[FIX] biology/bioperl: enable tests, https HOMEPAGE

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[FIX] biology/bioperl: enable tests, https HOMEPAGE

Charlene Wendling

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.

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.

biology/p5-Bio-ASN1-EntrezGene could have been added but then it
creates a circular dependency.


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

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Re: [FIX] biology/bioperl: enable tests, https HOMEPAGE

Andrew Hewus Fresh
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.

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Re: [FIX] biology/bioperl: enable tests, https HOMEPAGE

Charlene Wendling
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