Updated build-prcess to be completely under automake control.

For the tutorial the old Makefiles are saved as Makefile.simple in all
the respective directories.

Use generated config.h instead of command-line passing of preprocessor
flags.

Updated support files from current automake.

eo/.cvsignore

@@ -1,17 +1,19 @@
-*.lo
 *.la
+*.lo
 .deps
 .libs
 Makefile
 Makefile.in
 aclocal.m4
+autom4te.cache
 confdefs.h
+config.cache
+config.cache
 config.h
 config.h.in
-configure
 config.log
-config.cache
 config.status
+configure
 libtool
 stamp-h
 stamp-h.in

eo/COPYING

@@ -291,7 +291,7 @@ convey the exclusion of warranty; and each file should have at least
 the "copyright" line and a pointer to where the full notice is found.
 
     <one line to give the program's name and a brief idea of what it does.>
-    Copyright (C) 19yy  <name of author>
+    Copyright (C) <year>  <name of author>
 
     This program is free software; you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -313,7 +313,7 @@ Also add information on how to contact you by electronic and paper mail.
 If the program is interactive, make it output a short notice like this
 when it starts in an interactive mode:
 
-    Gnomovision version 69, Copyright (C) 19yy name of author
+    Gnomovision version 69, Copyright (C) year  name of author
     Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
     This is free software, and you are welcome to redistribute it
     under certain conditions; type `show c' for details.

eo/INSTALL

@@ -1,27 +1,8 @@
-                      EO INSTALL FILE
+Copyright 1994, 1995, 1996, 1999, 2000, 2001, 2002 Free Software
-=======================================================================
+Foundation, Inc.
-           check latest news at http://eodev.sourceforge.net/
-=======================================================================
 
-This file contains the standard installation instructions for packages
+   This file is free documentation; the Free Software Foundation gives
-built using GNU package management facilities.
+unlimited permission to copy, distribute and modify it.
-
-You should not need to read this file unless something goes wrong when
-doing the basic install which goes:
-
-- go to the EO directory - that was created when you unzipped the
-  archive file.
-
-- run 
-            ./autogen.sh
-
-- run 
-            make
-
-and that's it. You should probably go to the tutorial and start
-learning about EO features and programming.
-
-=======================================================================
 
 Basic Installation
 ==================
@@ -33,20 +14,27 @@ various system-dependent variables used during compilation.  It uses
 those values to create a `Makefile' in each directory of the package.
 It may also create one or more `.h' files containing system-dependent
 definitions.  Finally, it creates a shell script `config.status' that
-you can run in the future to recreate the current configuration, a file
+you can run in the future to recreate the current configuration, and a
-`config.cache' that saves the results of its tests to speed up
+file `config.log' containing compiler output (useful mainly for
-reconfiguring, and a file `config.log' containing compiler output
+debugging `configure').
-(useful mainly for debugging `configure').
+
+   It can also use an optional file (typically called `config.cache'
+and enabled with `--cache-file=config.cache' or simply `-C') that saves
+the results of its tests to speed up reconfiguring.  (Caching is
+disabled by default to prevent problems with accidental use of stale
+cache files.)
 
    If you need to do unusual things to compile the package, please try
 to figure out how `configure' could check whether to do them, and mail
 diffs or instructions to the address given in the `README' so they can
-be considered for the next release.  If at some point `config.cache'
+be considered for the next release.  If you are using the cache, and at
-contains results you don't want to keep, you may remove or edit it.
+some point `config.cache' contains results you don't want to keep, you
+may remove or edit it.
 
-   The file `configure.in' is used to create `configure' by a program
+   The file `configure.ac' (or `configure.in') is used to create
-called `autoconf'.  You only need `configure.in' if you want to change
+`configure' by a program called `autoconf'.  You only need
-it or regenerate `configure' using a newer version of `autoconf'.
+`configure.ac' if you want to change it or regenerate `configure' using
+a newer version of `autoconf'.
 
 The simplest way to compile this package is:
 
@@ -80,14 +68,16 @@ Compilers and Options
 =====================
 
    Some systems require unusual options for compilation or linking that
-the `configure' script does not know about.  You can give `configure'
+the `configure' script does not know about.  Run `./configure --help'
-initial values for variables by setting them in the environment.  Using
+for details on some of the pertinent environment variables.
-a Bourne-compatible shell, you can do that on the command line like
-this:
-     CC=c89 CFLAGS=-O2 LIBS=-lposix ./configure
 
-Or on systems that have the `env' program, you can do it like this:
+   You can give `configure' initial values for configuration parameters
-     env CPPFLAGS=-I/usr/local/include LDFLAGS=-s ./configure
+by setting variables in the command line or in the environment.  Here
+is an example:
+
+     ./configure CC=c89 CFLAGS=-O2 LIBS=-lposix
+
+   *Note Defining Variables::, for more details.
 
 Compiling For Multiple Architectures
 ====================================
@@ -100,11 +90,11 @@ directory where you want the object files and executables to go and run
 the `configure' script.  `configure' automatically checks for the
 source code in the directory that `configure' is in and in `..'.
 
-   If you have to use a `make' that does not supports the `VPATH'
+   If you have to use a `make' that does not support the `VPATH'
-variable, you have to compile the package for one architecture at a time
+variable, you have to compile the package for one architecture at a
-in the source code directory.  After you have installed the package for
+time in the source code directory.  After you have installed the
-one architecture, use `make distclean' before reconfiguring for another
+package for one architecture, use `make distclean' before reconfiguring
-architecture.
+for another architecture.
 
