*/*: sync with upstream

Taken from: FreeBSD
snape7997 · Dec 20, 2016 · 9de83d5 · 9de83d5
1 parent ebed948
commit 9de83d5
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diff --git a/archivers/kf5-karchive/distinfo b/archivers/kf5-karchive/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1475424075
-SHA256 (KDE/frameworks/5.27.0/karchive-5.27.0.tar.xz) = 7f387fa2e0f5360870524d0f2b352179f191d0ed0ea78ec3456964ffab8bebb0
-SIZE (KDE/frameworks/5.27.0/karchive-5.27.0.tar.xz) = 110736
+TIMESTAMP = 1480934869
+SHA256 (KDE/frameworks/5.29.0/karchive-5.29.0.tar.xz) = 9091bba1683eefcae6e27ecce6c7236ac792c173d3efa15f255e5890909c2986
+SIZE (KDE/frameworks/5.29.0/karchive-5.29.0.tar.xz) = 111712
diff --git a/archivers/zstd/Makefile b/archivers/zstd/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	zstd
-PORTVERSION=	1.1.1
+PORTVERSION=	1.1.2
 DISTVERSIONPREFIX=	v
 CATEGORIES=	archivers
 
@@ -23,6 +23,5 @@ MAKE_ARGS=	MANDIR="${PREFIX}/man/man1" \
 		INCLUDEDIR="${PREFIX}/include"
 
 BROKEN_FreeBSD_9=	missing builtin bswap32 and bswap64
-MAKE_JOBS_UNSAFE=	yes
 
 .include <bsd.port.mk>
diff --git a/archivers/zstd/distinfo b/archivers/zstd/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1478078796
-SHA256 (facebook-zstd-v1.1.1_GH0.tar.gz) = a92965a2480fecc6b7bf491106e93cbf69a298b865b6d623755b3a482d77e614
-SIZE (facebook-zstd-v1.1.1_GH0.tar.gz) = 734872
+TIMESTAMP = 1482085591
+SHA256 (facebook-zstd-v1.1.2_GH0.tar.gz) = 980b8febb0118e22f6ed70d23b5b3e600995dbf7489c1f6d6122c1411cdda8d8
+SIZE (facebook-zstd-v1.1.2_GH0.tar.gz) = 769017
diff --git a/archivers/zstd/files/patch-lib_Makefile b/archivers/zstd/files/patch-lib_Makefile
@@ -1,29 +1,29 @@
 --- lib/Makefile.orig	2016-11-01 18:13:22 UTC
 +++ lib/Makefile
-@@ -90,16 +90,16 @@ libzstd.pc: libzstd.pc.in
+@@ -106,16 +106,16 @@ libzstd.pc: libzstd.pc.in
               $< >$@
 
