Date: Fri, 07 Jul 2006 17:53:35 -0700 From: Scott Flatman <sf@slappy.org> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/99901: Maintainer Update: biology/avida Message-ID: <44AF020F.1050507@slappy.org> Resent-Message-ID: <200607080100.k6810bpw029720@freefall.freebsd.org>
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>Number: 99901
>Category: ports
>Synopsis: Adopt port. Update version.
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Sat Jul 08 01:00:36 GMT 2006
>Closed-Date:
>Last-Modified:
>Originator: Scott Flatman
>Release: FreeBSD 6.1-STABLE i386
>Organization:
>Environment:
FreeBSD emerald.foo.kom 6.1-STABLE FreeBSD 6.1-STABLE #28: Sat Jul 1 17:22:41 PDT 2006 sf@emerald.foo.kom:/home/obj/home/src6s/sys/EMERALD12 i386
>Description:
Adopt port.
Update version.
>How-To-Repeat:
>Fix:
-*- avida patch begins here -*-
diff -ruN avida.orig/Makefile avida/Makefile
--- avida.orig/Makefile Sun May 28 12:07:36 2006
+++ avida/Makefile Fri Jul 7 17:43:10 2006
@@ -6,50 +6,47 @@
#
PORTNAME= avida
-PORTVERSION= 2.0b7
+PORTVERSION= 2.4.3
CATEGORIES= biology
MASTER_SITES= ${MASTER_SITE_SOURCEFORGE}
MASTER_SITE_SUBDIR= ${PORTNAME}
+DISTNAME= ${PORTNAME}-src-${PORTVERSION}
-MAINTAINER= ports@FreeBSD.org
+MAINTAINER= sf@slappy.org
COMMENT= Avida is an auto-adaptive genetic system designed for ALife research
-USE_GMAKE= yes
-GNU_CONFIGURE= yes
-CONFIGURE_ARGS= --enable-standard-prefix --datadir=${DATADIR} --enable-viewer
-CONFIGURE_TARGET= --build=${MACHINE_ARCH}-portbld-freebsd${OSREL}
-USE_PERL5_BUILD= yes
-
-.if !defined(WITHOUT_QT)
-BUILD_DEPENDS+= qmake:${PORTSDIR}/devel/qmake
-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
-
-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|" \
- ${WRKSRC}/Makefile.in
-.endif
+BUILD_DEPENDS= cmake:${PORTSDIR}/devel/cmake
+
+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}
+
+do-build:
+ @(cd ${BUILD_WRKSRC}; \
+ mkdir -p build build/work; \
+ cd build; \
+ cmake ${CMAKE_ARGS} ..; \
+ make)
+
+do-install:
+ @(cd ${BUILD_WRKSRC}; \
+ cd build; \
+ make install)
-.if !defined(WITHOUT_QT)
post-install:
- ${INSTALL_PROGRAM} ${WRKSRC}/work/qt-viewer ${PREFIX}/bin
+ ${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} )
+.if !defined(NOPORTDOCS)
+ ${MKDIR} ${PREFIX}/share/doc/${PORTNAME}
+ (cp -RP ${WRKSRC}/documentation/ ${PREFIX}/share/doc/${PORTNAME})
.endif
.include <bsd.port.mk>
diff -ruN avida.orig/distinfo avida/distinfo
--- avida.orig/distinfo Fri Dec 9 20:57:33 2005
+++ avida/distinfo Fri Jul 7 17:43:10 2006
@@ -1,3 +1,3 @@
-MD5 (avida-2.0b7.tar.gz) = 908985c3f54e19e003e6e744a941b3cb
-SHA256 (avida-2.0b7.tar.gz) = f8a7ff62f4cc6cbd34833785b7bf8af591ece7a9c595ede211ed5745ad776a6f
-SIZE (avida-2.0b7.tar.gz) = 829131
+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
diff -ruN avida.orig/files/patch-ab avida/files/patch-ab
--- avida.orig/files/patch-ab Sat Apr 20 08:17:46 2002
+++ avida/files/patch-ab Wed Dec 31 16:00:00 1969
@@ -1,10 +0,0 @@
---- source/main/fitness_matrix.hh.orig Thu Apr 18 08:54:04 2002
-+++ source/main/fitness_matrix.hh Thu Apr 18 08:54:15 2002
-@@ -7,6 +7,7 @@
- #include <vector>
- #include <map>
- #include <list>
-+#include <sys/types.h>
- #include <sys/timeb.h>
-
- #include "../cpu/cpu.hh"
diff -ruN avida.orig/files/patch-configure avida/files/patch-configure
--- avida.orig/files/patch-configure Fri May 21 06:24:56 2004
+++ avida/files/patch-configure Wed Dec 31 16:00:00 1969
@@ -1,20 +0,0 @@
---- configure.orig Thu Oct 16 19:31:57 2003
-+++ configure Sun May 9 09:54:12 2004
-@@ -3488,7 +3488,7 @@
- enableval="$enable_debug"
- CPPFLAGS="-g -Wall -pedantic -DDEBUG"; qmake_debug="debug"
- else
-- CPPFLAGS="-O3 -ffast-math"; qmake_debug="release"
-+ CPPFLAGS+="-ffast-math"; qmake_debug="release"
- fi;
-
- # Check whether --enable-gnu-debug or --disable-gnu-debug was given.
