4 files changed, 40 insertions, 150 deletions

diff --git a/biology/avida/Makefile b/biology/avida/Makefile
index 1109de14ea97..a4ab1cfc8bb7 100644
--- a/biology/avida/Makefile
+++ b/biology/avida/Makefile
@@ -6,47 +6,32 @@
 #
 
 PORTNAME=	avida
-PORTVERSION=	2.4.3
+PORTVERSION=	2.8.1
 CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
-MASTER_SITE_SUBDIR=	${PORTNAME}
-DISTNAME=	${PORTNAME}-src-${PORTVERSION}
+MASTER_SITES=	SF
+DISTNAME=	${PORTNAME}-${PORTVERSION}-src
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Avida is an auto-adaptive genetic system designed for ALife research
 
-BUILD_DEPENDS=	cmake:${PORTSDIR}/devel/cmake
+USE_CMAKE=	yes
+USE_GCC=	4.2+
 
-CMAKE_ARGS=	-DPROJECT_BINARY_DIR=${WRKSRC}/build/work \
-		-DAVD_CONSISTENCY_TEST_PRIMITIVE:BOOL=OFF \
-		-DAVD_GUI_NCURSES:BOOL=ON \
-		-DAVD_PRIMITIVE:BOOL=ON \
-		-DAVD_UNIT_TESTS:BOOL=OFF\
-		-DCMAKE_BUILD_TYPE:STRING=Release
+WRKSRC=		${WRKDIR}/${PORTNAME}-src-${PORTVERSION}
 
-WRKSRC=		${WRKDIR}/${PORTNAME}
+PORTDOCS=	*
 
-do-build:
-	@(cd ${BUILD_WRKSRC}; \
-	${MKDIR} build build/work; \
-	cd build; \
-	cmake ${CMAKE_ARGS} ..; \
-	${MAKE})
-
-do-install:
-	@(cd ${BUILD_WRKSRC}; \
-	cd build; \
-	${MAKE} install)
+post-extract:
+	@${RM} -f ${WRKSRC}/documentation/.[D_]*
 
 post-install:
-	${MKDIR} ${PREFIX}/share/${PORTNAME}
-	(cd ${WRKSRC}/build/work/work; \
-	${INSTALL_PROGRAM} AvidaConsole ${PREFIX}/bin; \
-	${INSTALL_PROGRAM} task_event_gen ${PREFIX}/bin; \
-	${INSTALL_DATA} analyze.cfg environment.cfg events.cfg genesis genesis.4stack inst_set.4stack inst_set.default organism.default ${PREFIX}/share/${PORTNAME} )
+	${INSTALL_PROGRAM} ${WRKSRC}/work/avida ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/work/avida-viewer ${PREFIX}/bin
+	${MKDIR} ${DATADIR}
+	${INSTALL_DATA} ${WRKSRC}/work/*.cfg ${WRKSRC}/work/*.org ${DATADIR}
 .if !defined(NOPORTDOCS)
 	${MKDIR} ${DOCSDIR}
-	(${CP} -RP ${WRKSRC}/documentation/ ${DOCSDIR})
+	cd ${WRKSRC}/documentation && ${COPYTREE_SHARE} . ${DOCSDIR}
 .endif
 
