Date: Fri, 19 Apr 2002 21:01:35 -0700 (PDT) From: Jeremy Karlson <karlj000@unbc.ca> To: <FreeBSD-gnats-submit@FreeBSD.org> Subject: ports/37268: New Port: biology/avida: Avida is an auto-adaptive genetic system designed for ALife research Message-ID: <Pine.LNX.4.33.0204192101060.3669-100000@ugrad.unbc.ca>
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>Number: 37268
>Category: ports
>Synopsis: New Port: biology/avida: Avida is an auto-adaptive genetic system designed for ALife research
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Fri Apr 19 21:10:01 PDT 2002
>Closed-Date:
>Last-Modified:
>Originator: Jeremy
>Release: FreeBSD 4.5-STABLE i386
>Organization:
>Environment:
System: FreeBSD lucretia.karlson.ca 4.5-STABLE FreeBSD 4.5-STABLE #1: Thu Mar 7 17:28:13 PST 2002 carpathia@lucretia.karlson.ca:/usr/obj/usr/src/sys/LUCRETIA i386
>Description:
New Port: biology/avida
New Port: biology/avida: Avida is an auto-adaptive genetic system designed for ALife research
>How-To-Repeat:
>Fix:
The following shar file contains the complete port:
# This is a shell archive. Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file". Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
# /usr/ports/biology/avida
# /usr/ports/biology/avida/files
# /usr/ports/biology/avida/files/patch-aa
# /usr/ports/biology/avida/files/patch-ab
# /usr/ports/biology/avida/files/patch-ac
# /usr/ports/biology/avida/files/patch-ad
# /usr/ports/biology/avida/files/patch-ae
# /usr/ports/biology/avida/pkg-plist
# /usr/ports/biology/avida/distinfo
# /usr/ports/biology/avida/pkg-descr
# /usr/ports/biology/avida/pkg-comment
# /usr/ports/biology/avida/Makefile
#
echo c - /usr/ports/biology/avida
mkdir -p /usr/ports/biology/avida > /dev/null 2>&1
echo c - /usr/ports/biology/avida/files
mkdir -p /usr/ports/biology/avida/files > /dev/null 2>&1
echo x - /usr/ports/biology/avida/files/patch-aa
sed 's/^X//' >/usr/ports/biology/avida/files/patch-aa << 'END-of-/usr/ports/biology/avida/files/patch-aa'
X--- source/event/event_base.hh.orig Wed Apr 17 21:26:31 2002
X+++ source/event/event_base.hh Wed Apr 17 21:26:41 2002
X@@ -18,6 +18,7 @@
X
X #include "../defs.hh"
X #include <values.h>
X+#include <float.h>
X //#include "event_defs.hh"
X
X enum eTriggerVariable { UPDATE, GENERATION, IMMEDIATE, UNDEFINED };
END-of-/usr/ports/biology/avida/files/patch-aa
echo x - /usr/ports/biology/avida/files/patch-ab
sed 's/^X//' >/usr/ports/biology/avida/files/patch-ab << 'END-of-/usr/ports/biology/avida/files/patch-ab'
X--- source/main/fitness_matrix.hh.orig Thu Apr 18 08:54:04 2002
X+++ source/main/fitness_matrix.hh Thu Apr 18 08:54:15 2002
X@@ -7,6 +7,7 @@
X #include <vector>
X #include <map>
X #include <list>
X+#include <sys/types.h>
X #include <sys/timeb.h>
X
X #include "../cpu/cpu.hh"
END-of-/usr/ports/biology/avida/files/patch-ab
echo x - /usr/ports/biology/avida/files/patch-ac
sed 's/^X//' >/usr/ports/biology/avida/files/patch-ac << 'END-of-/usr/ports/biology/avida/files/patch-ac'
X--- source/defs.hh.orig Thu Apr 18 18:42:56 2002
X+++ source/defs.hh Thu Apr 18 18:43:14 2002
X@@ -8,7 +8,7 @@
X #ifndef DEFS_HH
X #define DEFS_HH
X
X-#define DEFAULT_DIR "../work/"
X+#define DEFAULT_DIR "%%PREFIX%%/share/%%PORTNAME%%/"
X
X // -= Remove bugfixes that change execution
X //#define REMOVE_SIZE_RANGE_FIX // had only affected upper limit in heads
END-of-/usr/ports/biology/avida/files/patch-ac
echo x - /usr/ports/biology/avida/files/patch-ad
sed 's/^X//' >/usr/ports/biology/avida/files/patch-ad << 'END-of-/usr/ports/biology/avida/files/patch-ad'
X--- source/support/genesis.orig Fri Apr 19 20:00:53 2002
X+++ source/support/genesis Fri Apr 19 20:02:24 2002
X@@ -13,7 +13,7 @@
X RANDOM_SEED 0 # Random number seed. (0 for based on time)
X
X ### Configuration Files ###
X-DEFAULT_DIR ../work/ # Directory in which config files can be found.