-@@ -3545,7 +3545,7 @@
- CPPFLAGS="${CPPFLAGS} -pedantic"
- fi;
-
--htmldir='${datadir}/doc_html'
-+htmldir='${prefix}/share/doc/avida'
- HTMLDIR=${htmldir}
-
- # Check whether --enable-primitive or --disable-primitive was given.
diff -ruN avida.orig/files/patch-source::main::config.cc avida/files/patch-source::main::config.cc
--- avida.orig/files/patch-source::main::config.cc Fri May 21 06:24:56 2004
+++ avida/files/patch-source::main::config.cc Wed Dec 31 16:00:00 1969
@@ -1,23 +0,0 @@
---- ./source/main/config.cc.orig Thu Oct 16 18:15:17 2003
-+++ ./source/main/config.cc Mon May 10 20:39:45 2004
-@@ -132,15 +132,15 @@
-
- file_group->Add(default_dir, DEFAULT_DIR, "DEFAULT_DIR",
- "Directory in which config files are found");
-- file_group->Add(inst_filename, "inst_set.default", "INST_SET",
-+ file_group->Add(inst_filename, "../work/inst_set.default", "INST_SET",
- "File containing instruction set");
-- file_group->Add(event_filename, "events.cfg", "EVENT_FILE",
-+ file_group->Add(event_filename, "../work/events.cfg", "EVENT_FILE",
- "File containing list of events during run");
-- file_group->Add(analyze_filename, "analyze.cfg", "ANALYZE_FILE",
-+ file_group->Add(analyze_filename, "../work/analyze.cfg", "ANALYZE_FILE",
- "File used for analysis mode");
-- file_group->Add(env_filename, "environment.cfg", "ENVIRONMENT_FILE",
-+ file_group->Add(env_filename, "../work/environment.cfg", "ENVIRONMENT_FILE",
- "File that describes the environment");
-- file_group->Add(start_creature, "organism.default", "START_CREATURE",
-+ file_group->Add(start_creature, "../work/organism.default", "START_CREATURE",
- "Organism to seed the soup");
-
- // Reproduction group.
diff -ruN avida.orig/files/patch-source::support::genesis avida/files/patch-source::support::genesis
--- avida.orig/files/patch-source::support::genesis Fri May 21 06:24:56 2004
+++ avida/files/patch-source::support::genesis Wed Dec 31 16:00:00 1969
@@ -1,19 +0,0 @@
---- source/support/genesis.orig Thu Oct 16 02:45:16 2003
-+++ source/support/genesis Sun May 9 23:40:24 2004
-@@ -22,11 +22,11 @@
-
- ### Configuration Files ###
- DEFAULT_DIR ../work/ # Directory in which config files are found
--INST_SET inst_set.default # File containing instruction set
--EVENT_FILE events.cfg # File containing list of events during run
--ANALYZE_FILE analyze.cfg # File used for analysis mode
--ENVIRONMENT_FILE environment.cfg # File that describes the environment
--START_CREATURE organism.default # Organism to seed the soup
-+INST_SET ../work/inst_set.default # File containing instruction set
-+EVENT_FILE ../work/events.cfg # File containing list of events during run
-+ANALYZE_FILE ../work/analyze.cfg # File used for analysis mode
-+ENVIRONMENT_FILE ../work/environment.cfg # File that describes the environment
-+START_CREATURE ../work/organism.default # Organism to seed the soup
-
- ### Reproduction ###
- BIRTH_METHOD 4 # 0 = Replace random organism in neighborhood
diff -ruN avida.orig/files/patch-source::tools::data_entry.hh avida/files/patch-source::tools::data_entry.hh
--- avida.orig/files/patch-source::tools::data_entry.hh Sat Sep 18 01:12:28 2004
+++ avida/files/patch-source::tools::data_entry.hh Wed Dec 31 16:00:00 1969
@@ -1,44 +0,0 @@
---- source/tools/data_entry.hh.orig Fri Sep 17 16:43:13 2004
-+++ source/tools/data_entry.hh Fri Sep 17 16:45:30 2004
-@@ -94,19 +94,19 @@