 Installation Names
 ==================
@@ -148,21 +138,31 @@ Specifying the System Type
 ==========================
 
    There may be some features `configure' cannot figure out
-automatically, but needs to determine by the type of host the package
+automatically, but needs to determine by the type of machine the package
-will run on.  Usually `configure' can figure that out, but if it prints
+will run on.  Usually, assuming the package is built to be run on the
-a message saying it can not guess the host type, give it the
+_same_ architectures, `configure' can figure that out, but if it prints
-`--host=TYPE' option.  TYPE can either be a short name for the system
+a message saying it cannot guess the machine type, give it the
-type, such as `sun4', or a canonical name with three fields:
+`--build=TYPE' option.  TYPE can either be a short name for the system
+type, such as `sun4', or a canonical name which has the form:
+
      CPU-COMPANY-SYSTEM
 
+where SYSTEM can have one of these forms:
+
+     OS KERNEL-OS
+
    See the file `config.sub' for the possible values of each field.  If
 `config.sub' isn't included in this package, then this package doesn't
-need to know the host type.
+need to know the machine type.
 
-   If you are building compiler tools for cross-compiling, you can also
+   If you are _building_ compiler tools for cross-compiling, you should
 use the `--target=TYPE' option to select the type of system they will
-produce code for and the `--build=TYPE' option to select the type of
+produce code for.
-system on which you are compiling the package.
+
+   If you want to _use_ a cross compiler, that generates code for a
+platform different from the build platform, you should specify the
+"host" platform (i.e., that on which the generated programs will
+eventually be run) with `--host=TYPE'.
 
 Sharing Defaults
 ================
@@ -175,20 +175,44 @@ default values for variables like `CC', `cache_file', and `prefix'.
 `CONFIG_SITE' environment variable to the location of the site script.
 A warning: not all `configure' scripts look for a site script.
 
-Operation Controls
+Defining Variables
 ==================
 
+   Variables not defined in a site shell script can be set in the
+environment passed to `configure'.  However, some packages may run
+configure again during the build, and the customized values of these
+variables may be lost.  In order to avoid this problem, you should set
+them in the `configure' command line, using `VAR=value'.  For example:
+
+     ./configure CC=/usr/local2/bin/gcc
+
+will cause the specified gcc to be used as the C compiler (unless it is
+overridden in the site shell script).
+
+`configure' Invocation
+======================
+
    `configure' recognizes the following options to control how it
 operates.
 
-`--cache-file=FILE'
-     Use and save the results of the tests in FILE instead of
-     `./config.cache'.  Set FILE to `/dev/null' to disable caching, for
-     debugging `configure'.
-
 `--help'
+`-h'
      Print a summary of the options to `configure', and exit.
 
+`--version'
+`-V'
+     Print the version of Autoconf used to generate the `configure'
+     script, and exit.
+
+`--cache-file=FILE'
+     Enable the cache: use and save the results of the tests in FILE,
+     traditionally `config.cache'.  FILE defaults to `/dev/null' to
+     disable caching.
+
+`--config-cache'
+`-C'
+     Alias for `--cache-file=config.cache'.
+
 `--quiet'
 `--silent'
 `-q'
@@ -200,8 +224,6 @@ operates.
      Look for the package's source code in directory DIR.  Usually
      `configure' can determine that directory automatically.
 
-`--version'
+`configure' also accepts some other, not widely useful, options.  Run
-     Print the version of Autoconf used to generate the `configure'
+`configure --help' for more details.
-     script, and exit.
 
-`configure' also accepts some other, not widely useful, options.

eo/Makefile.am

@@ -5,32 +5,42 @@
 ###############################################################################
 
 SUBDIRS = src test app tutorial
+
 #Directory for documents
 DOCDIR = ~/public_html/eodocs
+
 #Directory for indices -- not useful for the user
 IDXDIR = ~/index
 
-EXTRA_DIST=LICENSE 
+# EXTRA_DIST=LICENSE 
 
-###############################################################################
 
-lib:	
+
-	cd src; $(MAKE) all; cd ..
+# special targets
+app:
+	cd app; $(MAKE) all; cd ..
 
 # so that make doc always compiles the doc ...
 doc:    doc/eo.cfg
 	cd doc; $(MAKE) doc; touch eo.cfg; cd ..
 
 tutorial:
-	cd tutorial; $(MAKE) all; cd ..
+	cd $(srcdir)/tutorial; $(MAKE) all; cd ..
+
 
-app:
-	cd app; $(MAKE) all; cd ..
 
