Reassign biology/ perl modules to perl@.

While here:

Regenerate p5-AcePerl's patches using makepatch.
Make p5-Bio-ASN1-EntrezGene depend on p5-bioperl, instead of the
other way around. Bump PORTREVISION on those two ports.

8 files changed, 22 insertions, 21 deletions

diff --git a/biology/p5-AcePerl/Makefile b/biology/p5-AcePerl/Makefile
index c7b07b302ece..7c3dadd6a917 100644
--- a/biology/p5-AcePerl/Makefile
+++ b/biology/p5-AcePerl/Makefile
@@ -8,7 +8,7 @@ CATEGORIES=	biology databases perl5
 MASTER_SITES=	CPAN/Ace
 PKGNAMEPREFIX=	p5-
 
-MAINTAINER=	ports@FreeBSD.org
+MAINTAINER=	perl@FreeBSD.org
 COMMENT=	Perl5 interface to the ACEDB genome database system
 
 LICENSE=	ART10 GPLv1
diff --git a/biology/p5-AcePerl/files/patch-Makefile.PL b/biology/p5-AcePerl/files/patch-Makefile.PL
index 719769644488..b9ff2e5e66b4 100644
--- a/biology/p5-AcePerl/files/patch-Makefile.PL
+++ b/biology/p5-AcePerl/files/patch-Makefile.PL
@@ -1,20 +1,20 @@
---- Makefile.PL.orig	Fri Sep 28 16:13:04 2001
-+++ Makefile.PL	Fri Jan 25 14:11:26 2002
-@@ -2,7 +2,7 @@
- use ExtUtils::MakeMaker qw(prompt WriteMakefile);
+--- Makefile.PL.orig	2006-01-04 15:18:10 UTC
++++ Makefile.PL
+@@ -3,7 +3,7 @@ use ExtUtils::MakeMaker qw(prompt WriteM
  use File::Path;
+ require 5.8.0;
  
 -my $choice;
 +my $choice = 3;
  while (!$choice) {
    $reply = prompt(
  		  "\nWhat do you want to build?\n\n" .
-@@ -22,8 +22,6 @@
+@@ -23,8 +23,6 @@ my @extlib = ();
  push @extlib,'Freesubs' if $choice >= 2;
  push @extlib,'RPC'      if $choice >= 3;
  
 -print "\n";
 -setup_sitedefs() if prompt("Do you want to install Ace::Browser? ","n") =~ /[yY]/;
  
- my $headers  = "./ace/wh";
+ my $headers  = "./acelib/wh";
  WriteMakefile(
diff --git a/biology/p5-AcePerl/files/patch-RPC__RPC.xs b/biology/p5-AcePerl/files/patch-RPC__RPC.xs
index b2869ae8408f..f8089abbe630 100644
--- a/biology/p5-AcePerl/files/patch-RPC__RPC.xs
+++ b/biology/p5-AcePerl/files/patch-RPC__RPC.xs
@@ -1,6 +1,6 @@
---- ./RPC/RPC.xs.orig	2014-08-21 20:31:10.000000000 -0400
-+++ ./RPC/RPC.xs	2014-08-21 20:31:34.000000000 -0400
-@@ -153,7 +153,7 @@
+--- RPC/RPC.xs.orig	2000-06-13 17:17:19 UTC
++++ RPC/RPC.xs
+@@ -153,7 +153,7 @@ int arg;
  	break;
      case '_':
  	if (strEQ(name, "_ACECLIENT_"))
diff --git a/biology/p5-AcePerl/files/patch-acelib_memsubs.c b/biology/p5-AcePerl/files/patch-acelib_memsubs.c
index 982bdef30f4c..adb2d1ef6dc4 100644
--- a/biology/p5-AcePerl/files/patch-acelib_memsubs.c
+++ b/biology/p5-AcePerl/files/patch-acelib_memsubs.c
@@ -1,5 +1,5 @@
---- acelib/memsubs.c.orig	Mon Jan 11 02:01:29 1999
-+++ acelib/memsubs.c	Thu Jul 27 17:18:45 2000
+--- acelib/memsubs.c.orig	2002-11-24 19:24:23 UTC
++++ acelib/memsubs.c
 @@ -21,7 +21,7 @@
  #if defined(NEXT) || defined(HP) || defined(MACINTOSH) 
  extern void* malloc(mysize_t size) ;
diff --git a/biology/p5-AcePerl/files/patch-acelib_wh_mydirent.h b/biology/p5-AcePerl/files/patch-acelib_wh_mydirent.h
index 376d287b34d2..ef03e1540c4c 100644
--- a/biology/p5-AcePerl/files/patch-acelib_wh_mydirent.h
+++ b/biology/p5-AcePerl/files/patch-acelib_wh_mydirent.h
@@ -1,5 +1,5 @@
---- acelib/wh/mydirent.h.orig	Mon Jul 16 23:04:45 2001
-+++ acelib/wh/mydirent.h	Mon Aug 13 12:41:59 2001
+--- acelib/wh/mydirent.h.orig	2002-11-14 20:00:06 UTC
++++ acelib/wh/mydirent.h
 @@ -55,7 +55,7 @@
  extern char *getwd(char *pathname) ;
  #endif /* HP || SOLARIS || WIN32 */
diff --git a/biology/p5-AcePerl/files/patch-acelib_wh_mystdlib.h b/biology/p5-AcePerl/files/patch-acelib_wh_mystdlib.h
index 09c42b7c0fee..b1906a8347ac 100644
--- a/biology/p5-AcePerl/files/patch-acelib_wh_mystdlib.h
+++ b/biology/p5-AcePerl/files/patch-acelib_wh_mystdlib.h
@@ -1,6 +1,6 @@
---- 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 @@
+--- acelib/wh/mystdlib.h.orig	2002-11-14 20:00:06 UTC
++++ acelib/wh/mystdlib.h
+@@ -161,7 +161,8 @@ char *DosToPosix(char *path) ; /* define
  #endif
  
