Stagify, remove BROKEN.

2 files changed, 107 insertions, 112 deletions

diff --git a/biology/p5-Bio-Graphics/Makefile b/biology/p5-Bio-Graphics/Makefile
index 6374f4bdc281..4486196f86d1 100644
--- a/biology/p5-Bio-Graphics/Makefile
+++ b/biology/p5-Bio-Graphics/Makefile
@@ -13,7 +13,6 @@ COMMENT=	Generate GD Images of Bio::Seq Objects
 LICENSE=	ART10 GPLv1
 LICENSE_COMB=	dual
 
-BROKEN=		not staged
 BUILD_DEPENDS=	p5-Bio-SCF>=1.01:${PORTSDIR}/biology/p5-Bio-SCF \
 		p5-GD>=2.30:${PORTSDIR}/graphics/p5-GD \
 		p5-GD-SVG>=0.32:${PORTSDIR}/graphics/p5-GD-SVG \
@@ -24,110 +23,4 @@ RUN_DEPENDS:=	${BUILD_DEPENDS}
 USES=		perl5
 USE_PERL5=	configure
 
-MAN1=		contig_draw.pl.1 \
-		feature_draw.pl.1 \
-		frend.pl.1 \
-		search_overview.pl.1
-MAN3=		Bio::Graphics.3 \
-		Bio::Graphics::ConfiguratorI.3 \
-		Bio::Graphics::DrawTransmembrane.3 \
-		Bio::Graphics::Feature.3 \
-		Bio::Graphics::FeatureBase.3 \
-		Bio::Graphics::FeatureDir.3 \
-		Bio::Graphics::FeatureFile.3 \
-		Bio::Graphics::FeatureFile::Iterator.3 \
-		Bio::Graphics::Glyph.3 \
-		Bio::Graphics::Glyph::Factory.3 \
-		Bio::Graphics::Glyph::alignment.3 \
-		Bio::Graphics::Glyph::allele_tower.3 \
-		Bio::Graphics::Glyph::anchored_arrow.3 \
-		Bio::Graphics::Glyph::arrow.3 \
-		Bio::Graphics::Glyph::box.3 \
-		Bio::Graphics::Glyph::broken_line.3 \
-		Bio::Graphics::Glyph::cds.3 \
-		Bio::Graphics::Glyph::christmas_arrow.3 \
-		Bio::Graphics::Glyph::crossbox.3 \
-		Bio::Graphics::Glyph::dashed_line.3 \
-		Bio::Graphics::Glyph::decorated_gene.3 \
-		Bio::Graphics::Glyph::decorated_transcript.3 \
-		Bio::Graphics::Glyph::diamond.3 \
-		Bio::Graphics::Glyph::dna.3 \
-		Bio::Graphics::Glyph::dot.3 \
-		Bio::Graphics::Glyph::dumbbell.3 \
-		Bio::Graphics::Glyph::ellipse.3 \
-		Bio::Graphics::Glyph::ex.3 \
-		Bio::Graphics::Glyph::extending_arrow.3 \
-		Bio::Graphics::Glyph::fb_shmiggle.3 \
-		Bio::Graphics::Glyph::fixedwidth.3 \
-		Bio::Graphics::Glyph::flag.3 \
-		Bio::Graphics::Glyph::gene.3 \
-		Bio::Graphics::Glyph::generic.3 \
-		Bio::Graphics::Glyph::graded_segments.3 \
-		Bio::Graphics::Glyph::group.3 \
-		Bio::Graphics::Glyph::hat.3 \
-		Bio::Graphics::Glyph::heat_map.3 \
-		Bio::Graphics::Glyph::heat_map_ideogram.3 \
-		Bio::Graphics::Glyph::heterogeneous_segments.3 \
-		Bio::Graphics::Glyph::hidden.3 \
-		Bio::Graphics::Glyph::hybrid_plot.3 \
-		Bio::Graphics::Glyph::ideogram.3 \
-		Bio::Graphics::Glyph::image.3 \
-		Bio::Graphics::Glyph::lightning.3 \
-		Bio::Graphics::Glyph::line.3 \
-		Bio::Graphics::Glyph::merge_parts.3 \
-		Bio::Graphics::Glyph::merged_alignment.3 \
-		Bio::Graphics::Glyph::minmax.3 \
-		Bio::Graphics::Glyph::operon.3 \
-		Bio::Graphics::Glyph::oval.3 \
-		Bio::Graphics::Glyph::pairplot.3 \
-		Bio::Graphics::Glyph::pentagram.3 \
-		Bio::Graphics::Glyph::phylo_align.3 \
-		Bio::Graphics::Glyph::pinsertion.3 \
-		Bio::Graphics::Glyph::primers.3 \
-		Bio::Graphics::Glyph::processed_transcript.3 \
-		Bio::Graphics::Glyph::protein.3 \
-		Bio::Graphics::Glyph::ragged_ends.3 \
-		Bio::Graphics::Glyph::rainbow_gene.3 \
-		Bio::Graphics::Glyph::redgreen_box.3 \
-		Bio::Graphics::Glyph::redgreen_segment.3 \
-		Bio::Graphics::Glyph::repeating_shape.3 \
-		Bio::Graphics::Glyph::rndrect.3 \
-		Bio::Graphics::Glyph::ruler_arrow.3 \
-		Bio::Graphics::Glyph::saw_teeth.3 \
-		Bio::Graphics::Glyph::scale.3 \
-		Bio::Graphics::Glyph::segmented_keyglyph.3 \
-		Bio::Graphics::Glyph::segments.3 \
-		Bio::Graphics::Glyph::so_transcript.3 \
-		Bio::Graphics::Glyph::span.3 \
-		Bio::Graphics::Glyph::spectrogram.3 \
-		Bio::Graphics::Glyph::splice_site.3 \
-		Bio::Graphics::Glyph::stackedplot.3 \
-		Bio::Graphics::Glyph::ternary_plot.3 \
-		Bio::Graphics::Glyph::text_in_box.3 \
-		Bio::Graphics::Glyph::three_letters.3 \
-		Bio::Graphics::Glyph::tic_tac_toe.3 \
-		Bio::Graphics::Glyph::toomany.3 \
-		Bio::Graphics::Glyph::trace.3 \
-		Bio::Graphics::Glyph::track.3 \
-		Bio::Graphics::Glyph::transcript.3 \
-		Bio::Graphics::Glyph::transcript2.3 \
-		Bio::Graphics::Glyph::translation.3 \
-		Bio::Graphics::Glyph::triangle.3 \
-		Bio::Graphics::Glyph::two_bolts.3 \
-		Bio::Graphics::Glyph::vista_plot.3 \
-		Bio::Graphics::Glyph::wave.3 \
-		Bio::Graphics::Glyph::weighted_arrow.3 \
-		Bio::Graphics::Glyph::whiskerplot.3 \
-		Bio::Graphics::Glyph::wiggle_box.3 \