-all:
-	for i in $(SUBDIRS); do cd $$i && $(MAKE) all; cd ..; done
 
-clean:
+
-	for i in $(SUBDIRS); do cd $$i && $(MAKE) clean; cd ..; done
+###############################################################################
+
+#lib:	
+#	cd src; $(MAKE) all; cd ..
+
+
+#all:
+#	for i in $(SUBDIRS); do cd $$i && $(MAKE) all; cd ..; done
+
+#clean:
+#	for i in $(SUBDIRS); do cd $$i && $(MAKE) clean; cd ..; done
 
 ###############################################################################

eo/app/mastermind/Makefile.am

@@ -8,7 +8,7 @@ DEPS = $(top_builddir)/src/libeo.a $(top_builddir)/src/utils/libeoutils.a
 
 ###############################################################################
 
-INCLUDES = -I$(top_builddir)/src
+INCLUDES = -I$(top_builddir)/src -I$(top_srcdir)/src
 LDADDS = $(top_builddir)/src/libeo.a $(top_builddir)/src/utils/libeoutils.a
 
 ###############################################################################

eo/app/mastermind/mastermind.cpp

@@ -7,7 +7,8 @@
 #include <iostream>                // cerr cout
 #include <fstream>                 // ifstream
 #include <string>                  // string
-#include <eo>                      // all usefull eo stuff
+#include <eo>                      // all usefull eo stuff\
+
 #include "mastermind.h"            // Chrom eoChromInit eoChromMutation eoChromXover eoChromEvaluator
 
 using namespace std;

eo/autogen.sh

@@ -29,32 +29,26 @@ if test "$DIE" -eq 1; then
     exit 1
 fi
 
-if test -z "$*"; then
+set aclocalinclude="$ACLOCAL_FLAGS"
-    echo "I am going to run ./configure with no arguments - if you wish"
+aclocal $aclocalinclude
-    echo "to pass any to it, please specify them on the $0 command line."
+unset $aclocalinclude
-fi
+autoheader
-
+automake
-for dir in .
-do
-    echo processing $dir
-    (
-	cd $dir; \
-	aclocalinclude="$ACLOCAL_FLAGS"; \
-	aclocal $aclocalinclude; \
-	autoheader; \
-	automake; \
 autoconf
-    )
-done
 
-./configure "$@"
+# if test -z "$*"; then
+#     echo "I am going to run ./configure with no arguments - if you wish"
+#     echo "to pass any to it, please specify them on the $0 command line."
+# fi
+#
+# ./configure "$@"
 
 # we want doc to be recompiled - and it keeps saying it's up to date!!!
 touch doc/eo.cfg
 
 echo
 echo "Now type 'make' to compile $PROG."
-echo "And if you have Doxygen installed, type 'make doc' to generate $PROG documentation."
+echo "If you have Doxygen installed, type 'make doc' to generate $PROG documentation."
 echo
 #echo "WARNING: Compiling all test programs can take some time."
 #echo "But you don't have to: you can simply type"

eo/configure.in

@@ -4,6 +4,8 @@ AC_INIT(src/eo)
 dnl Change the version number here
 AM_INIT_AUTOMAKE(eo, 0.9.3)
 
+AM_CONFIG_HEADER([config.h])
+
 dnl Checks for maintainer mode
 AM_MAINTAINER_MODE
 
@@ -15,13 +17,9 @@ AC_PROG_MAKE_SET
 AC_PROG_RANLIB
 
 dnl Checks for libraries.
-dnl Replace `main' with a function in -leo:
 AC_CHECK_LIB(eo, main)
-dnl Replace `main' with a function in -leoutils:
 AC_CHECK_LIB(eoutils, main)
-dnl Replace `main' with a function in -lm:
+AC_CHECK_LIB(m, cos)
-AC_CHECK_LIB(m, main)
-
 
 dnl Checks for header files.
 AC_HEADER_STDC
@@ -36,5 +34,24 @@ AC_TYPE_SIZE_T
 dnl Checks for library functions.
 AC_CHECK_FUNCS(select)
 
-AC_OUTPUT(doc/Makefile src/Makefile src/utils/Makefile src/other/Makefile win/Makefile src/gp/Makefile src/es/Makefile src/ga/Makefile test/Makefile contrib/Makefile Makefile app/Makefile app/mastermind/Makefile app/gpsymreg/Makefile src/do/Makefile)
+AC_OUTPUT(Makefile \
-#app/gprop/Makefile is in the sinbin 
+          src/Makefile \
+          src/do/Makefile \
+          src/es/Makefile \
+          src/gp/Makefile \
+          src/ga/Makefile \
+          src/other/Makefile \
+          src/utils/Makefile \
+          contrib/Makefile \
+          doc/Makefile \
+          win/Makefile \
+          test/Makefile \
+          tutorial/Makefile \
+          tutorial/Lesson1/Makefile \
+          tutorial/Lesson2/Makefile \
+          tutorial/Lesson3/Makefile \
+          tutorial/Lesson4/Makefile \
+          tutorial/Lesson5/Makefile \
+          app/Makefile \
+          app/mastermind/Makefile \
+          app/gpsymreg/Makefile)

eo/depcomp

@@ -212,13 +212,17 @@ tru64)
    # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
    # dependencies in `foo.d' instead, so we check for that too.
    # Subdirectories are respected.
+   dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+   test "x$dir" = "x$object" && dir=
+   base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
 
-   base=`echo "$object" | sed -e 's/\.o$//' -e 's/\.lo$//'`
-   tmpdepfile1="$base.o.d"
-   tmpdepfile2="$base.d"
    if test "$libtool" = yes; then
+      tmpdepfile1="$dir.libs/$base.lo.d"
+      tmpdepfile2="$dir.libs/$base.d"
       "$@" -Wc,-MD
    else
+      tmpdepfile1="$dir$base.o.d"
+      tmpdepfile2="$dir$base.d"
       "$@" -MD
    fi
 
