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
> Here is a diff that fixes that. While here, i've moved HOMEPAGE to
> https.
>
> Before:
> Failed 333/334 test programs. 0/0 subtests failed.
>
> After:
> Failed 1/334 test programs. 1/22057 subtests failed.
We also need this patch to make the tests pass, and this module to work,
not sure what perl version this code worked in, but not the one we have
now.
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;
}
We might also want this patch to 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);
> 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.
> Any comment?
>
> 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 8 Feb 2019 21:21:39 -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 +55,10 @@ 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
>
--
andrew - http://afresh1.com
Real programmers don't document.
If it was hard to write, it should be hard to understand.