- install: libzstd libzstd.pc
+ install: libzstd.a libzstd libzstd.pc
 -	@install -d -m 755 $(DESTDIR)$(LIBDIR)/pkgconfig/ $(DESTDIR)$(INCLUDEDIR)/
--	@install -m 755 libzstd.$(SHARED_EXT_VER) $(DESTDIR)$(LIBDIR)/libzstd.$(SHARED_EXT_VER)
+-	@install -m 755 libzstd.$(SHARED_EXT_VER) $(DESTDIR)$(LIBDIR)
 -	@cp -a libzstd.$(SHARED_EXT_MAJOR) $(DESTDIR)$(LIBDIR)
 -	@cp -a libzstd.$(SHARED_EXT) $(DESTDIR)$(LIBDIR)
 -	@cp -a libzstd.pc $(DESTDIR)$(LIBDIR)/pkgconfig/
--	@install -m 644 libzstd.a $(DESTDIR)$(LIBDIR)/libzstd.a
--	@install -m 644 zstd.h $(DESTDIR)$(INCLUDEDIR)/zstd.h
--	@install -m 644 common/zstd_errors.h $(DESTDIR)$(INCLUDEDIR)/zstd_errors.h
--	@install -m 644 common/zbuff.h $(DESTDIR)$(INCLUDEDIR)/zbuff.h   # Deprecated streaming functions
--	@install -m 644 dictBuilder/zdict.h $(DESTDIR)$(INCLUDEDIR)/zdict.h
+-	@install -m 644 libzstd.a $(DESTDIR)$(LIBDIR)
+-	@install -m 644 zstd.h $(DESTDIR)$(INCLUDEDIR)
+-	@install -m 644 common/zstd_errors.h $(DESTDIR)$(INCLUDEDIR)
+-	@install -m 644 deprecated/zbuff.h $(DESTDIR)$(INCLUDEDIR)     # prototypes generate deprecation warnings
+-	@install -m 644 dictBuilder/zdict.h $(DESTDIR)$(INCLUDEDIR)
 +	@install -d -m 755 $(DESTDIR)$(PREFIX)/libdata/pkgconfig/ $(DESTDIR)$(INCLUDEDIR)/
-+	@$(BSD_INSTALL_LIB) libzstd.$(SHARED_EXT_VER) $(DESTDIR)$(LIBDIR)/libzstd.$(SHARED_EXT_VER)
++	@$(BSD_INSTALL_LIB) libzstd.$(SHARED_EXT_VER) $(DESTDIR)$(LIBDIR)
 +	@ln -sf libzstd.$(SHARED_EXT_VER) $(DESTDIR)$(LIBDIR)/libzstd.$(SHARED_EXT_MAJOR)
 +	@ln -sf libzstd.$(SHARED_EXT_VER) $(DESTDIR)$(LIBDIR)/libzstd.$(SHARED_EXT)
 +	@$(BSD_INSTALL_DATA) libzstd.pc $(DESTDIR)$(PREFIX)/libdata/pkgconfig/
-+	@$(BSD_INSTALL_LIB) libzstd.a $(DESTDIR)$(LIBDIR)/libzstd.a
-+	@$(BSD_INSTALL_DATA) zstd.h $(DESTDIR)$(INCLUDEDIR)/zstd.h
-+	@$(BSD_INSTALL_DATA) common/zstd_errors.h $(DESTDIR)$(INCLUDEDIR)/zstd_errors.h
-+	@$(BSD_INSTALL_DATA) common/zbuff.h $(DESTDIR)$(INCLUDEDIR)/zbuff.h   # Deprecated streaming functions
-+	@$(BSD_INSTALL_DATA) dictBuilder/zdict.h $(DESTDIR)$(INCLUDEDIR)/zdict.h
++	@$(BSD_INSTALL_LIB) libzstd.a $(DESTDIR)$(LIBDIR)
++	@$(BSD_INSTALL_DATA) zstd.h $(DESTDIR)$(INCLUDEDIR)
++	@$(BSD_INSTALL_DATA) common/zstd_errors.h $(DESTDIR)$(INCLUDEDIR)
++	@$(BSD_INSTALL_DATA) deprecated/zbuff.h $(DESTDIR)$(INCLUDEDIR)     # prototypes generate deprecation warnings
++	@$(BSD_INSTALL_DATA) dictBuilder/zdict.h $(DESTDIR)$(INCLUDEDIR)
  	@echo zstd static and shared library installed
 