@@ -250,34 +254,40 @@ tru64)
 
 dashmstdout)
   # Important note: in order to support this mode, a compiler *must*
-  # always write the proprocessed file to stdout, regardless of -o,
+  # always write the proprocessed file to stdout, regardless of -o.
-  # because we must use -o when running libtool.
+  "$@" || exit $?
-  test -z "$dashmflag" && dashmflag=-M
+
-  ( IFS=" "
+  # Remove the call to Libtool.
-    case " $* " in
+  if test "$libtool" = yes; then
-    *" --mode=compile "*) # this is libtool, let us make it quiet
+    while test $1 != '--mode=compile'; do
+      shift
+    done
+    shift
+  fi
+
+  # Remove `-o $object'.  We will use -o /dev/null later,
+  # however we can't do the remplacement now because
+  # `-o $object' might simply not be used
+  IFS=" "
   for arg
-      do # cycle over the arguments
+  do
-        case "$arg" in
+    case $arg in
-	"--mode=compile")
+    -o)
-	  # insert --quiet before "--mode=compile"
+      shift
-	  set fnord "$@" --quiet
-	  shift # fnord
       ;;
-	esac
+    $object)
+      shift
+      ;;
+    *)
       set fnord "$@" "$arg"
       shift # fnord
-	shift # "$arg"
+      shift # $arg
-      done
       ;;
     esac
-    "$@" $dashmflag | sed 's:^[^:]*\:[ 	]*:'"$object"'\: :' > "$tmpdepfile"
+  done
-  ) &
+
-  proc=$!
+  test -z "$dashmflag" && dashmflag=-M
-  "$@"
+  "$@" -o /dev/null $dashmflag | sed 's:^[^:]*\:[ 	]*:'"$object"'\: :' > "$tmpdepfile"
-  stat=$?
-  wait "$proc"
-  if test "$stat" != 0; then exit $stat; fi
   rm -f "$depfile"
   cat < "$tmpdepfile" > "$depfile"
   tr ' ' '
@@ -295,14 +305,15 @@ dashXmstdout)
   ;;
 
 makedepend)
+  "$@" || exit $?
   # X makedepend
-  (
   shift
   cleared=no
   for arg in "$@"; do
-      case $cleared in no)
+    case $cleared in
+    no)
       set ""; shift
-	cleared=yes
+      cleared=yes ;;
     esac
     case "$arg" in
     -D*|-I*)
@@ -315,13 +326,7 @@ makedepend)
   done
   obj_suffix="`echo $object | sed 's/^.*\././'`"
   touch "$tmpdepfile"
-    ${MAKEDEPEND-makedepend} 2>/dev/null -o"$obj_suffix" -f"$tmpdepfile" "$@"
+  ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
-  ) &
-  proc=$!
-  "$@"
-  stat=$?
-  wait "$proc"
-  if test "$stat" != 0; then exit $stat; fi
   rm -f "$depfile"
   cat < "$tmpdepfile" > "$depfile"
   sed '1,2d' "$tmpdepfile" | tr ' ' '
@@ -334,35 +339,39 @@ makedepend)
 
 cpp)
   # Important note: in order to support this mode, a compiler *must*
-  # always write the proprocessed file to stdout, regardless of -o,
+  # always write the proprocessed file to stdout.
-  # because we must use -o when running libtool.
+  "$@" || exit $?
-  ( IFS=" "
+
-    case " $* " in
+  # Remove the call to Libtool.
-    *" --mode=compile "*)
+  if test "$libtool" = yes; then
+    while test $1 != '--mode=compile'; do
+      shift
+    done
+    shift
+  fi
+
+  # Remove `-o $object'.
+  IFS=" "
   for arg
-      do # cycle over the arguments
+  do
     case $arg in
-	"--mode=compile")
+    -o)
-	  # insert --quiet before "--mode=compile"
+      shift
-	  set fnord "$@" --quiet
-	  shift # fnord
       ;;
-	esac
+    $object)
+      shift
+      ;;
+    *)
       set fnord "$@" "$arg"
       shift # fnord
-	shift # "$arg"
+      shift # $arg
-      done
       ;;
     esac
+  done
+
   "$@" -E |
     sed -n '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
     sed '$ s: \\$::' > "$tmpdepfile"
-  ) &
-  proc=$!
-  "$@"
-  stat=$?
-  wait "$proc"
-  if test "$stat" != 0; then exit $stat; fi
   rm -f "$depfile"
   echo "$object : \\" > "$depfile"
   cat < "$tmpdepfile" >> "$depfile"
@@ -374,24 +383,8 @@ msvisualcpp)
   # Important note: in order to support this mode, a compiler *must*
   # always write the proprocessed file to stdout, regardless of -o,
   # because we must use -o when running libtool.
-  ( IFS=" "
+  "$@" || exit $?
-    case " $* " in
+  IFS=" "
-    *" --mode=compile "*)
-      for arg
-      do # cycle over the arguments
-        case $arg in
-	"--mode=compile")
-	  # insert --quiet before "--mode=compile"
-	  set fnord "$@" --quiet
-	  shift # fnord
-	  ;;
-	esac
-	set fnord "$@" "$arg"
-	shift # fnord
-	shift # "$arg"
-      done
-      ;;
-    esac
   for arg
   do
     case "$arg" in
@@ -409,12 +402,6 @@ msvisualcpp)
   done
   "$@" -E |
   sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile"
-  ) &
-  proc=$!
-  "$@"
-  stat=$?
-  wait "$proc"
-  if test "$stat" != 0; then exit $stat; fi
   rm -f "$depfile"
   echo "$object : \\" > "$depfile"
   . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::	\1 \\:p' >> "$depfile"

eo/install-sh

@@ -109,7 +109,7 @@ then
 	echo "install:	no input file specified"
 	exit 1
 else
-	true
+	:
 fi
 
 if [ x"$dir_arg" != x ]; then
@@ -118,8 +118,9 @@ if [ x"$dir_arg" != x ]; then
 	
 	if [ -d $dst ]; then
 		instcmd=:
+		chmodcmd=""
 	else
-		instcmd=mkdir
+		instcmd=$mkdirprog
 	fi
 else
 
