7 files changed, 128 insertions, 113 deletions

diff --git a/biology/avida/Makefile b/biology/avida/Makefile
index 19d47b805bdd..12958cc330e6 100644
--- a/biology/avida/Makefile
+++ b/biology/avida/Makefile
@@ -6,42 +6,50 @@
 #
 
 PORTNAME=	avida
-PORTVERSION=	1.6.0
-PORTREVISION=	1
+PORTVERSION=	2.0b7
 CATEGORIES=	biology
-MASTER_SITES=	http://dllab.caltech.edu/avida/files/
+MASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
+MASTER_SITE_SUBDIR=	${PORTNAME}
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Avida is an auto-adaptive genetic system designed for ALife research
 
-WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION:C/\.[[:alnum:]]+$//}
 USE_GMAKE=	yes
 GNU_CONFIGURE=	yes
-CONFIGURE_ARGS=	--enable-viewer --enable-standard-prefix --prefix=${PREFIX} --datadir=${PREFIX}/share/${PORTNAME}
+CONFIGURE_ARGS=	--enable-standard-prefix --datadir=${DATADIR} --enable-viewer
+CONFIGURE_TARGET=	--build=${MACHINE_ARCH}-portbld-freebsd${OSREL}
+USE_PERL5_BUILD=	yes
+USE_REINPLACE=	yes
+
+.if !defined(WITHOUT_QT)
+USE_QT_VER=		3
+CONFIGURE_ARGS+=	--enable-qt-viewer
+CONFIGURE_ENV+=	QTDIR="${LOCALBASE}"
+MAKE_ENV+=	QMAKESPEC="${LOCALBASE}/share/qt/mkspecs/freebsd-g++"		\
+		QTDIR="${X11BASE}"
+PLIST_SUB=	QT=""
+.else
+PLIST_SUB=	QT="@comment "
+.endif
 
-.include <bsd.port.pre.mk>
+DIR2FIX=	source/main/functional_testsuites/default.md5sum/genesis	\
+		source/main/functional_testsuites/default.tail/genesis		\
+		source/main/functional_testsuites/tedious.tail/genesis		\
+		source/qt-viewer/setup_genesis.cc source/support/genesis	\
+		source/support/genesis.4stack source/main/config.cc source/defs.hh
+
+pre-configure:
+.for src in ${DIR2FIX}
+	@${REINPLACE_CMD} -e "s|../work/|${DATADIR}/|" ${WRKSRC}/${src}
+.endfor
+.if defined(NOPORTDOCS)
+	@${REINPLACE_CMD} -e "s|SUBDIRS = source doc|SUBDIRS = source|"		\
+		${WRKSRC}/Makefile.in
+.endif
 
-.if ${OSVERSION} >= 500113
-BROKEN=		"Does not compile (bad C++ code)"
+.if !defined(WITHOUT_QT)
+post-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/work/qt-viewer ${PREFIX}/bin
 .endif
 