X+DEFAULT_DIR %%PREFIX%%/share/%%PORTNAME%%/ # Directory in which config files can be found.
X INST_SET inst_set.28.base # File containing instruction set.
X TASK_SET task_set # File containing task set.
X RESOURCE_SET resource_set # File containing resource set.
END-of-/usr/ports/biology/avida/files/patch-ad
echo x - /usr/ports/biology/avida/files/patch-ae
sed 's/^X//' >/usr/ports/biology/avida/files/patch-ae << 'END-of-/usr/ports/biology/avida/files/patch-ae'
X--- source/support/genesis.heads.orig Fri Apr 19 20:01:09 2002
X+++ source/support/genesis.heads Fri Apr 19 20:02:47 2002
X@@ -13,7 +13,7 @@
X RANDOM_SEED 0 # Random number seed. (0 for based on time)
X
X ### Configuration Files ###
X-DEFAULT_DIR ../work/ # Directory in which config files can be found.
X+DEFAULT_DIR %%PREFIX%%/share/%%PORTNAME%%/ # Directory in which config files can be found.
X INST_SET inst_set.26.heads.new # File containing instruction set.
X TASK_SET task_set # File containing task set.
X RESOURCE_SET resource_set # File containing resource set.
END-of-/usr/ports/biology/avida/files/patch-ae
echo x - /usr/ports/biology/avida/pkg-plist
sed 's/^X//' >/usr/ports/biology/avida/pkg-plist << 'END-of-/usr/ports/biology/avida/pkg-plist'
Xbin/avida
Xshare/avida/creature.base
Xshare/avida/creature.heads
Xshare/avida/creature.heads.new
Xshare/avida/genesis
Xshare/avida/genesis.heads
Xshare/avida/inst_set.19.short
Xshare/avida/inst_set.24.base
Xshare/avida/inst_set.26.heads.new
Xshare/avida/inst_set.27.multi
Xshare/avida/inst_set.27.no-nop
Xshare/avida/inst_set.27.parasite
Xshare/avida/inst_set.28.base
Xshare/avida/inst_set.28.const
Xshare/avida/inst_set.28.dir-match
Xshare/avida/inst_set.29.base_memsize
Xshare/avida/inst_set.31.multi
Xshare/avida/inst_set.32.heads
Xshare/avida/inst_set.84.long
Xshare/avida/inst_set.args
Xshare/avida/inst_set.big
Xshare/avida/inst_set.dev
Xshare/avida/inst_set.full
Xshare/avida/inst_set.long
Xshare/avida/inst_set.re
Xshare/avida/inst_set.red
Xshare/avida/inst_set.short
Xshare/avida/inst_set.test
Xshare/avida/inst_set.tiny
Xshare/avida/inst_set.travc
Xshare/avida/event_list
Xshare/avida/resource_set
Xshare/avida/task_set
Xshare/avida/analyze.cfg
X@dirrm share/avida
END-of-/usr/ports/biology/avida/pkg-plist
echo x - /usr/ports/biology/avida/distinfo
sed 's/^X//' >/usr/ports/biology/avida/distinfo << 'END-of-/usr/ports/biology/avida/distinfo'
XMD5 (avida-1.6.0.tar.gz) = 2294af061f200c486de2ed889e0e17af
END-of-/usr/ports/biology/avida/distinfo
echo x - /usr/ports/biology/avida/pkg-descr
sed 's/^X//' >/usr/ports/biology/avida/pkg-descr << 'END-of-/usr/ports/biology/avida/pkg-descr'
XThe computer program avida is an auto-adaptive genetic system designed
Xprimarily for use as a platform in Digital or Artificial Life research. The
Xavida system is based on concepts similar to those employed by the tierra
Xprogram developed by Tom Ray. It is a population of self-reproducing strings
Xwith a Turing-complete genetic basis subjected to Poisson-random mutations.
