diff options
author | rafan <rafan@FreeBSD.org> | 2006-07-08 11:36:36 +0800 |
---|---|---|
committer | rafan <rafan@FreeBSD.org> | 2006-07-08 11:36:36 +0800 |
commit | b2b987e2248bf35cf8cc85fe5b08b67e910b70df (patch) | |
tree | 129c2f58cdf3d69c3245c003a4a0d034bf6cbf99 /biology | |
parent | a53c31625070df75e3c6a38bc719be13773ace81 (diff) | |
download | freebsd-ports-gnome-b2b987e2248bf35cf8cc85fe5b08b67e910b70df.tar.gz freebsd-ports-gnome-b2b987e2248bf35cf8cc85fe5b08b67e910b70df.tar.zst freebsd-ports-gnome-b2b987e2248bf35cf8cc85fe5b08b67e910b70df.zip |
- Update to 2.4.3
- Pass maintainersip to submitter
PR: 99901
Submitted by: Scott Flatman <sf slappy.org>
Approved by: delphij (mentor, implicit)
Diffstat (limited to 'biology')
-rw-r--r-- | biology/avida/Makefile | 67 | ||||
-rw-r--r-- | biology/avida/distinfo | 6 | ||||
-rw-r--r-- | biology/avida/files/patch-ab | 10 | ||||
-rw-r--r-- | biology/avida/files/patch-configure | 20 | ||||
-rw-r--r-- | biology/avida/files/patch-source::main::config.cc | 23 | ||||
-rw-r--r-- | biology/avida/files/patch-source::support::genesis | 19 | ||||
-rw-r--r-- | biology/avida/files/patch-source::tools::data_entry.hh | 44 | ||||
-rw-r--r-- | biology/avida/pkg-plist | 192 |
8 files changed, 147 insertions, 234 deletions
diff --git a/biology/avida/Makefile b/biology/avida/Makefile index 475e81256547..ed3566b71966 100644 --- a/biology/avida/Makefile +++ b/biology/avida/Makefile @@ -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="${X11BASE}" -PLIST_SUB= QT="" -.else -PLIST_SUB= QT="@comment " -.endif +BUILD_DEPENDS= cmake:${PORTSDIR}/devel/cmake -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|" \ - ${WRKSRC}/Makefile.in -.endif +CMAKE_ARGS= -DPROJECT_BINARY_DIR=${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} 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} ${DOCSDIR} + (${CP} -RP ${WRKSRC}/documentation/ ${DOCSDIR}) .endif .include <bsd.port.mk> diff --git a/biology/avida/distinfo b/biology/avida/distinfo index b46b679ba1a1..78b88df49b32 100644 --- a/biology/avida/distinfo +++ b/biology/avida/distinfo @@ -1,3 +1,3 @@ -MD5 (avida-2.0b7.tar.gz) = 908985c3f54e19e003e6e744a941b3cb -SHA256 (avida-2.0b7.tar.gz) = f8a7ff62f4cc6cbd34833785b7bf8af591ece7a9c595ede211ed5745ad776a6f -SIZE (avida-2.0b7.tar.gz) = 829131 +MD5 (avida-src-2.4.3.tar.gz) = 44c3f1df0fe5d62a08cb0a64dc9c5ac2 +SHA256 (avida-src-2.4.3.tar.gz) = 4a883138d9da57c99defe521de96e7851f453e1a003c978a6dbb178c8a51ba11 +SIZE (avida-src-2.4.3.tar.gz) = 1725948 diff --git a/biology/avida/files/patch-ab b/biology/avida/files/patch-ab deleted file mode 100644 index 453635356a94..000000000000 --- a/biology/avida/files/patch-ab +++ /dev/null @@ -1,10 +0,0 @@ ---- source/main/fitness_matrix.hh.orig Thu Apr 18 08:54:04 2002 -+++ source/main/fitness_matrix.hh Thu Apr 18 08:54:15 2002 -@@ -7,6 +7,7 @@ - #include <vector> - #include <map> - #include <list> -+#include <sys/types.h> - #include <sys/timeb.h> - - #include "../cpu/cpu.hh" diff --git a/biology/avida/files/patch-configure b/biology/avida/files/patch-configure deleted file mode 100644 index 789380563b84..000000000000 --- a/biology/avida/files/patch-configure +++ /dev/null @@ -1,20 +0,0 @@ ---- configure.orig Thu Oct 16 19:31:57 2003 -+++ configure Sun May 9 09:54:12 2004 -@@ -3488,7 +3488,7 @@ - enableval="$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 --git a/biology/avida/files/patch-source::main::config.cc b/biology/avida/files/patch-source::main::config.cc deleted file mode 100644 index ef4cea87bd04..000000000000 --- a/biology/avida/files/patch-source::main::config.cc +++ /dev/null @@ -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 --git a/biology/avida/files/patch-source::support::genesis b/biology/avida/files/patch-source::support::genesis deleted file mode 100644 index ccc0ce6681f2..000000000000 --- a/biology/avida/files/patch-source::support::genesis +++ /dev/null @@ -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 --git a/biology/avida/files/patch-source::tools::data_entry.hh b/biology/avida/files/patch-source::tools::data_entry.hh deleted file mode 100644 index 71ab0df011bf..000000000000 --- a/biology/avida/files/patch-source::tools::data_entry.hh +++ /dev/null @@ -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 --git a/biology/avida/pkg-plist b/biology/avida/pkg-plist index d16f43387a78..13ccc4b91474 100644 --- a/biology/avida/pkg-plist +++ b/biology/avida/pkg-plist @@ -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 -%%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 @@ -81,10 +8,115 @@ bin/viewer %%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%%%%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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