On Fri, 15 Feb 2019 15:23:48 -0700
Andrew Hewus Fresh wrote:
> On Fri, Feb 08, 2019 at 10:43:27PM +0100, Charlene Wendling wrote:
> >
> > I've noticed (since too long already) when testing reverse depends
> > that only one of the biology/bioperl tests is ran, due to a lack of
> > TEST_DEPENDS.
>
>
> OK afresh1@, with the below patch
>
I added them.
> > biology/p5-Bio-ASN1-EntrezGene could have been added but then it
> > creates a circular dependency.
>
> Can it just be a TEST_DEPENDS and not a BUILD_DEPENDS?
> or is there some RUN_DEPENDS conflict you meant?
>
> Just adding it to TEST_DEPENDS worked for me.
>
A straight 'make test' for biology/bioperl doesn't work:
Can't install p5-Bio-ASN1-EntrezGene-1.10p2v0: can't resolve
bioperl-1.6.924p1
You need to install biology/bioperl before really testing it. I don't
know if it's acceptable, i added it though.
I'm letting the diff here for more comments.
Charlène.
Index: Makefile
===================================================================
RCS file: /cvs/ports/biology/bioperl/Makefile,v
retrieving revision 1.19
diff -u -p -u -p -r1.19 Makefile
--- Makefile 5 Apr 2016 12:21:41 -0000 1.19
+++ Makefile 18 Feb 2019 23:18:49 -0000
@@ -3,11 +3,11 @@
COMMENT= perl tools for bioinformatics
DISTNAME= BioPerl-1.6.924
-REVISION= 0
+REVISION= 1
PKGNAME= ${DISTNAME:L}# No p5-prefix here.
CATEGORIES= biology
-HOMEPAGE= http://bioperl.org/
+HOMEPAGE= https://bioperl.org/
# perl
PERMIT_PACKAGE_CDROM= Yes
@@ -55,6 +55,11 @@ RUN_DEPENDS= biology/AcePerl \
www/p5-SOAP-Lite \
www/p5-URI \
www/p5-libwww
+TEST_DEPENDS= biology/p5-Bio-ASN1-EntrezGene \
+ devel/p5-Test-Most \
+ www/p5-HTML-TableExtract
+
+MAKE_ENV += TEST_POD=Yes
# Optional (not ported) dependencies:
# Postscript-TextBlock
Index: patches/patch-Bio_Tools_Alignment_Consed_pm
===================================================================
RCS file: patches/patch-Bio_Tools_Alignment_Consed_pm
diff -N patches/patch-Bio_Tools_Alignment_Consed_pm
--- /dev/null 1 Jan 1970 00:00:00 -0000
+++ patches/patch-Bio_Tools_Alignment_Consed_pm 18 Feb 2019 23:18:49 -0000
@@ -0,0 +1,15 @@
+$OpenBSD$
+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 $r_destination;
+ }
Index: patches/patch-Bio_Tools_SiRNA_Ruleset_tuschl_pm
===================================================================
RCS file: patches/patch-Bio_Tools_SiRNA_Ruleset_tuschl_pm
diff -N patches/patch-Bio_Tools_SiRNA_Ruleset_tuschl_pm
--- /dev/null 1 Jan 1970 00:00:00 -0000
+++ patches/patch-Bio_Tools_SiRNA_Ruleset_tuschl_pm 18 Feb 2019 23:18:49
-0000
@@ -0,0 +1,16 @@
+$OpenBSD$
+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);
+
Index: patches/patch-maintenance_symlink_script_pl
===================================================================
RCS file:
/cvs/ports/biology/bioperl/patches/patch-maintenance_symlink_script_pl,v
retrieving revision 1.1
diff -u -p -u -p -r1.1 patch-maintenance_symlink_script_pl
--- patches/patch-maintenance_symlink_script_pl 23 Mar 2014 13:10:22 -0000
1.1
+++ patches/patch-maintenance_symlink_script_pl 18 Feb 2019 23:18:49 -0000
@@ -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
+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