  uninstall:
diff --git a/archivers/zstd/files/patch-programs_Makefile b/archivers/zstd/files/patch-programs_Makefile
@@ -1,13 +1,17 @@
 --- programs/Makefile.orig	2016-08-31 16:09:10 UTC
 +++ programs/Makefile
-@@ -129,11 +129,11 @@ ifneq (,$(filter $(shell uname),Linux Da
+@@ -157,13 +157,13 @@ ifneq (,$(filter $(shell uname),Linux Da
  install: zstd
  	@echo Installing binaries
  	@install -d -m 755 $(DESTDIR)$(BINDIR)/ $(DESTDIR)$(MANDIR)/
--	@install -m 755 zstd$(EXT) $(DESTDIR)$(BINDIR)/zstd$(EXT)
-+	@$(BSD_INSTALL_PROGRAM) zstd$(EXT) $(DESTDIR)$(BINDIR)/zstd$(EXT)
- 	@ln -sf zstd$(EXT) $(DESTDIR)$(BINDIR)/zstdcat
- 	@ln -sf zstd$(EXT) $(DESTDIR)$(BINDIR)/unzstd
+-	@install -m 755 zstd $(DESTDIR)$(BINDIR)/zstd
++	@$(BSD_INSTALL_PROGRAM) zstd $(DESTDIR)$(BINDIR)/zstd
+ 	@ln -sf zstd $(DESTDIR)$(BINDIR)/zstdcat
+ 	@ln -sf zstd $(DESTDIR)$(BINDIR)/unzstd
+-	@install -m 755 zstdless $(DESTDIR)$(BINDIR)/zstdless
+-	@install -m 755 zstdgrep $(DESTDIR)$(BINDIR)/zstdgrep
++	@$(BSD_INSTALL_SCRIPT) zstdless $(DESTDIR)$(BINDIR)/zstdless
++	@$(BSD_INSTALL_SCRIPT) zstdgrep $(DESTDIR)$(BINDIR)/zstdgrep
  	@echo Installing man pages
 -	@install -m 644 zstd.1 $(DESTDIR)$(MANDIR)/zstd.1
 +	@$(BSD_INSTALL_MAN) zstd.1 $(DESTDIR)$(MANDIR)/zstd.1

diff --git a/archivers/zstd/pkg-plist b/archivers/zstd/pkg-plist
@@ -1,6 +1,8 @@
 bin/unzstd
 bin/zstd
 bin/zstdcat
+bin/zstdgrep
+bin/zstdless
 include/zbuff.h
 include/zdict.h
 include/zstd.h

diff --git a/astro/libosmium/Makefile b/astro/libosmium/Makefile
@@ -26,6 +26,12 @@ GH_ACCOUNT=	osmcode
 USES=		cmake compiler:c++11-lib
 CMAKE_ARGS=	-DBUILD_EXAMPLES:BOOL=OFF
 
+# if/when corresponding ports appear in the tree, these will need to
+# be turned from depends
+CMAKE_ARGS+=	-DINSTALL_GDALCPP:BOOL=ON \
+		-DINSTALL_PROTOZERO:BOOL=ON \
+		-DINSTALL_UTFCPP:BOOL=ON
+
 # though it builds tests, the library itself is header-only
 NO_ARCH=	yes
 

diff --git a/astro/libosmium/pkg-plist b/astro/libosmium/pkg-plist
@@ -1,3 +1,4 @@
+include/gdalcpp.hpp
 include/osmium/area/assembler.hpp
 include/osmium/area/detail/node_ref_segment.hpp
 include/osmium/area/detail/proto_ring.hpp
@@ -175,3 +176,18 @@ include/osmium/util/timer.hpp
 include/osmium/util/verbose_output.hpp
 include/osmium/version.hpp
 include/osmium/visitor.hpp
+include/protozero/byteswap.hpp
+include/protozero/config.hpp
+include/protozero/exception.hpp
+include/protozero/iterators.hpp
+include/protozero/pbf_builder.hpp
+include/protozero/pbf_message.hpp
+include/protozero/pbf_reader.hpp
+include/protozero/pbf_writer.hpp
+include/protozero/types.hpp
+include/protozero/varint.hpp
+include/protozero/version.hpp
+include/utf8.h
+include/utf8/checked.h
+include/utf8/core.h
+include/utf8/unchecked.h
diff --git a/biology/Makefile b/biology/Makefile
@@ -58,6 +58,7 @@
     SUBDIR += njplot
     SUBDIR += p5-AcePerl
     SUBDIR += p5-Bio-ASN1-EntrezGene
+    SUBDIR += p5-Bio-Coordinate
     SUBDIR += p5-Bio-Das
     SUBDIR += p5-Bio-Das-Lite
     SUBDIR += p5-Bio-GFF3

diff --git a/biology/jellyfish/Makefile b/biology/jellyfish/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	jellyfish
-PORTVERSION=	2.2.4
+PORTVERSION=	2.2.6
 DISTVERSIONPREFIX=	v
 CATEGORIES=	biology
 