XThe population adapts to the combination of an intrinsic fitness landscape
X(self-reproduction) and an externally imposed (extrinsic) fitness function
Xprovided by the researcher. By studying this system, one can examine
Xevolutionary adaptation, general traits of living systems (such as
Xself-organization), and other issues pertaining to theoretical or
Xevolutionary biology and dynamic systems.
X
XWWW: http://dllab.caltech.edu/avida/
X
XJeremy
Xkarlj000@unbc.ca
END-of-/usr/ports/biology/avida/pkg-descr
echo x - /usr/ports/biology/avida/pkg-comment
sed 's/^X//' >/usr/ports/biology/avida/pkg-comment << 'END-of-/usr/ports/biology/avida/pkg-comment'
XAvida is an auto-adaptive genetic system designed for ALife research
END-of-/usr/ports/biology/avida/pkg-comment
echo x - /usr/ports/biology/avida/Makefile
sed 's/^X//' >/usr/ports/biology/avida/Makefile << 'END-of-/usr/ports/biology/avida/Makefile'
X# New ports collection makefile for: avida
X# Date created: 17 April 2002
X# Whom: Jeremy <karlj000@unbc.ca>
X#
X# $FreeBSD:$
X#
X
XPORTNAME= avida
XPORTVERSION= 1.6.0
XCATEGORIES= science biology
XMASTER_SITES= http://dllab.caltech.edu/avida/versions/
X
XMAINTAINER= karlj000@unbc.ca
X
XWRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION:C/\.[[:alnum:]]+$//}
XUSE_GMAKE= yes
XGNU_CONFIGURE= yes
XCONFIGURE_ARGS= --enable-viewer --enable-standard-prefix --prefix=${PREFIX} --datadir=${PREFIX}/share/${PORTNAME}
X
Xpost-patch:
X # Change source/defs.hh prefix and port name.
X @ ${MV} ${WRKSRC}/source/defs.hh ${WRKSRC}/source/defs.hh.presed
X @ ${SED} -e 's#%%PREFIX%%#${PREFIX}#g' ${WRKSRC}/source/defs.hh.presed \
X | ${SED} -e 's#%%PORTNAME%%#${PORTNAME}#g' \
X > ${WRKSRC}/source/defs.hh
X
X # Change source/support/genesis prefix and port name.
X @ ${MV} ${WRKSRC}/source/support/genesis ${WRKSRC}/source/support/genesis.presed
X @ ${SED} -e 's#%%PREFIX%%#${PREFIX}#g' ${WRKSRC}/source/support/genesis.presed \
X | ${SED} -e 's#%%PORTNAME%%#${PORTNAME}#g' \
X > ${WRKSRC}/source/support/genesis
X
X # Change source/support/genesis.heads prefix and port name.
X @ ${MV} ${WRKSRC}/source/support/genesis.heads ${WRKSRC}/source/support/genesis.heads.presed
X @ ${SED} -e 's#%%PREFIX%%#${PREFIX}#g' ${WRKSRC}/source/support/genesis.heads.presed \
X | ${SED} -e 's#%%PORTNAME%%#${PORTNAME}#g' \
X > ${WRKSRC}/source/support/genesis.heads
X
X.include <bsd.port.mk>
END-of-/usr/ports/biology/avida/Makefile
exit
>Release-Note:
>Audit-Trail:
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