-post-patch:
-	# Change source/defs.hh prefix and port name.
-	@ ${MV} ${WRKSRC}/source/defs.hh ${WRKSRC}/source/defs.hh.presed
-	@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#g' ${WRKSRC}/source/defs.hh.presed \
-	| ${SED} -e 's#%%PORTNAME%%#${PORTNAME}#g' \
-	> ${WRKSRC}/source/defs.hh
-
-	# Change source/support/genesis prefix and port name.
-	@ ${MV} ${WRKSRC}/source/support/genesis ${WRKSRC}/source/support/genesis.presed
-	@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#g' ${WRKSRC}/source/support/genesis.presed \
-	| ${SED} -e 's#%%PORTNAME%%#${PORTNAME}#g' \
-	> ${WRKSRC}/source/support/genesis
-
-	# Change source/support/genesis.heads prefix and port name.
-	@ ${MV} ${WRKSRC}/source/support/genesis.heads ${WRKSRC}/source/support/genesis.heads.presed
-	@ ${SED} -e 's#%%PREFIX%%#${PREFIX}#g' ${WRKSRC}/source/support/genesis.heads.presed \
-	| ${SED} -e 's#%%PORTNAME%%#${PORTNAME}#g' \
-	> ${WRKSRC}/source/support/genesis.heads
-
-.include <bsd.port.post.mk>
+.include <bsd.port.mk>
diff --git a/biology/avida/distinfo b/biology/avida/distinfo
index a50226c2e50f..0892a2bff7c6 100644
--- a/biology/avida/distinfo
+++ b/biology/avida/distinfo
@@ -1,2 +1,2 @@
-MD5 (avida-1.6.0.tar.gz) = 2294af061f200c486de2ed889e0e17af
-SIZE (avida-1.6.0.tar.gz) = 345669
+MD5 (avida-2.0b7.tar.gz) = 908985c3f54e19e003e6e744a941b3cb
+SIZE (avida-2.0b7.tar.gz) = 829131
diff --git a/biology/avida/files/patch-aa b/biology/avida/files/patch-aa
deleted file mode 100644
index 0c36d6c47ed9..000000000000
--- a/biology/avida/files/patch-aa
+++ /dev/null
@@ -1,11 +0,0 @@
---- source/event/event_base.hh.orig	Wed Apr 17 21:26:31 2002
-+++ source/event/event_base.hh	Wed Apr 17 21:26:41 2002
-@@ -18,6 +18,7 @@
- 
- #include "../defs.hh"
--#include <values.h>
-+#include <limits.h>
-+#include <float.h>
- //#include "event_defs.hh"
- 
- enum eTriggerVariable { UPDATE, GENERATION, IMMEDIATE, UNDEFINED };
diff --git a/biology/avida/files/patch-ac b/biology/avida/files/patch-ac
deleted file mode 100644
index 980deaebc657..000000000000
--- a/biology/avida/files/patch-ac
+++ /dev/null
@@ -1,11 +0,0 @@
---- source/defs.hh.orig	Thu Apr 18 18:42:56 2002
-+++ source/defs.hh	Thu Apr 18 18:43:14 2002
-@@ -8,7 +8,7 @@
- #ifndef DEFS_HH
- #define DEFS_HH
- 
--#define DEFAULT_DIR "../work/"
-+#define DEFAULT_DIR "%%PREFIX%%/share/%%PORTNAME%%/"
- 
- // -= Remove bugfixes that change execution
- //#define REMOVE_SIZE_RANGE_FIX      // had only affected upper limit in heads
diff --git a/biology/avida/files/patch-ad b/biology/avida/files/patch-ad
deleted file mode 100644
index 0440d2e48130..000000000000
--- a/biology/avida/files/patch-ad
+++ /dev/null
@@ -1,11 +0,0 @@
---- source/support/genesis.orig	Fri Apr 19 20:00:53 2002
-+++ source/support/genesis	Fri Apr 19 20:02:24 2002
-@@ -13,7 +13,7 @@
- RANDOM_SEED 0		# Random number seed. (0 for based on time)
- 
- ### Configuration Files ###
--DEFAULT_DIR ../work/         # Directory in which config files can be found.
-+DEFAULT_DIR %%PREFIX%%/share/%%PORTNAME%%/ # Directory in which config files can be found.
- INST_SET inst_set.28.base    # File containing instruction set.
- TASK_SET task_set            # File containing task set.
- RESOURCE_SET resource_set    # File containing resource set.
diff --git a/biology/avida/files/patch-ae b/biology/avida/files/patch-ae
deleted file mode 100644
index 34a692b7cbca..000000000000
--- a/biology/avida/files/patch-ae
+++ /dev/null
@@ -1,11 +0,0 @@
---- source/support/genesis.heads.orig	Fri Apr 19 20:01:09 2002
-+++ source/support/genesis.heads	Fri Apr 19 20:02:47 2002
-@@ -13,7 +13,7 @@
- RANDOM_SEED 0		# Random number seed. (0 for based on time)
- 
- ### Configuration Files ###
--DEFAULT_DIR ../work/         # Directory in which config files can be found.
-+DEFAULT_DIR %%PREFIX%%/share/%%PORTNAME%%/ # Directory in which config files can be found.
- INST_SET inst_set.26.heads.new    # File containing instruction set.
- TASK_SET task_set            # File containing task set.
- RESOURCE_SET resource_set            # File containing resource set.
diff --git a/biology/avida/pkg-plist b/biology/avida/pkg-plist
index ca5b88fca552..d16f43387a78 100644
--- a/biology/avida/pkg-plist
+++ b/biology/avida/pkg-plist
@@ -1,39 +1,90 @@
-bin/avida
-share/avida/creature.base
-share/avida/creature.heads
-share/avida/creature.heads.new
-share/avida/genesis
-share/avida/genesis.heads
-share/avida/genesis.heads.orig
-share/avida/genesis.heads.presed
-share/avida/genesis.orig
-share/avida/genesis.presed
-share/avida/inst_set.19.short
-share/avida/inst_set.24.base
-share/avida/inst_set.26.heads.new
-share/avida/inst_set.27.multi
-share/avida/inst_set.27.no-nop
-share/avida/inst_set.27.parasite
-share/avida/inst_set.28.base
-share/avida/inst_set.28.const
-share/avida/inst_set.28.dir-match
-share/avida/inst_set.29.base_memsize
-share/avida/inst_set.31.multi
-share/avida/inst_set.32.heads
