From 9e3da593d2b8eb711044789d0248d901ce4777a0 Mon Sep 17 00:00:00 2001 From: Ying-Chieh Liao Date: Sat, 20 Apr 2002 15:17:46 +0000 Subject: add avida 1.6.0 Avida is an auto-adaptive genetic system designed for ALife research PR: 37268 Submitted by: Jeremy Karlson --- biology/Makefile | 1 + biology/avida/Makefile | 39 +++++++++++++++++++++++++++++++++++++++ biology/avida/distinfo | 1 + biology/avida/files/patch-aa | 10 ++++++++++ biology/avida/files/patch-ab | 10 ++++++++++ biology/avida/files/patch-ac | 11 +++++++++++ biology/avida/files/patch-ad | 11 +++++++++++ biology/avida/files/patch-ae | 11 +++++++++++ biology/avida/pkg-comment | 1 + biology/avida/pkg-descr | 16 ++++++++++++++++ biology/avida/pkg-plist | 35 +++++++++++++++++++++++++++++++++++ 11 files changed, 146 insertions(+) create mode 100644 biology/avida/Makefile create mode 100644 biology/avida/distinfo create mode 100644 biology/avida/files/patch-aa create mode 100644 biology/avida/files/patch-ab create mode 100644 biology/avida/files/patch-ac create mode 100644 biology/avida/files/patch-ad create mode 100644 biology/avida/files/patch-ae create mode 100644 biology/avida/pkg-comment create mode 100644 biology/avida/pkg-descr create mode 100644 biology/avida/pkg-plist (limited to 'biology') diff --git a/biology/Makefile b/biology/Makefile index c66e42a81840..5be076006729 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -2,6 +2,7 @@ # SUBDIR += artemis + SUBDIR += avida SUBDIR += babel SUBDIR += biojava SUBDIR += chemeq diff --git a/biology/avida/Makefile b/biology/avida/Makefile new file mode 100644 index 000000000000..d02462e1fd4f --- /dev/null +++ b/biology/avida/Makefile @@ -0,0 +1,39 @@ +# New ports collection makefile for: avida +# Date created: 17 April 2002 +# Whom: Jeremy +# +# $FreeBSD$ +# + +PORTNAME= avida +PORTVERSION= 1.6.0 +CATEGORIES= biology +MASTER_SITES= http://dllab.caltech.edu/avida/versions/ + +MAINTAINER= karlj000@unbc.ca + +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} + +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 diff --git a/biology/avida/distinfo b/biology/avida/distinfo new file mode 100644 index 000000000000..d0e179ea3e42 --- /dev/null +++ b/biology/avida/distinfo @@ -0,0 +1 @@ +MD5 (avida-1.6.0.tar.gz) = 2294af061f200c486de2ed889e0e17af diff --git a/biology/avida/files/patch-aa b/biology/avida/files/patch-aa new file mode 100644 index 000000000000..554cac9efe93 --- /dev/null +++ b/biology/avida/files/patch-aa @@ -0,0 +1,10 @@ +--- 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 ++#include + //#include "event_defs.hh" + + enum eTriggerVariable { UPDATE, GENERATION, IMMEDIATE, UNDEFINED }; diff --git a/biology/avida/files/patch-ab b/biology/avida/files/patch-ab new file mode 100644 index 000000000000..453635356a94 --- /dev/null +++ b/biology/avida/files/patch-ab @@ -0,0 +1,10 @@ +--- 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 + #include + #include ++#include + #include + + #include "../cpu/cpu.hh" diff --git a/biology/avida/files/patch-ac b/biology/avida/files/patch-ac new file mode 100644 index 000000000000..980deaebc657 --- /dev/null +++ b/biology/avida/files/patch-ac @@ -0,0 +1,11 @@ +--- 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 new file mode 100644 index 000000000000..0440d2e48130 --- /dev/null +++ b/biology/avida/files/patch-ad @@ -0,0 +1,11 @@ +--- 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 new file mode 100644 index 000000000000..34a692b7cbca --- /dev/null +++ b/biology/avida/files/patch-ae @@ -0,0 +1,11 @@ +--- 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-comment b/biology/avida/pkg-comment new file mode 100644 index 000000000000..7d166f5a2674 --- /dev/null +++ b/biology/avida/pkg-comment @@ -0,0 +1 @@ +Avida is an auto-adaptive genetic system designed for ALife research diff --git a/biology/avida/pkg-descr b/biology/avida/pkg-descr new file mode 100644 index 000000000000..3f85f3975c88 --- /dev/null +++ b/biology/avida/pkg-descr @@ -0,0 +1,16 @@ +The computer program avida is an auto-adaptive genetic system designed +primarily for use as a platform in Digital or Artificial Life research. The +avida system is based on concepts similar to those employed by the tierra +program developed by Tom Ray. It is a population of self-reproducing strings +with a Turing-complete genetic basis subjected to Poisson-random mutations. +The population adapts to the combination of an intrinsic fitness landscape +(self-reproduction) and an externally imposed (extrinsic) fitness function +provided by the researcher. By studying this system, one can examine +evolutionary adaptation, general traits of living systems (such as +self-organization), and other issues pertaining to theoretical or +evolutionary biology and dynamic systems. + +WWW: http://dllab.caltech.edu/avida/ + +Jeremy +karlj000@unbc.ca diff --git a/biology/avida/pkg-plist b/biology/avida/pkg-plist new file mode 100644 index 000000000000..e7ce0d5f69bd --- /dev/null +++ b/biology/avida/pkg-plist @@ -0,0 +1,35 @@ +bin/avida +share/avida/creature.base +share/avida/creature.heads +share/avida/creature.heads.new +share/avida/genesis +share/avida/genesis.heads +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 -- cgit v1.2.3