@@ -127,9 +128,9 @@ else
 # might cause directories to be created, which would be especially bad 
 # if $src (and thus $dsttmp) contains '*'.
 
-	if [ -f $src -o -d $src ]
+	if [ -f "$src" ] || [ -d "$src" ]
 	then
-		true
+		:
 	else
 		echo "install:  $src does not exist"
 		exit 1
@@ -140,7 +141,7 @@ else
 		echo "install:	no destination specified"
 		exit 1
 	else
-		true
+		:
 	fi
 
 # If destination is a directory, append the input filename; if your system
@@ -150,7 +151,7 @@ else
 	then
 		dst="$dst"/`basename $src`
 	else
-		true
+		:
 	fi
 fi
 
@@ -182,7 +183,7 @@ while [ $# -ne 0 ] ; do
         then
 		$mkdirprog "${pathcomp}"
 	else
-		true
+		:
 	fi
 
 	pathcomp="${pathcomp}/"
@@ -193,10 +194,10 @@ if [ x"$dir_arg" != x ]
 then
 	$doit $instcmd $dst &&
 
-	if [ x"$chowncmd" != x ]; then $doit $chowncmd $dst; else true ; fi &&
+	if [ x"$chowncmd" != x ]; then $doit $chowncmd $dst; else : ; fi &&
-	if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dst; else true ; fi &&
+	if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dst; else : ; fi &&
-	if [ x"$stripcmd" != x ]; then $doit $stripcmd $dst; else true ; fi &&
+	if [ x"$stripcmd" != x ]; then $doit $stripcmd $dst; else : ; fi &&
-	if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dst; else true ; fi
+	if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dst; else : ; fi
 else
 
 # If we're going to rename the final executable, determine the name now.
@@ -215,7 +216,7 @@ else
 	then
 		dstfile=`basename $dst`
 	else
-		true
+		:
 	fi
 
 # Make a temp file name in the proper directory.
@@ -234,10 +235,10 @@ else
 # ignore errors from any of these, just make sure not to ignore
 # errors from the above "$doit $instcmd $src $dsttmp" command.
 
-	if [ x"$chowncmd" != x ]; then $doit $chowncmd $dsttmp; else true;fi &&
+	if [ x"$chowncmd" != x ]; then $doit $chowncmd $dsttmp; else :;fi &&
-	if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dsttmp; else true;fi &&
+	if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dsttmp; else :;fi &&
-	if [ x"$stripcmd" != x ]; then $doit $stripcmd $dsttmp; else true;fi &&
+	if [ x"$stripcmd" != x ]; then $doit $stripcmd $dsttmp; else :;fi &&
-	if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dsttmp; else true;fi &&
+	if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dsttmp; else :;fi &&
 
 # Now rename the file to the real destination.
 

eo/missing

@@ -1,7 +1,7 @@
 #! /bin/sh
 # Common stub for a few missing GNU programs while installing.
-# Copyright (C) 1996, 1997 Free Software Foundation, Inc.
+# Copyright (C) 1996, 1997, 1999, 2000, 2002 Free Software Foundation, Inc.
-# Franc,ois Pinard <pinard@iro.umontreal.ca>, 1996.
+# Originally by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
 
 # This program is free software; you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -18,11 +18,37 @@
 # Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
 # 02111-1307, USA.
 
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
 if test $# -eq 0; then
   echo 1>&2 "Try \`$0 --help' for more information"
   exit 1
 fi
 
+run=:
+
+# In the cases where this matters, `missing' is being run in the
+# srcdir already.
+if test -f configure.ac; then
+  configure_ac=configure.ac
+else
+  configure_ac=configure.in
+fi
+
+case "$1" in
+--run)
+  # Try to run requested program, and just exit if it succeeds.
+  run=
+  shift
+  "$@" && exit 0
+  ;;
+esac
+
+# If it does not exist, or fails to run (possibly an outdated version),
+# try to emulate it.
 case "$1" in
 
   -h|--h|--he|--hel|--help)
@@ -35,6 +61,7 @@ error status if there is no known handling for PROGRAM.
 Options:
   -h, --help      display this help and exit
   -v, --version   output version information and exit
+  --run           try to run the given command, and emulate it if it fails
 
 Supported PROGRAM values:
   aclocal      touch file \`aclocal.m4'
@@ -43,13 +70,15 @@ Supported PROGRAM values:
   automake     touch all \`Makefile.in' files
   bison        create \`y.tab.[ch]', if possible, from existing .[ch]
   flex         create \`lex.yy.c', if possible, from existing .c
+  help2man     touch the output file
   lex          create \`lex.yy.c', if possible, from existing .c
   makeinfo     touch the output file
+  tar          try tar, gnutar, gtar, then tar without non-portable flags
   yacc         create \`y.tab.[ch]', if possible, from existing .[ch]"
     ;;
 