  #if defined(POSIX) || defined(LINUX) || defined(SOLARIS) || defined(SGI) || \
diff --git a/biology/p5-Bio-ASN1-EntrezGene/Makefile b/biology/p5-Bio-ASN1-EntrezGene/Makefile
index d154cee9a960..2b00d8f2545a 100644
--- a/biology/p5-Bio-ASN1-EntrezGene/Makefile
+++ b/biology/p5-Bio-ASN1-EntrezGene/Makefile
@@ -3,16 +3,18 @@
 
 PORTNAME=	Bio-ASN1-EntrezGene
 PORTVERSION=	1.70
+PORTREVISION=	1
 PORTEPOCH=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
 PKGNAMEPREFIX=	p5-
 
-MAINTAINER=	ports@FreeBSD.org
+MAINTAINER=	perl@FreeBSD.org
 COMMENT=	Regular expression-based Perl Parser for NCBI Entrez Gene
 
-WRKSRC=		${WRKDIR}/Bio-ASN1-EntrezGene-${PORTVERSION}
+BUILD_DEPENDS=	p5-bioperl>=0:${PORTSDIR}/biology/p5-bioperl
+RUN_DEPENDS:=	${BUILD_DEPENDS}
 
 USES=		perl5
 USE_PERL5=	configure
diff --git a/biology/p5-bioperl/Makefile b/biology/p5-bioperl/Makefile
index 3430fe8c7d1e..cd42295c1c57 100644
--- a/biology/p5-bioperl/Makefile
+++ b/biology/p5-bioperl/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	bioperl
 PORTVERSION=	1.6.924
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	biology perl5
 MASTER_SITES=	CPAN
 MASTER_SITE_SUBDIR=	CPAN:CJFIELDS
@@ -18,7 +18,6 @@ LICENSE_COMB=	dual
 
 BUILD_DEPENDS=	p5-Algorithm-Munkres>=0:${PORTSDIR}/math/p5-Algorithm-Munkres \
 		p5-Array-Compare>=0:${PORTSDIR}/misc/p5-Array-Compare \
-		p5-Bio-ASN1-EntrezGene>=0:${PORTSDIR}/biology/p5-Bio-ASN1-EntrezGene \
 		p5-Class-AutoClass>=0:${PORTSDIR}/devel/p5-Class-AutoClass \
 		p5-Clone>=0:${PORTSDIR}/devel/p5-Clone \
 		p5-Convert-Binary-C>=0:${PORTSDIR}/converters/p5-Convert-Binary-C \