-		Bio::Graphics::Glyph::wiggle_density.3 \
-		Bio::Graphics::Glyph::wiggle_xyplot.3 \
-		Bio::Graphics::Glyph::xyplot.3 \
-		Bio::Graphics::Panel.3 \
-		Bio::Graphics::Pictogram.3 \
-		Bio::Graphics::RendererI.3 \
-		Bio::Graphics::Util.3 \
-		Bio::Graphics::Wiggle.3 \
-		Bio::Graphics::Wiggle::Loader.3
-
-NO_STAGE=	yes
 .include <bsd.port.mk>
diff --git a/biology/p5-Bio-Graphics/pkg-plist b/biology/p5-Bio-Graphics/pkg-plist
index 2e0544503bc1..e08c6069432c 100644
--- a/biology/p5-Bio-Graphics/pkg-plist
+++ b/biology/p5-Bio-Graphics/pkg-plist
@@ -4,6 +4,106 @@ bin/frend.pl
 bin/glyph_help.pl
 bin/render_msa.pl
 bin/search_overview.pl
+%%PERL5_MAN3%%/Bio::Graphics.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::ConfiguratorI.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::DrawTransmembrane.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Feature.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::FeatureBase.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::FeatureDir.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::FeatureFile.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::FeatureFile::Iterator.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::Factory.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::alignment.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::allele_tower.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::anchored_arrow.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::arrow.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::box.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::broken_line.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::cds.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::christmas_arrow.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::crossbox.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::dashed_line.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::decorated_gene.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::decorated_transcript.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::diamond.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::dna.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::dot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::dumbbell.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::ellipse.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::ex.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::extending_arrow.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::fb_shmiggle.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::fixedwidth.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::flag.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::gene.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::generic.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::graded_segments.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::group.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::hat.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::heat_map.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::heat_map_ideogram.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::heterogeneous_segments.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::hidden.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::hybrid_plot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::ideogram.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::image.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::lightning.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::line.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::merge_parts.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::merged_alignment.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::minmax.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::operon.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::oval.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::pairplot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::pentagram.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::phylo_align.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::pinsertion.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::primers.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::processed_transcript.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::protein.