r_source) {
return $r_destination;
}

16
biology/bioperl/patches/patch-Bio_Tools_SiRNA_Ruleset_tuschl_pm Normal file
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@ -0,0 +1,16 @@
$OpenBSD: patch-Bio_Tools_SiRNA_Ruleset_tuschl_pm,v 1.1 2019/02/21 10:25:48 cwen Exp $
Avoid some of the super annoying warnings about deprecated braces
Index: Bio/Tools/SiRNA/Ruleset/tuschl.pm
--- Bio/Tools/SiRNA/Ruleset/tuschl.pm.orig
+++ Bio/Tools/SiRNA/Ruleset/tuschl.pm
@@ -178,8 +178,8 @@ sub _get_oligos {
my $target = $2;
# check for too many Gs (or Cs on the other strand)
- next if ( $target =~ /G{ $self->gstring,}/io );
- next if ( $target =~ /C{ $self->gstring,}/io );
+ next if ( $target =~ /G\{ $self->gstring,\}/io );
+ next if ( $target =~ /C\{ $self->gstring,\}/io );
# skip Ns (for filtering)
next if ( $target =~ /N/i);

9
biology/bioperl/patches/patch-maintenance_symlink_script_pl
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@ -1,7 +1,8 @@
$OpenBSD: patch-maintenance_symlink_script_pl,v 1.1 2014/03/23 13:10:22 nigel Exp $
--- maintenance/symlink_script.pl.orig Tue Sep 29 17:33:45 2009
+++ maintenance/symlink_script.pl Sat Mar 22 22:54:28 2014
@@ -12,7 +13,9 @@ my %symlink_scripts = ('bp_bulk_load_gff.pl' => 'bp_pg
$OpenBSD: patch-maintenance_symlink_script_pl,v 1.2 2019/02/21 10:25:48 cwen Exp $
Index: maintenance/symlink_script.pl
--- maintenance/symlink_script.pl.orig
+++ maintenance/symlink_script.pl
@@ -12,7 +12,9 @@ my %symlink_scripts = ('bp_bulk_load_gff.pl' => 'bp_pg
# installation process installs the symlink as the actual file, so we may as
# well have just done a copy