- DataSet(_funS), DataCompare(_funC) { ; }
-
- bool Print(std::ostream & fp) const {
-- if (target == NULL) return false;
-- fp << (target->*DataRetrieval)();
-+ if (this->target == NULL) return false;
-+ fp << (this->target->*DataRetrieval)();
- return true;
- }
-
- //int Compare(T * other) const { return (target->*DataCompare)(other); }
- int Compare(T * other) const {
-- return (DataCompare)?((target->*DataCompare)(other)):(0);
-+ return (DataCompare)?((this->target->*DataCompare)(other)):(0);
- }
- bool Set(const cString & value) {
- OUT new_value(0);
- if (DataSet == 0) return false;
-- (target->*DataSet)( cStringUtil::Convert(value, new_value) );
-+ (this->target->*DataSet)( cStringUtil::Convert(value, new_value) );
- return true;
- }
- };
-@@ -128,14 +128,14 @@
- DataRetrieval(_funR), DataCompare(_funC), arg(_arg) { ; }
-
- bool Print(std::ostream & fp) const {
-- if (target == NULL) return false;
-- fp << (target->*DataRetrieval)(arg);
-+ if (this->target == NULL) return false;
-+ fp << (this->target->*DataRetrieval)(arg);
- return true;
- }
-
- //int Compare(T * other) const { return (target->*DataCompare)(other, arg); }
- int Compare(T * other) const {
-- return (DataCompare)?((target->*DataCompare)(other, arg)):(0);
-+ return (DataCompare)?((this->target->*DataCompare)(other, arg)):(0);
- }
- };
-
diff -ruN avida.orig/pkg-plist avida/pkg-plist
--- avida.orig/pkg-plist Mon May 10 12:26:42 2004
+++ avida/pkg-plist Fri Jul 7 17:43:10 2006
@@ -1,79 +1,6 @@
-bin/primitive
-%%QT%%bin/qt-viewer
-bin/viewer
+bin/AvidaConsole
+bin/task_event_gen
%%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
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-%%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
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-%%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
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-%%PORTDOCS%%%%DOCSDIR%%/print_data.html
-%%PORTDOCS%%%%DOCSDIR%%/screen.html
-%%PORTDOCS%%%%DOCSDIR%%/structure.html
%%DATADIR%%/environment.cfg
%%DATADIR%%/events.cfg
%%DATADIR%%/genesis
@@ -81,10 +8,115 @@
%%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%%
+%%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
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+%%PORTDOCS%%%%DOCSDIR%%/content/using/cpu_tour.html
+%%PORTDOCS%%%%DOCSDIR%%/content/using/cvs.html
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+%%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
+@dirrm %%PORTDOCS%%%%DOCSDIR%%/xdocs/images
+@dirrm %%PORTDOCS%%%%DOCSDIR%%/xdocs/admin
+@dirrm %%PORTDOCS%%%%DOCSDIR%%/xdocs
+@dirrm %%PORTDOCS%%%%DOCSDIR%%/forrest/translations
+@dirrm %%PORTDOCS%%%%DOCSDIR%%/forrest/classes
+@dirrm %%PORTDOCS%%%%DOCSDIR%%/forrest
+@dirrm %%PORTDOCS%%%%DOCSDIR%%/content/using/glossary
+@dirrm %%PORTDOCS%%%%DOCSDIR%%/content/using
+@dirrm %%PORTDOCS%%%%DOCSDIR%%/content
+@dirrm %%PORTDOCS%%%%DOCSDIR%%
@dirrm %%DATADIR%%
-*- avida patch ends here -*-
--------------080703020500020304020709--
>Release-Note:
>Audit-Trail:
>Unformatted:
This is a multi-part message in MIME format.
--------------080703020500020304020709
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 7bit
--------------080703020500020304020709
Content-Type: text/plain;
name="avida"
Content-Transfer-Encoding: 7bit
Content-Disposition: inline;
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