   -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
-    echo "missing - GNU libit 0.0"
+    echo "missing 0.4 - GNU automake"
     ;;
 
   -*)
@@ -58,50 +87,100 @@ Supported PROGRAM values:
     exit 1
     ;;
 
-  aclocal)
+  aclocal*)
+    if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+       # We have it, but it failed.
+       exit 1
+    fi
+
     echo 1>&2 "\
 WARNING: \`$1' is missing on your system.  You should only need it if
-         you modified \`acinclude.m4' or \`configure.in'.  You might want
+         you modified \`acinclude.m4' or \`${configure_ac}'.  You might want
          to install the \`Automake' and \`Perl' packages.  Grab them from
          any GNU archive site."
     touch aclocal.m4
     ;;
 
   autoconf)
+    if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+       # We have it, but it failed.
+       exit 1
+    fi
+
     echo 1>&2 "\
 WARNING: \`$1' is missing on your system.  You should only need it if
-         you modified \`configure.in'.  You might want to install the
+         you modified \`${configure_ac}'.  You might want to install the
          \`Autoconf' and \`GNU m4' packages.  Grab them from any GNU
          archive site."
     touch configure
     ;;
 
   autoheader)
+    if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+       # We have it, but it failed.
+       exit 1
+    fi
+
     echo 1>&2 "\
 WARNING: \`$1' is missing on your system.  You should only need it if
-         you modified \`acconfig.h' or \`configure.in'.  You might want
+         you modified \`acconfig.h' or \`${configure_ac}'.  You might want
          to install the \`Autoconf' and \`GNU m4' packages.  Grab them
          from any GNU archive site."
-    files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER([^):]*:\([^)]*\)).*/\1/p' configure.in`
+    files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
-    if test -z "$files"; then
+    test -z "$files" && files="config.h"
-      files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^):]*\)).*/\1/p' configure.in`
+    touch_files=
-      test -z "$files" || files="$files.in"
+    for f in $files; do
-    else
+      case "$f" in
-      files=`echo "$files" | sed -e 's/:/ /g'`
+      *:*) touch_files="$touch_files "`echo "$f" |
-    fi
+				       sed -e 's/^[^:]*://' -e 's/:.*//'`;;
-    test -z "$files" && files="config.h.in"
+      *) touch_files="$touch_files $f.in";;
-    touch $files
+      esac
+    done
+    touch $touch_files
     ;;
 
-  automake)
+  automake*)
+    if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+       # We have it, but it failed.
+       exit 1
+    fi
+
     echo 1>&2 "\
 WARNING: \`$1' is missing on your system.  You should only need it if
-         you modified \`Makefile.am', \`acinclude.m4' or \`configure.in'.
+         you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
          You might want to install the \`Automake' and \`Perl' packages.
          Grab them from any GNU archive site."
-    find . -type f -name Makefile.am -print \
+    find . -type f -name Makefile.am -print |
-      | sed 's/^\(.*\).am$/touch \1.in/' \
+	   sed 's/\.am$/.in/' |
-      | sh
+	   while read f; do touch "$f"; done
+    ;;
+
+  autom4te)
+    if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+       # We have it, but it failed.
+       exit 1
+    fi
+
+    echo 1>&2 "\
+WARNING: \`$1' is needed, and you do not seem to have it handy on your
+         system.  You might have modified some files without having the
+         proper tools for further handling them.
+         You can get \`$1Help2man' as part of \`Autoconf' from any GNU
+         archive site."
+
+    file=`echo "$*" | sed -n 's/.*--output[ =]*\([^ ]*\).*/\1/p'`
+    test -z "$file" && file=`echo "$*" | sed -n 's/.*-o[ ]*\([^ ]*\).*/\1/p'`
+    if test -f "$file"; then
+	touch $file
+    else
+	test -z "$file" || exec >$file
+	echo "#! /bin/sh"
+	echo "# Created by GNU Automake missing as a replacement of"
+	echo "#  $ $@"
+	echo "exit 0"
+	chmod +x $file
+	exit 1
+    fi
     ;;
 
   bison|yacc)
@@ -157,7 +236,37 @@ WARNING: \`$1' is missing on your system.  You should only need it if
     fi
     ;;
 
+  help2man)
+    if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+       # We have it, but it failed.
+       exit 1
+    fi
+
+    echo 1>&2 "\
+WARNING: \`$1' is missing on your system.  You should only need it if
+	 you modified a dependency of a manual page.  You may need the
+	 \`Help2man' package in order for those modifications to take
+	 effect.  You can get \`Help2man' from any GNU archive site."
+
+    file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'`
+    if test -z "$file"; then
+	file=`echo "$*" | sed -n 's/.*--output=\([^ ]*\).*/\1/p'`
+    fi
+    if [ -f "$file" ]; then
+	touch $file
+    else
+	test -z "$file" || exec >$file
+	echo ".ab help2man is required to generate this page"
+	exit 1
+    fi
+    ;;
+
   makeinfo)
+    if test -z "$run" && (makeinfo --version) > /dev/null 2>&1; then
+       # We have makeinfo, but it failed.
+       exit 1
+    fi
+
     echo 1>&2 "\
 WARNING: \`$1' is missing on your system.  You should only need it if
          you modified a \`.texi' or \`.texinfo' file, or any other file
@@ -173,6 +282,45 @@ WARNING: \`$1' is missing on your system.  You should only need it if
     touch $file
     ;;
 