@@ -16,8 +16,7 @@ BUILD_DEPENDS=	yaggo:devel/yaggo
 
 GNU_CONFIGURE=	yes
 
-USES=		autoreconf compiler:c++11-lib gmake \
-		libtool pathfix pkgconfig
+USES=		autoreconf compiler:c++11-lib gmake libtool pathfix pkgconfig
 USE_LDCONFIG=	yes
 
 USE_GITHUB=	yes
@@ -26,7 +25,9 @@ GH_PROJECT=	Jellyfish
 
 INSTALL_TARGET=	install-strip
 
-BROKEN_FreeBSD_9_i386=	multiple code issues on i386 < 10.0-RELEASE
+PLIST_SUB=	VER=${PORTVERSION}
+
+BROKEN_FreeBSD_9_i386=	Multiple code issues on i386 < 10.0-RELEASE
 BROKEN_aarch64=		Fails to compile: error: variable res is uninitialized
 
 .include <bsd.port.pre.mk>

diff --git a/biology/jellyfish/distinfo b/biology/jellyfish/distinfo
@@ -1,2 +1,3 @@
-SHA256 (gmarcais-Jellyfish-v2.2.4_GH0.tar.gz) = 44b6478aed63b859b8287d72b4f9bfb5d513fed334efbc8a9e5783da12ecb3ec
-SIZE (gmarcais-Jellyfish-v2.2.4_GH0.tar.gz) = 658653
+TIMESTAMP = 1482069678
+SHA256 (gmarcais-Jellyfish-v2.2.6_GH0.tar.gz) = 800bc60aaec273dc04296ee7493e714457f2fe88551f76693e5d9f9a679dd35e
+SIZE (gmarcais-Jellyfish-v2.2.6_GH0.tar.gz) = 660858
diff --git a/biology/jellyfish/pkg-plist b/biology/jellyfish/pkg-plist
@@ -1,52 +1,52 @@
 bin/jellyfish
-include/jellyfish-2.2.4/jellyfish/allocators_mmap.hpp
-include/jellyfish-2.2.4/jellyfish/atomic_bits_array.hpp
-include/jellyfish-2.2.4/jellyfish/atomic_field.hpp
-include/jellyfish-2.2.4/jellyfish/atomic_gcc.hpp
-include/jellyfish-2.2.4/jellyfish/backtrace.hpp
-include/jellyfish-2.2.4/jellyfish/binary_dumper.hpp
-include/jellyfish-2.2.4/jellyfish/bloom_common.hpp
-include/jellyfish-2.2.4/jellyfish/bloom_counter2.hpp
-include/jellyfish-2.2.4/jellyfish/bloom_filter.hpp
-include/jellyfish-2.2.4/jellyfish/circular_buffer.hpp
-include/jellyfish-2.2.4/jellyfish/compare_and_swap.hpp
-include/jellyfish-2.2.4/jellyfish/cooperative_pool.hpp
-include/jellyfish-2.2.4/jellyfish/cooperative_pool2.hpp
-include/jellyfish-2.2.4/jellyfish/cpp_array.hpp
-include/jellyfish-2.2.4/jellyfish/divisor.hpp
-include/jellyfish-2.2.4/jellyfish/dumper.hpp
-include/jellyfish-2.2.4/jellyfish/err.hpp
-include/jellyfish-2.2.4/jellyfish/file_header.hpp
-include/jellyfish-2.2.4/jellyfish/generator_manager.hpp
-include/jellyfish-2.2.4/jellyfish/generic_file_header.hpp
-include/jellyfish-2.2.4/jellyfish/hash_counter.hpp
-include/jellyfish-2.2.4/jellyfish/int128.hpp
-include/jellyfish-2.2.4/jellyfish/jellyfish.hpp
-include/jellyfish-2.2.4/jellyfish/json.h
-include/jellyfish-2.2.4/jellyfish/large_hash_array.hpp
-include/jellyfish-2.2.4/jellyfish/large_hash_iterator.hpp
-include/jellyfish-2.2.4/jellyfish/locks_pthread.hpp
-include/jellyfish-2.2.4/jellyfish/mapped_file.hpp
-include/jellyfish-2.2.4/jellyfish/mer_dna.hpp
-include/jellyfish-2.2.4/jellyfish/mer_dna_bloom_counter.hpp
-include/jellyfish-2.2.4/jellyfish/mer_heap.hpp
-include/jellyfish-2.2.4/jellyfish/mer_iterator.hpp
-include/jellyfish-2.2.4/jellyfish/mer_overlap_sequence_parser.hpp
-include/jellyfish-2.2.4/jellyfish/mer_qual_iterator.hpp
-include/jellyfish-2.2.4/jellyfish/misc.hpp
-include/jellyfish-2.2.4/jellyfish/offsets_key_value.hpp
-include/jellyfish-2.2.4/jellyfish/rectangular_binary_matrix.hpp
-include/jellyfish-2.2.4/jellyfish/simple_circular_buffer.hpp
-include/jellyfish-2.2.4/jellyfish/sorted_dumper.hpp
-include/jellyfish-2.2.4/jellyfish/stdio_filebuf.hpp
-include/jellyfish-2.2.4/jellyfish/storage.hpp
-include/jellyfish-2.2.4/jellyfish/stream_iterator.hpp
-include/jellyfish-2.2.4/jellyfish/stream_manager.hpp
-include/jellyfish-2.2.4/jellyfish/text_dumper.hpp
-include/jellyfish-2.2.4/jellyfish/thread_exec.hpp
-include/jellyfish-2.2.4/jellyfish/time.hpp
-include/jellyfish-2.2.4/jellyfish/token_ring.hpp
-include/jellyfish-2.2.4/jellyfish/whole_sequence_parser.hpp
+include/jellyfish-%%VER%%/jellyfish/allocators_mmap.hpp
+include/jellyfish-%%VER%%/jellyfish/atomic_bits_array.hpp
+include/jellyfish-%%VER%%/jellyfish/atomic_field.hpp
+include/jellyfish-%%VER%%/jellyfish/atomic_gcc.hpp
+include/jellyfish-%%VER%%/jellyfish/backtrace.hpp
+include/jellyfish-%%VER%%/jellyfish/binary_dumper.hpp
+include/jellyfish-%%VER%%/jellyfish/bloom_common.hpp
+include/jellyfish-%%VER%%/jellyfish/bloom_counter2.hpp
+include/jellyfish-%%VER%%/jellyfish/bloom_filter.hpp
+include/jellyfish-%%VER%%/jellyfish/circular_buffer.hpp
+include/jellyfish-%%VER%%/jellyfish/compare_and_swap.hpp
+include/jellyfish-%%VER%%/jellyfish/cooperative_pool.hpp
+include/jellyfish-%%VER%%/jellyfish/cooperative_pool2.hpp
+include/jellyfish-%%VER%%/jellyfish/cpp_array.hpp
+include/jellyfish-%%VER%%/jellyfish/divisor.hpp
+include/jellyfish-%%VER%%/jellyfish/dumper.hpp
+include/jellyfish-%%VER%%/jellyfish/err.hpp
+include/jellyfish-%%VER%%/jellyfish/file_header.hpp
+include/jellyfish-%%VER%%/jellyfish/generator_manager.hpp
+include/jellyfish-%%VER%%/jellyfish/generic_file_header.hpp
+include/jellyfish-%%VER%%/jellyfish/hash_counter.hpp
+include/jellyfish-%%VER%%/jellyfish/int128.hpp
+include/jellyfish-%%VER%%/jellyfish/jellyfish.hpp
+include/jellyfish-%%VER%%/jellyfish/json.h
+include/jellyfish-%%VER%%/jellyfish/large_hash_array.hpp
+include/jellyfish-%%VER%%/jellyfish/large_hash_iterator.hpp
+include/jellyfish-%%VER%%/jellyfish/locks_pthread.hpp
+include/jellyfish-%%VER%%/jellyfish/mapped_file.hpp
+include/jellyfish-%%VER%%/jellyfish/mer_dna.hpp
+include/jellyfish-%%VER%%/jellyfish/mer_dna_bloom_counter.hpp
+include/jellyfish-%%VER%%/jellyfish/mer_heap.hpp
+include/jellyfish-%%VER%%/jellyfish/mer_iterator.hpp
+include/jellyfish-%%VER%%/jellyfish/mer_overlap_sequence_parser.hpp
+include/jellyfish-%%VER%%/jellyfish/mer_qual_iterator.hpp
+include/jellyfish-%%VER%%/jellyfish/misc.hpp
+include/jellyfish-%%VER%%/jellyfish/offsets_key_value.hpp
+include/jellyfish-%%VER%%/jellyfish/rectangular_binary_matrix.hpp
+include/jellyfish-%%VER%%/jellyfish/simple_circular_buffer.hpp
+include/jellyfish-%%VER%%/jellyfish/sorted_dumper.hpp
+include/jellyfish-%%VER%%/jellyfish/stdio_filebuf.hpp
+include/jellyfish-%%VER%%/jellyfish/storage.hpp
+include/jellyfish-%%VER%%/jellyfish/stream_iterator.hpp
+include/jellyfish-%%VER%%/jellyfish/stream_manager.hpp
+include/jellyfish-%%VER%%/jellyfish/text_dumper.hpp
+include/jellyfish-%%VER%%/jellyfish/thread_exec.hpp
+include/jellyfish-%%VER%%/jellyfish/time.hpp
+include/jellyfish-%%VER%%/jellyfish/token_ring.hpp
+include/jellyfish-%%VER%%/jellyfish/whole_sequence_parser.hpp
 lib/libjellyfish-2.0.a
 lib/libjellyfish-2.0.so
 lib/libjellyfish-2.0.so.2

diff --git a/biology/p5-Bio-Coordinate/Makefile b/biology/p5-Bio-Coordinate/Makefile
@@ -0,0 +1,24 @@
+# Created by: Sunpoet Po-Chuan Hsieh <[email protected]>
+# $FreeBSD$
+
+PORTNAME=	Bio-Coordinate
+PORTVERSION=	1.007001
+CATEGORIES=	biology perl5
+MASTER_SITES=	CPAN
+PKGNAMEPREFIX=	p5-
+
+MAINTAINER=	[email protected]
+COMMENT=	Modules for working with biological coordinates
+
+LICENSE=	ART10 GPLv1
+LICENSE_COMB=	dual
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+BUILD_DEPENDS=	p5-BioPerl>=1.007000:biology/p5-BioPerl
+RUN_DEPENDS:=	${BUILD_DEPENDS}
+
+NO_ARCH=	yes
+USE_PERL5=	configure
+USES=		perl5
+
+.include <bsd.port.mk>
diff --git a/biology/p5-Bio-Coordinate/distinfo b/biology/p5-Bio-Coordinate/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1482042798
+SHA256 (Bio-Coordinate-1.007001.tar.gz) = 63c0a652ec60a2a905d71c85c08b96fcfb12fc784cac8a5d029eb9647d45d619
+SIZE (Bio-Coordinate-1.007001.tar.gz) = 44111
diff --git a/biology/p5-Bio-Coordinate/pkg-descr b/biology/p5-Bio-Coordinate/pkg-descr
@@ -0,0 +1,4 @@
+Bio::Coordinate classes are used for working with various biological coordinate
+systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.
+
+WWW: http://search.cpan.org/dist/Bio-Coordinate/
diff --git a/biology/p5-Bio-Coordinate/pkg-plist b/biology/p5-Bio-Coordinate/pkg-plist
@@ -0,0 +1,26 @@
+%%SITE_PERL%%/Bio/Coordinate.pm
+%%SITE_PERL%%/Bio/Coordinate/Chain.pm
+%%SITE_PERL%%/Bio/Coordinate/Collection.pm
+%%SITE_PERL%%/Bio/Coordinate/ExtrapolatingPair.pm
+%%SITE_PERL%%/Bio/Coordinate/GeneMapper.pm
+%%SITE_PERL%%/Bio/Coordinate/Graph.pm
+%%SITE_PERL%%/Bio/Coordinate/MapperI.pm
+%%SITE_PERL%%/Bio/Coordinate/Pair.pm
+%%SITE_PERL%%/Bio/Coordinate/Result.pm
+%%SITE_PERL%%/Bio/Coordinate/Result/Gap.pm
+%%SITE_PERL%%/Bio/Coordinate/Result/Match.pm
+%%SITE_PERL%%/Bio/Coordinate/ResultI.pm
+%%SITE_PERL%%/Bio/Coordinate/Utils.pm
+%%PERL5_MAN3%%/Bio::Coordinate.3.gz
+%%PERL5_MAN3%%/Bio::Coordinate::Chain.3.gz
+%%PERL5_MAN3%%/Bio::Coordinate::Collection.3.gz
+%%PERL5_MAN3%%/Bio::Coordinate::ExtrapolatingPair.3.gz
+%%PERL5_MAN3%%/Bio::Coordinate::GeneMapper.3.gz
+%%PERL5_MAN3%%/Bio::Coordinate::Graph.3.gz
+%%PERL5_MAN3%%/Bio::Coordinate::MapperI.3.gz
+%%PERL5_MAN3%%/Bio::Coordinate::Pair.3.gz
+%%PERL5_MAN3%%/Bio::Coordinate::Result.3.gz
+%%PERL5_MAN3%%/Bio::Coordinate::Result::Gap.3.gz
+%%PERL5_MAN3%%/Bio::Coordinate::Result::Match.3.gz
+%%PERL5_MAN3%%/Bio::Coordinate::ResultI.3.gz
+%%PERL5_MAN3%%/Bio::Coordinate::Utils.3.gz
diff --git a/biology/p5-Bio-Graphics/Makefile b/biology/p5-Bio-Graphics/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	Bio-Graphics
 PORTVERSION=	2.40
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 PKGNAMEPREFIX=	p5-
@@ -13,8 +14,9 @@ COMMENT=	Generate GD Images of Bio::Seq Objects
 LICENSE=	ART10 GPLv1
 LICENSE_COMB=	dual
 
-BUILD_DEPENDS=	p5-Bio-SCF>=1.01:biology/p5-Bio-SCF \
-		p5-BioPerl>=1.6.0:biology/p5-BioPerl \
+BUILD_DEPENDS=	p5-Bio-Coordinate>=1.007000:biology/p5-Bio-Coordinate \
+		p5-Bio-SCF>=1.01:biology/p5-Bio-SCF \
+		p5-BioPerl>=1.007000:biology/p5-BioPerl \
 		p5-GD>=2.30:graphics/p5-GD \
 		p5-GD-SVG>=0.32:graphics/p5-GD-SVG \
 		p5-Statistics-Descriptive>=2.6:math/p5-Statistics-Descriptive