Index: head/biology/p5-AcePerl/Makefile =================================================================== --- head/biology/p5-AcePerl/Makefile (revision 161223) +++ head/biology/p5-AcePerl/Makefile (revision 161224) @@ -1,53 +1,60 @@ # New ports collection makefile for: p5-AcePerl # Date created: 26 July 2000 # Whom: Johann Visagie # # $FreeBSD$ # PORTNAME= AcePerl -PORTVERSION= 1.83 +PORTVERSION= 1.89 CATEGORIES= biology databases perl5 MASTER_SITES= ${MASTER_SITE_PERL_CPAN} MASTER_SITE_SUBDIR= Ace PKGNAMEPREFIX= p5- MAINTAINER= pgollucci@p6m7g8.com COMMENT= Perl5 interface to the ACEDB genome database system -BUILD_DEPENDS= ${SITE_PERL}/${PERL_ARCH}/Digest/MD5.pm:${PORTSDIR}/security/p5-Digest-MD5 -RUN_DEPENDS= ${BUILD_DEPENDS} +RUN_DEPENDS= ${SITE_PERL}/${PERL_ARCH}/Digest/MD5.pm:${PORTSDIR}/security/p5-Digest-MD5 \ + ${SITE_PERL}/${PERL_ARCH}/Scalar/Util.pm:${PORTSDIR}/lang/p5-Scalar-List-Utils \ + ${SITE_PERL}/Cache/Cache.pm:${PORTSDIR}/devel/p5-Cache-Cache +BUILD_DEPENDS= ${RUN_DEPENDS} PERL_CONFIGURE= yes +MAN1= ace.pl.1 MAN3= Ace.3 Ace::Browser::AceSubs.3 Ace::Browser::SearchSubs.3 \ Ace::Browser::SiteDefs.3 Ace::Graphics::Fk.3 \ Ace::Graphics::Glyph.3 Ace::Graphics::Glyph::anchored_arrow.3 \ Ace::Graphics::Glyph::arrow.3 Ace::Graphics::Glyph::box.3 \ Ace::Graphics::Glyph::dot.3 Ace::Graphics::Glyph::ex.3 \ Ace::Graphics::Glyph::graded_segments.3 \ Ace::Graphics::Glyph::group.3 Ace::Graphics::Glyph::line.3 \ Ace::Graphics::Glyph::primers.3 \ Ace::Graphics::Glyph::segments.3 Ace::Graphics::Glyph::span.3 \ Ace::Graphics::Glyph::toomany.3 \ Ace::Graphics::Glyph::transcript.3 \ Ace::Graphics::Glyph::triangle.3 \ Ace::Graphics::GlyphFactory.3 Ace::Graphics::Panel.3 \ Ace::Graphics::Track.3 Ace::Iterator.3 Ace::Local.3 \ Ace::Model.3 Ace::Object.3 Ace::Sequence.3 \ Ace::Sequence::Feature.3 Ace::Sequence::FeatureList.3 \ Ace::Sequence::GappedAlignment.3 Ace::Sequence::Gene.3 \ Ace::Sequence::Homol.3 Ace::Sequence::Multi.3 \ Ace::Sequence::Transcript.3 .include +.if ${PERL_LEVEL} < 500600 +IGNORE= requires Perl 5.6.0 +.endif + .if ${ARCH} == "amd64" || ${ARCH} == "ia64" -BROKEN= "Does not compile on amd64 or ia64 (missing -fPIC)" +BROKEN= Does not compile on amd64 or ia64 (missing -fPIC) .endif post-patch: @ ${SED} -e 's|XX__CC__XX|${CC}|' < ${FILESDIR}/FREEBSD_DEF \ - > ${WRKSRC}/ace/wmake/FREEBSD_DEF + > ${WRKSRC}/acelib/wmake/FREEBSD_DEF .include Property changes on: head/biology/p5-AcePerl/Makefile ___________________________________________________________________ Modified: cvs2svn:cvs-rev ## -1 +1 ## -1.13 \ No newline at end of property +1.14 \ No newline at end of property Index: head/biology/p5-AcePerl/distinfo =================================================================== --- head/biology/p5-AcePerl/distinfo (revision 161223) +++ head/biology/p5-AcePerl/distinfo (revision 161224) @@ -1,3 +1,3 @@ -MD5 (AcePerl-1.83.tar.gz) = d1cc9e852ce7fb23a0f2eac739b040fb -SHA256 (AcePerl-1.83.tar.gz) = 58164fff2977f37ad1298492b8ef74dca8adb314611ec99d6ef466f5d55300cc -SIZE (AcePerl-1.83.tar.gz) = 294151 +MD5 (AcePerl-1.89.tar.gz) = 547da3ca59894e99448408cfe9a8ae6e +SHA256 (AcePerl-1.89.tar.gz) = f3be1f9d31756761f7e1a6043e86b6b39d746fc6cc2bb52663860c31d4e7d64a +SIZE (AcePerl-1.89.tar.gz) = 299210 Property changes on: head/biology/p5-AcePerl/distinfo ___________________________________________________________________ Modified: cvs2svn:cvs-rev ## -1 +1 ## -1.8 \ No newline at end of property +1.9 \ No newline at end of property Index: head/biology/p5-AcePerl/files/patch-aa =================================================================== --- head/biology/p5-AcePerl/files/patch-aa (revision 161223) +++ head/biology/p5-AcePerl/files/patch-aa (revision 161224) @@ -1,23 +1,23 @@ ---- ace/wh/mystdlib.h.orig Mon Jul 16 23:04:45 2001 -+++ ace/wh/mystdlib.h Mon Aug 13 12:42:25 2001 +--- acelib/wh/mystdlib.h.orig Mon Jul 16 23:04:45 2001 ++++ acelib/wh/mystdlib.h Mon Aug 13 12:42:25 2001 @@ -161,7 +161,8 @@ #endif #if defined(POSIX) || defined(LINUX) || defined(SOLARIS) || defined(SGI) || \ - defined(HP) || defined(WIN32) || defined(INTEL_SOLARIS) + defined(HP) || defined(WIN32) || defined(INTEL_SOLARIS) || \ + defined(FREEBSD) #ifdef WIN32 #include ---- ace/wh/mydirent.h.orig Mon Jul 16 23:04:45 2001 -+++ ace/wh/mydirent.h Mon Aug 13 12:41:59 2001 +--- acelib/wh/mydirent.h.orig Mon Jul 16 23:04:45 2001 ++++ acelib/wh/mydirent.h Mon Aug 13 12:41:59 2001 @@ -55,7 +55,7 @@ extern char *getwd(char *pathname) ; #endif /* HP || SOLARIS || WIN32 */ -#if defined (POSIX) || defined(SUN) || defined(SUNSVR4) || defined(SOLARIS) || defined(DEC) || defined(ALPHA) || defined(SGI) || defined(LINUX) || defined(HP) || defined (INTEL_SOLARIS) +#if defined (POSIX) || defined(SUN) || defined(SUNSVR4) || defined(SOLARIS) || defined(DEC) || defined(ALPHA) || defined(SGI) || defined(LINUX) || defined(HP) || defined (INTEL_SOLARIS) || defined (FREEBSD) #include typedef struct dirent MYDIRENT ; #endif Property changes on: head/biology/p5-AcePerl/files/patch-aa ___________________________________________________________________ Modified: cvs2svn:cvs-rev ## -1 +1 ## -1.2 \ No newline at end of property +1.3 \ No newline at end of property Index: head/biology/p5-AcePerl/files/patch-ab =================================================================== --- head/biology/p5-AcePerl/files/patch-ab (revision 161223) +++ head/biology/p5-AcePerl/files/patch-ab (revision 161224) @@ -1,11 +1,11 @@ ---- ace/memsubs.c.orig Mon Jan 11 02:01:29 1999 -+++ ace/memsubs.c Thu Jul 27 17:18:45 2000 +--- acelib/memsubs.c.orig Mon Jan 11 02:01:29 1999 ++++ acelib/memsubs.c Thu Jul 27 17:18:45 2000 @@ -21,7 +21,7 @@ #if defined(NEXT) || defined(HP) || defined(MACINTOSH) extern void* malloc(mysize_t size) ; - #elif !defined(WIN32) + #elif !defined(WIN32) && !defined(DARWIN) -#include /* normal machines */ +#include /* normal machines */ #endif /********** primary type definition **************/ Property changes on: head/biology/p5-AcePerl/files/patch-ab ___________________________________________________________________ Modified: cvs2svn:cvs-rev ## -1 +1 ## -1.1 \ No newline at end of property +1.2 \ No newline at end of property Index: head/biology/p5-AcePerl/files/patch-weaken =================================================================== --- head/biology/p5-AcePerl/files/patch-weaken (nonexistent) +++ head/biology/p5-AcePerl/files/patch-weaken (revision 161224) @@ -0,0 +1,33 @@ +--- Ace.pm.orig Tue May 2 17:32:55 2006 ++++ Ace.pm Tue May 2 17:33:12 2006 +@@ -2,7 +2,7 @@ + + use strict; + use Carp qw(croak carp cluck); +-use WeakRef; ++use Scalar::Util qw(weaken); + + use vars qw($VERSION @ISA @EXPORT @EXPORT_OK $Error); + +--- ChangeLog.orig Tue May 2 17:33:12 2006 ++++ ChangeLog Tue May 2 17:33:22 2006 +@@ -1,7 +1,7 @@ + 1.89 Wed Mar 9 18:25:45 EST 2005 + 1. Added caching code. + 2. Now requires ace binaries 4_9s or later. +- 3. Requires CACHE::CACHE and WeakRef for caching. ++ 3. Requires CACHE::CACHE and Scalar::Util for caching. + + 1.87 10/3/03 + 1. Fixed unreadable GIF images produced by recent versions of GifAceServer. +--- Makefile.PL.orig Tue May 2 17:33:22 2006 ++++ Makefile.PL Tue May 2 17:33:32 2006 +@@ -35,7 +35,7 @@ + 'INC' => "-I$headers", + PREREQ_PM => { + 'Digest::MD5' => 2.0, +- 'WeakRef' => 0.01, ++ 'Scalar::Util' => 1, + 'Cache::Cache' => 1.03, + }, + 'dist' => {'COMPRESS'=>'gzip -9f', Property changes on: head/biology/p5-AcePerl/files/patch-weaken ___________________________________________________________________ Added: cvs2svn:cvs-rev ## -0,0 +1 ## +1.1 \ No newline at end of property Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Index: head/biology/p5-AcePerl/pkg-plist =================================================================== --- head/biology/p5-AcePerl/pkg-plist (revision 161223) +++ head/biology/p5-AcePerl/pkg-plist (revision 161224) @@ -1,121 +1,125 @@ +bin/ace.pl %%SITE_PERL%%/%%PERL_ARCH%%/Ace.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser/AceSubs.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser/GeneSubs.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser/SearchSubs.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser/SiteDefs.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser/TreeSubs.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Freesubs.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Fk.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/anchored_arrow.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/arrow.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/box.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/crossbox.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/dot.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/ex.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/graded_segments.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/group.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/line.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/primers.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/segments.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/span.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/toomany.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/transcript.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph/triangle.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/GlyphFactory.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Panel.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Track.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Iterator.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Local.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Model.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Object.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Object/Wormbase.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/RPC.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/Feature.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/FeatureList.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/GappedAlignment.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/Gene.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/Homol.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/Multi.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence/Transcript.pm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/SocketServer.pm %%SITE_PERL%%/%%PERL_ARCH%%/GFF/Filehandle.pm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/.packlist %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Freesubs/Freesubs.bs %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Freesubs/Freesubs.so %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_asAce.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_asHTML.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_asTable.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_asXML.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_default_makeHTML.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_insert.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_special_dump.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_to_ace_date.al +%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/_xmlNumber.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/add_row.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/add_tree.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asAce.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asDNA.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asGif.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asHTML.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asPeptide.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asString.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asTable.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/asXML.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/autosplit.ix %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/comment.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/commit.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/date_style.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/debug.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/delete.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/escapeXML.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/isComment.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/kill.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/replace.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/rollback.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/tags.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object/timestamp.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/RPC/RPC.bs %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/RPC/RPC.so %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature/autosplit.ix %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Sequence/autosplit.ix %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/_register_iterator.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/_restore_iterator.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/_save_iterator.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/_unregister_iterator.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/auto_save.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/autosplit.ix %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/class_count.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/classes.al -%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/count.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/date.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/date_style.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/datetime.al +%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/debug.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/fetch_many.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/find.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/freeprotect.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/grep.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/layout.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/new.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/parse.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/parse_file.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/parse_longtext.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/pick.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/ping.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/put.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/split.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/status.al %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/timestamps.al +%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/title.al +%%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/version.al @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Sequence @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/RPC @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Object @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace/Freesubs @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/auto/Ace @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/GFF @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Sequence @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Object @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics/Glyph @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Graphics @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace/Browser @dirrm %%SITE_PERL%%/%%PERL_ARCH%%/Ace Property changes on: head/biology/p5-AcePerl/pkg-plist ___________________________________________________________________ Modified: cvs2svn:cvs-rev ## -1 +1 ## -1.7 \ No newline at end of property +1.8 \ No newline at end of property