+  tar)
+    shift
+    if test -n "$run"; then
+      echo 1>&2 "ERROR: \`tar' requires --run"
+      exit 1
+    fi
+
+    # We have already tried tar in the generic part.
+    # Look for gnutar/gtar before invocation to avoid ugly error
+    # messages.
+    if (gnutar --version > /dev/null 2>&1); then
+       gnutar "$@" && exit 0
+    fi
+    if (gtar --version > /dev/null 2>&1); then
+       gtar "$@" && exit 0
+    fi
+    firstarg="$1"
+    if shift; then
+	case "$firstarg" in
+	*o*)
+	    firstarg=`echo "$firstarg" | sed s/o//`
+	    tar "$firstarg" "$@" && exit 0
+	    ;;
+	esac
+	case "$firstarg" in
+	*h*)
+	    firstarg=`echo "$firstarg" | sed s/h//`
+	    tar "$firstarg" "$@" && exit 0
+	    ;;
+	esac
+    fi
+
+    echo 1>&2 "\
+WARNING: I can't seem to be able to run \`tar' with the given arguments.
+         You may want to install GNU tar or Free paxutils, or check the
+         command line arguments."
+    exit 1
+    ;;
+
   *)
     echo 1>&2 "\
 WARNING: \`$1' is needed, and you do not seem to have it handy on your

eo/mkinstalldirs

@@ -4,9 +4,53 @@
 # Created: 1993-05-16
 # Public domain
 
-# $Id: mkinstalldirs,v 5.1 1999-02-12 17:39:01 gustavo Exp $
-
 errstatus=0
+dirmode=""
+
+usage="\
+Usage: mkinstalldirs [-h] [--help] [-m mode] dir ..."
+
+# process command line arguments
+while test $# -gt 0 ; do
+   case "${1}" in
+     -h | --help | --h* )			# -h for help
+	echo "${usage}" 1>&2; exit 0 ;;
+     -m )					# -m PERM arg
+	shift
+	test $# -eq 0 && { echo "${usage}" 1>&2; exit 1; }
+	dirmode="${1}"
+	shift ;;
+     -- ) shift; break ;;			# stop option processing
+     -* ) echo "${usage}" 1>&2; exit 1 ;;	# unknown option
+     * )  break ;;				# first non-opt arg
+   esac
+done
+
+for file
+do
+  if test -d "$file"; then
+    shift
+  else
+    break
+  fi
+done
+
+case $# in
+0) exit 0 ;;
+esac
+
+case $dirmode in
+'')
+  if mkdir -p -- . 2>/dev/null; then
+    echo "mkdir -p -- $*"
+    exec mkdir -p -- "$@"
+  fi ;;
+*)
+  if mkdir -m "$dirmode" -p -- . 2>/dev/null; then
+    echo "mkdir -m $dirmode -p -- $*"
+    exec mkdir -m "$dirmode" -p -- "$@"
+  fi ;;
+esac
 
 for file
 do
@@ -22,12 +66,23 @@ do
      esac
 
      if test ! -d "$pathcomp"; then
-        echo "mkdir $pathcomp" 1>&2
+	echo "mkdir $pathcomp"
 
 	mkdir "$pathcomp" || lasterr=$?
 
 	if test ! -d "$pathcomp"; then
 	  errstatus=$lasterr
+	else
+	  if test ! -z "$dirmode"; then
+	     echo "chmod $dirmode $pathcomp"
+
+	     lasterr=""
+	     chmod "$dirmode" "$pathcomp" || lasterr=$?
+
+	     if test ! -z "$lasterr"; then
+	       errstatus=$lasterr
+	     fi
+	  fi
 	fi
      fi
 
@@ -37,4 +92,8 @@ done
 
 exit $errstatus
 
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 3
+# End:
 # mkinstalldirs ends here

eo/src/Makefile.am

@@ -4,12 +4,22 @@
 ##
 ###############################################################################
 
+INCLUDES = -I$(top_srcdir)/src
+
 SUBDIRS = es ga gp utils other do
+
 CPPFLAGS = -O2
 
 lib_LIBRARIES = libeo.a
-libeo_a_SOURCES = eoFunctorStore.cpp eoPersistent.cpp eoPrintable.cpp eoCtrlCContinue.cpp eoParetoFitness.cpp eoScalarFitnessAssembled.cpp  
+
+libeo_a_SOURCES = eoFunctorStore.cpp \
+		eoPersistent.cpp \
+		eoPrintable.cpp \
+		eoCtrlCContinue.cpp \
+		eoParetoFitness.cpp \
+		eoScalarFitnessAssembled.cpp  
 
 libeoincdir = $(includedir)/eo
-libeoinc_HEADERS = *.h eo do/*.h 
+
+libeoinc_HEADERS = $(srcdir)/*.h $(srcdir)/eo $(srcdir)/do/*.h 
 

eo/src/eoVariableLengthCrossover.h

@@ -26,6 +26,8 @@
 #ifndef _eoVariableLengthCrossover_h
 #define _eoVariableLengthCrossover_h
 