-share/avida/inst_set.84.long
-share/avida/inst_set.args
-share/avida/inst_set.big
-share/avida/inst_set.dev
-share/avida/inst_set.full
-share/avida/inst_set.long
-share/avida/inst_set.re
-share/avida/inst_set.red
-share/avida/inst_set.short
-share/avida/inst_set.test
-share/avida/inst_set.tiny
-share/avida/inst_set.travc
-share/avida/event_list
-share/avida/resource_set
-share/avida/task_set
-share/avida/analyze.cfg
-@dirrm share/avida
+bin/primitive
+%%QT%%bin/qt-viewer
+bin/viewer
+%%DATADIR%%/analyze.cfg
+%%PORTDOCS%%%%DOCSDIR%%/analyze_mode.html
+%%PORTDOCS%%%%DOCSDIR%%/analyze_samples.html
+%%PORTDOCS%%%%DOCSDIR%%/code_c++_intro.html
+%%PORTDOCS%%%%DOCSDIR%%/code_death_birth.html
+%%PORTDOCS%%%%DOCSDIR%%/code_environment.html
+%%PORTDOCS%%%%DOCSDIR%%/code_events.html
+%%PORTDOCS%%%%DOCSDIR%%/code_genesis.html
+%%PORTDOCS%%%%DOCSDIR%%/code_genome.html
+%%PORTDOCS%%%%DOCSDIR%%/code_init_file.html
+%%PORTDOCS%%%%DOCSDIR%%/code_instruction.html
+%%PORTDOCS%%%%DOCSDIR%%/code_life_cycle.html
+%%PORTDOCS%%%%DOCSDIR%%/code_task.html
+%%PORTDOCS%%%%DOCSDIR%%/cpu2.gif
+%%PORTDOCS%%%%DOCSDIR%%/cpu_tour.html
+%%PORTDOCS%%%%DOCSDIR%%/cvs.html
+%%PORTDOCS%%%%DOCSDIR%%/devel.html
+%%PORTDOCS%%%%DOCSDIR%%/environment.html
+%%PORTDOCS%%%%DOCSDIR%%/events.html
+%%PORTDOCS%%%%DOCSDIR%%/genesis.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/components.help
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Bitwise.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.CPU-cycle.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.CPU.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Complement-Template.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Genome.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Genotype.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Heads.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.IO.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Input-Output.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Instruction.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Logic.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Memory.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Mutation.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Nop-Head-Notation.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Nop-Register-Notation.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Organism.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Population.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Registers.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Stack.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Tasks.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.Template.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.add.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.dec.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.h-alloc.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.h-copy.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.h-divide.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.h-search.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.if-label.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.if-less.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.if-n-equ.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.inc.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.jmp-head.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.mov-head.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.nand.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.nop-instructions.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.pop.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.push.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.set-flow.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.shift-l.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.shift-r.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.sub.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.swap-stk.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/help.swap.html
+%%PORTDOCS%%%%DOCSDIR%%/glossary/inst.help
+%%PORTDOCS%%%%DOCSDIR%%/glossary/notations.help
+%%PORTDOCS%%%%DOCSDIR%%/glossary/todo.help
+%%PORTDOCS%%%%DOCSDIR%%/index.html
+%%PORTDOCS%%%%DOCSDIR%%/inst_set.html
+%%PORTDOCS%%%%DOCSDIR%%/level_map.html
+%%PORTDOCS%%%%DOCSDIR%%/print_data.html
+%%PORTDOCS%%%%DOCSDIR%%/screen.html
+%%PORTDOCS%%%%DOCSDIR%%/structure.html
+%%DATADIR%%/environment.cfg
+%%DATADIR%%/events.cfg
+%%DATADIR%%/genesis
+%%DATADIR%%/genesis.4stack
+%%DATADIR%%/inst_set.4stack
+%%DATADIR%%/inst_set.default
+%%DATADIR%%/organism.default
+%%DATADIR%%/preset_organisms/dummy
+%%DATADIR%%/preset_organisms/organism.4stack
+%%DATADIR%%/preset_organisms/organism.parasite
+@dirrm %%DATADIR%%/preset_organisms
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/glossary
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
+@dirrm %%DATADIR%%