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::ragged_ends.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::rainbow_gene.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::redgreen_box.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::redgreen_segment.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::repeating_shape.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::rndrect.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::ruler_arrow.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::saw_teeth.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::scale.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::segmented_keyglyph.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::segments.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::so_transcript.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::span.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::spectrogram.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::splice_site.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::stackedplot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::ternary_plot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::text_in_box.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::three_letters.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::tic_tac_toe.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::toomany.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::trace.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::track.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::transcript.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::transcript2.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::translation.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::triangle.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::two_bolts.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::vista_plot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::wave.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::weighted_arrow.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::whiskerplot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::wiggle_box.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::wiggle_density.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::wiggle_xyplot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Glyph::xyplot.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Panel.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Pictogram.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::RendererI.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Util.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Wiggle.3.gz
+%%PERL5_MAN3%%/Bio::Graphics::Wiggle::Loader.3.gz
 %%SITE_PERL%%/Bio/Graphics.pm
 %%SITE_PERL%%/Bio/Graphics/ConfiguratorI.pm
 %%SITE_PERL%%/Bio/Graphics/DrawTransmembrane.pm
@@ -12,6 +112,7 @@ bin/search_overview.pl
 %%SITE_PERL%%/Bio/Graphics/FeatureDir.pm
 %%SITE_PERL%%/Bio/Graphics/FeatureFile.pm
 %%SITE_PERL%%/Bio/Graphics/FeatureFile/Iterator.pm
+%%SITE_PERL%%/Bio/Graphics/GDWrapper.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph/Factory.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph/alignment.pm
@@ -105,7 +206,6 @@ bin/search_overview.pl
 %%SITE_PERL%%/Bio/Graphics/Glyph/wiggle_xyplot.pm
 %%SITE_PERL%%/Bio/Graphics/Glyph/xyplot.pm
 %%SITE_PERL%%/Bio/Graphics/Layout.pm
-%%SITE_PERL%%/Bio/Graphics/GDWrapper.pm
 %%SITE_PERL%%/Bio/Graphics/Panel.pm
 %%SITE_PERL%%/Bio/Graphics/Pictogram.pm
 %%SITE_PERL%%/Bio/Graphics/RendererI.pm
@@ -113,10 +213,12 @@ bin/search_overview.pl
 %%SITE_PERL%%/Bio/Graphics/Wiggle.pm
 %%SITE_PERL%%/Bio/Graphics/Wiggle/Loader.pm
 %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Graphics/.packlist
-@dirrmtry %%SITE_PERL%%/Bio/Graphics/Wiggle
-@dirrmtry %%SITE_PERL%%/Bio/Graphics/Glyph
+man/man1/contig_draw.pl.1.gz
+man/man1/feature_draw.pl.1.gz
+man/man1/frend.pl.1.gz
+man/man1/search_overview.pl.1.gz
 @dirrmtry %%SITE_PERL%%/Bio/Graphics/FeatureFile
+@dirrmtry %%SITE_PERL%%/Bio/Graphics/Glyph
+@dirrmtry %%SITE_PERL%%/Bio/Graphics/Wiggle
 @dirrmtry %%SITE_PERL%%/Bio/Graphics
-@dirrmtry %%SITE_PERL%%/Bio
 @dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/Graphics
-@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio