6 files changed, 88 insertions, 61 deletions

diff --git a/biology/p5-AcePerl/Makefile b/biology/p5-AcePerl/Makefile
index 11e90f57696a..d11118087a95 100644
--- a/biology/p5-AcePerl/Makefile
+++ b/biology/p5-AcePerl/Makefile
@@ -6,16 +6,17 @@
 #
 
 PORTNAME=	AcePerl
-PORTVERSION=	1.62
+PORTVERSION=	1.67
 CATEGORIES=	biology databases perl5
 MASTER_SITES=	http://stein.cshl.org/AcePerl/archive/ \
 		${MASTER_SITE_PERL_CPAN}
 MASTER_SITE_SUBDIR=Ace
 PKGNAMEPREFIX=	p5-
 
-MAINTAINER=	johann@egenetics.com
+MAINTAINER=	bio@freebsd.net
 
 USE_PERL5=	YES
+PERL_CONFIGURE=	YES
 
 MAN3=		Ace::Sequence::Feature.3 \
 		Ace::Sequence.3 \
@@ -30,8 +31,8 @@ MAN3=		Ace::Sequence::Feature.3 \
 
 MANPREFIX=	${PREFIX}/lib/perl5/${PERL_VERSION}
 
-do-configure:
-	${CP} ${FILESDIR}/FREEBSD_DEF ${WRKSRC}/ace/wmake/
-	@ cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL
+post-patch:
+	@ ${SED} -e 's/XX__CC__XX/${CC}/' < ${FILESDIR}/FREEBSD_DEF \
+	  > ${WRKSRC}/ace/wmake/FREEBSD_DEF
 
 .include <bsd.port.mk>
diff --git a/biology/p5-AcePerl/distinfo b/biology/p5-AcePerl/distinfo
index 9f0e26a085ea..9576df0586fd 100644
--- a/biology/p5-AcePerl/distinfo
+++ b/biology/p5-AcePerl/distinfo
@@ -1 +1 @@
-MD5 (AcePerl-1.62.tar.gz) = d9978077a8e1857b94216d5a28bc38ef
+MD5 (AcePerl-1.67.tar.gz) = 46c9bc547f4c8e73480ddac7cbf79d95
diff --git a/biology/p5-AcePerl/files/FREEBSD_DEF b/biology/p5-AcePerl/files/FREEBSD_DEF
index 685175adcd87..a6e06d157158 100644
--- a/biology/p5-AcePerl/files/FREEBSD_DEF
+++ b/biology/p5-AcePerl/files/FREEBSD_DEF
@@ -8,10 +8,10 @@
 #####   following the explanations given in wmake/truemake  #####
 #################################################################
 
-CFLAGS+= -g -Wall -O2 -DACEDB4
 NAME = FREEBSD
-COMPILER = gcc ${CFLAGS}
-LINKER = gcc -g
+CFLAGS+= -g -Wall -O2 -DACEDB4
+COMPILER = XX__CC__XX ${CFLAGS}
+LINKER = XX__CC__XX -g
 
 LIBS = -lm
 Xt_LIBS = -L/usr/X11R6/lib -lXaw -lXt -lXmu -lXext -lX11
diff --git a/biology/p5-AcePerl/files/patch-ac b/biology/p5-AcePerl/files/patch-ac
new file mode 100644
index 000000000000..90194f8b38d7
--- /dev/null
+++ b/biology/p5-AcePerl/files/patch-ac
@@ -0,0 +1,11 @@
+--- Makefile.PL.orig	Thu Aug 31 19:02:21 2000
++++ Makefile.PL	Mon Oct  9 16:43:32 2000
+@@ -1,7 +1,7 @@
+ use Config;
+ use ExtUtils::MakeMaker qw(prompt WriteMakefile);
+ 
+-my $choice;
++my $choice = 3;
+ while (!$choice) {
+   $reply = prompt(
+ 		  "\nWhat do you want to build?\n\n" .
diff --git a/biology/p5-AcePerl/pkg-descr b/biology/p5-AcePerl/pkg-descr
index b282dac21cd5..766e14953e2a 100644
--- a/biology/p5-AcePerl/pkg-descr
+++ b/biology/p5-AcePerl/pkg-descr
@@ -2,7 +2,9 @@ AcePerl is an object-oriented Perl interface for the ACEDB genome database
 system. It provides functionality for connecting to remote ACEDB databases,
 performing queries, fetching ACE objects, and updating databases.
 
+Author:	Lincoln D. Stein <lstein@cshl.org>
 WWW: http://stein.cshl.org/AcePerl/
 
-- Johann
-johann@egenetics.com
+Port maintained by the FreeBSD bio-porters mailing list.
+
+-- FreeBSD bio-porters <bio@freebsd.net>
diff --git a/biology/p5-AcePerl/pkg-plist b/biology/p5-AcePerl/pkg-plist
index 0de06a9b8076..52e905370a94 100644
--- a/biology/p5-AcePerl/pkg-plist
+++ b/biology/p5-AcePerl/pkg-plist
@@ -1,73 +1,86 @@
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Ace.bs
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Ace.so
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Freesubs.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Iterator.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Local.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Feature.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Multi.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/FeatureList.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Homol.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Model.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Object.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Iterator.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/RPC.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Feature.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/FeatureList.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Homol.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence/Multi.pm
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/SocketServer.pm
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/GFF/Filehandle.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/fetch_many.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/auto_save.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/date_style.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/comment.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/isComment.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/.packlist
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Freesubs/Freesubs.bs
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Freesubs/Freesubs.so
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asAce.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asHTML.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asTable.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asXML.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_default_makeHTML.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_insert.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_special_dump.al
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_to_ace_date.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/date_style.al
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/add_row.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/delete.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asPeptide.al
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/add_tree.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asHTML.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/timestamp.al
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asAce.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asTable.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asTable.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asString.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/replace.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/debug.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_asAce.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_default_makeHTML.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/isTimestamp.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/tags.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asDNA.al
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asGif.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_special_dump.al
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asHTML.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/_insert.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/kill.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/rollback.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asDNA.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asPeptide.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asString.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asTable.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/asXML.al
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/autosplit.ix
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/comment.al
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/commit.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/status.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse_file.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/class_count.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/layout.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/pick.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/date_style.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/debug.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/delete.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/escapeXML.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/isComment.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/kill.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/replace.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/rollback.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/tags.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object/timestamp.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/RPC/RPC.bs
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/RPC/RPC.so
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature/autosplit.ix
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/autosplit.ix
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/grep.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/put.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/new.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/classes.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_unregister_iterator.al
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_register_iterator.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_restore_iterator.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_save_iterator.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/_unregister_iterator.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/auto_save.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/autosplit.ix
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/class_count.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/classes.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/count.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/date_style.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/fetch_many.al
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/find.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/freeprotect.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/grep.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/layout.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/new.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse_file.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse_longtext.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/pick.al
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/ping.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/count.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/autosplit.ix
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/put.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/split.al
+lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/status.al
 lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/timestamps.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/parse_longtext.al
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace.pm
-lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/.packlist
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace
-@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/GFF
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence/Feature
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Sequence
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/RPC
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Object
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace/Freesubs
 @dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Ace
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/GFF
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace/Sequence
+@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Ace