 .include <bsd.port.mk>
diff --git a/biology/avida/distinfo b/biology/avida/distinfo
index 78b88df49b32..43af8be95154 100644
--- a/biology/avida/distinfo
+++ b/biology/avida/distinfo
@@ -1,3 +1,3 @@
-MD5 (avida-src-2.4.3.tar.gz) = 44c3f1df0fe5d62a08cb0a64dc9c5ac2
-SHA256 (avida-src-2.4.3.tar.gz) = 4a883138d9da57c99defe521de96e7851f453e1a003c978a6dbb178c8a51ba11
-SIZE (avida-src-2.4.3.tar.gz) = 1725948
+MD5 (avida-2.8.1-src.tar.gz) = 99d9405921a23df1813e34c96106cd47
+SHA256 (avida-2.8.1-src.tar.gz) = 554a82081f550e49f795ecda34d6e19a91239e8dc500b6590f46d08839179ef7
+SIZE (avida-2.8.1-src.tar.gz) = 1609168
diff --git a/biology/avida/files/patch-source-main-cTaskLib.cc b/biology/avida/files/patch-source-main-cTaskLib.cc
new file mode 100644
index 000000000000..e250c4a81844
--- /dev/null
+++ b/biology/avida/files/patch-source-main-cTaskLib.cc
@@ -0,0 +1,12 @@
+--- source/main/cTaskLib.cc.orig	2007-09-05 23:53:07.000000000 +0400
++++ source/main/cTaskLib.cc	2008-10-13 19:32:10.000000000 +0400
+@@ -41,8 +41,8 @@
+ // Various workarounds for Visual Studio shortcomings
+ #if AVIDA_PLATFORM(WINDOWS)
+ # define llabs(x) _abs64(x)
+-# define log2(x) (log(x)/log(2.0))
+ #endif
++# define log2(x) (log(x)/log(2.0))
+ 
+ static const double dCastPrecision = 100000.0;
+ 
diff --git a/biology/avida/pkg-plist b/biology/avida/pkg-plist
index 13ccc4b91474..dd71eb55626a 100644
--- a/biology/avida/pkg-plist
+++ b/biology/avida/pkg-plist
@@ -1,122 +1,15 @@
-bin/AvidaConsole
-bin/task_event_gen
+bin/avida
+bin/avida-viewer
 %%DATADIR%%/analyze.cfg
+%%DATADIR%%/avida.cfg
+%%DATADIR%%/default-classic.org
+%%DATADIR%%/default-sex-classic.org
+%%DATADIR%%/default-smt.org
+%%DATADIR%%/default-transsmt.org
 %%DATADIR%%/environment.cfg
 %%DATADIR%%/events.cfg
-%%DATADIR%%/genesis
-%%DATADIR%%/genesis.4stack
-%%DATADIR%%/inst_set.4stack
-%%DATADIR%%/inst_set.default
-%%DATADIR%%/organism.default
-%%PORTDOCS%%%%DOCSDIR%%/content/using/CMakeLists.txt
-%%PORTDOCS%%%%DOCSDIR%%/content/using/analyze_mode.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/analyze_samples.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/code_c++_intro.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/code_death_birth.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/code_environment.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/code_events.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/code_genesis.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/code_genome.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/code_init_file.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/code_instruction.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/code_life_cycle.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/code_task.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/cpu2.gif
-%%PORTDOCS%%%%DOCSDIR%%/content/using/cpu_tour.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/cvs.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/devel.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/environment.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/events.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/genesis.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/CMakeLists.txt
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/components.help
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Bitwise.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.CPU-cycle.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.CPU.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Complement-Template.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Genome.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Genotype.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Heads.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.IO.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Input-Output.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Instruction.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Logic.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Memory.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Mutation.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Nop-Head-Notation.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Nop-Register-Notation.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Organism.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Population.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Registers.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Stack.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Tasks.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.Template.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.add.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.dec.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.h-alloc.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.h-copy.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.h-divide.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.h-search.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.if-label.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.if-less.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.if-n-equ.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.inc.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.jmp-head.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.mov-head.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.nand.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.nop-instructions.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.pop.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.push.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.set-flow.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.shift-l.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.shift-r.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.sub.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.swap-stk.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/help.swap.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/inst.help
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/notations.help
-%%PORTDOCS%%%%DOCSDIR%%/content/using/glossary/todo.help
-%%PORTDOCS%%%%DOCSDIR%%/content/using/index.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/inst_set.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/level_map.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/print_data.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/screen.html
-%%PORTDOCS%%%%DOCSDIR%%/content/using/structure.html
-%%PORTDOCS%%%%DOCSDIR%%/forrest/README.txt
-%%PORTDOCS%%%%DOCSDIR%%/forrest/classes/CatalogManager.properties
-%%PORTDOCS%%%%DOCSDIR%%/forrest/skinconf.xml
-%%PORTDOCS%%%%DOCSDIR%%/forrest/translations/langcode.xml
-%%PORTDOCS%%%%DOCSDIR%%/forrest/translations/languages_en.xml
-%%PORTDOCS%%%%DOCSDIR%%/forrest/translations/languages_es.xml
-%%PORTDOCS%%%%DOCSDIR%%/forrest/translations/menu.xml
-%%PORTDOCS%%%%DOCSDIR%%/forrest/translations/menu_af.xml
-%%PORTDOCS%%%%DOCSDIR%%/forrest/translations/menu_de.xml
-%%PORTDOCS%%%%DOCSDIR%%/forrest/translations/menu_es.xml
-%%PORTDOCS%%%%DOCSDIR%%/forrest/translations/menu_it.xml
-%%PORTDOCS%%%%DOCSDIR%%/forrest/translations/menu_no.xml
-%%PORTDOCS%%%%DOCSDIR%%/forrest/translations/menu_ru.xml
-%%PORTDOCS%%%%DOCSDIR%%/forrest/translations/menu_sk.xml
-%%PORTDOCS%%%%DOCSDIR%%/forrest/translations/tabs.xml
-%%PORTDOCS%%%%DOCSDIR%%/forrest/translations/tabs_es.xml
-%%PORTDOCS%%%%DOCSDIR%%/xdocs/admin/index.xml
-%%PORTDOCS%%%%DOCSDIR%%/xdocs/admin/third-party-osx.xml
-%%PORTDOCS%%%%DOCSDIR%%/xdocs/admin/third-party-win32.xml
-%%PORTDOCS%%%%DOCSDIR%%/xdocs/images/group-logo.gif
-%%PORTDOCS%%%%DOCSDIR%%/xdocs/images/group.svg
-%%PORTDOCS%%%%DOCSDIR%%/xdocs/images/icon.png
-%%PORTDOCS%%%%DOCSDIR%%/xdocs/images/project-logo.gif
-%%PORTDOCS%%%%DOCSDIR%%/xdocs/images/project.svg
-%%PORTDOCS%%%%DOCSDIR%%/xdocs/index.xml
-%%PORTDOCS%%%%DOCSDIR%%/xdocs/site.xml
-%%PORTDOCS%%%%DOCSDIR%%/xdocs/tabs.xml
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/xdocs/images
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/xdocs/admin
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/xdocs
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/forrest/translations
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/forrest/classes
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/forrest
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/content/using/glossary
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/content/using
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/content
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
+%%DATADIR%%/instset-classic.cfg
+%%DATADIR%%/instset-sex-classic.cfg
+%%DATADIR%%/instset-smt.cfg
+%%DATADIR%%/instset-transsmt.cfg
 @dirrm %%DATADIR%%