+#include <config.h>
+
 #include <eoFunctor.h>
 #include <eoOp.h>
 

eo/src/es/Makefile.am

@@ -4,7 +4,7 @@
 ##
 ###############################################################################
 
-INCLUDES = -I$(top_builddir)/src
+INCLUDES = -I$(top_builddir)/src -I$(top_srcdir)/src
 lib_LIBRARIES = libes.a
 libes_a_SOURCES = make_algo_scalar_es.cpp \
     make_algo_scalar_real.cpp \

eo/src/ga/Makefile.am

@@ -4,7 +4,7 @@
 ##
 ###############################################################################
 
-INCLUDES = -I$(top_builddir)/src
+INCLUDES = -I$(top_builddir)/src  -I$(top_srcdir)/src
 lib_LIBRARIES = libga.a
 libga_a_SOURCES = make_algo_scalar_ga.cpp \
     make_checkpoint_ga.cpp \

eo/src/pyeo/pickle.h

@@ -21,6 +21,8 @@
 #ifndef PICKLE_H
 #define PICKLE_h
 
+#include <config.h>
+
 #include <boost/python.hpp>
 #ifdef HAVE_SSTREAM
 #include <sstream>

eo/src/utils/Makefile.am

@@ -4,13 +4,13 @@
 ##
 ###############################################################################
 
-INCLUDES = -I$(top_builddir)/src
+INCLUDES = -I$(top_builddir)/src  -I$(top_srcdir)/src
 CPPFLAGS = -O2 -Wall
 lib_LIBRARIES = libeoutils.a
 libeoutils_a_SOURCES = eoParser.cpp eoRNG.cpp eoState.cpp eoUpdater.cpp eoFileMonitor.cpp eoStdoutMonitor.cpp eoRealBounds.cpp make_help.cpp
 
 libeoincdir = $(includedir)/eo/utils
-libeoinc_HEADERS = checkpointing *.h
+libeoinc_HEADERS = checkpointing $(srcdir)/*.h
 #compatibility.h eoCheckPoint.h eoData.h eoDistance.h eoFDCStat.h eoFileMonitor.h eoGnuplot1DMonitor.h eoGnuplot1DSnapshot.h eoHowMany.h eoMonitor.h eoParam.h eoParser.h eoRNG.h eoStat.h eoScalarFitnessStat.h eoState.h eoStdoutMonitor.h eoUpdatable.h eoUpdater.h rnd_generators.h eoRndGenerators.h selectors.h
 
 

eo/src/utils/eoFileSnapshot.h

@@ -27,6 +27,8 @@
 #ifndef _eoFileSnapshot_h
 #define _eoFileSnapshot_h
 
+#include <config.h>
+
 #include <string>
 #include <fstream>
 #include <utils/eoParam.h>

eo/src/utils/eoGnuplot.h

@@ -26,6 +26,8 @@
 #ifndef _eoGnuplot_H
 #define _eoGnuplot_H
 
+#include <config.h>
+
 #include <string>
 
 /**
@@ -150,7 +152,7 @@ inline void eoGnuplot::initGnuPlot(std::string _title, std::string _extra)
  * Created......: Mon Mar 13 13:50:11 1995
  * Description..: Communication par pipe bidirectionnel avec un autre process
  *
- * Ident........: $Id: eoGnuplot.h,v 1.9 2004-01-21 19:57:19 maartenkeijzer Exp $
+ * Ident........: $Id: eoGnuplot.h,v 1.10 2004-09-17 16:53:15 kuepper Exp $
  * ----------------------------------------------------------------------
  */
 

eo/src/utils/eoGnuplot1DMonitor.h

@@ -28,6 +28,8 @@
 #ifndef _eoGnuplot1DMonitor_H
 #define _eoGnuplot1DMonitor_H
 
+#include <config.h>
+
 #include <string>
 
 #include <utils/eoMonitor.h>

eo/src/utils/eoGnuplot1DSnapshot.h

@@ -28,8 +28,12 @@
 #ifndef _eoGnuplot1DSnapshot_H
 #define _eoGnuplot1DSnapshot_H
 
+#include <config.h>
+
 #include <string>
-// #include <sstream>
+#ifdef HAVE_SSTREAM
+#include <sstream>
+#endif
 
 #include <utils/eoFileSnapshot.h>
 #include <utils/eoGnuplot.h>

eo/src/utils/eoHowMany.h

@@ -63,6 +63,9 @@
  *
  * It is an eoPersistent because we need to be able to use eoParamValue<eoHowMany>
  */
+
+#include <config.h>
+
 #ifdef HAVE_SSTREAM
 #include <sstream>
 #else

eo/src/utils/eoParam.h

@@ -27,6 +27,8 @@
 #ifndef eoParam_h
 #define eoParam_h
 
+#include <config.h>
+
 //-----------------------------------------------------------------------------
 #include <math.h>		   // for floor
 #include <string>

eo/src/utils/eoPopStat.h

@@ -35,6 +35,8 @@ that can be used to dump to the screen
 #ifndef _eoPopStat_h
 #define _eoPopStat_h
 
+#include <config.h>
+
 #include <utils/eoStat.h>
 
 

eo/tutorial/.cvsignore

@@ -0,0 +1 @@
+Makefile.in

eo/tutorial/Lesson1/.cvsignore

@@ -0,0 +1 @@
+Makefile.in

eo/tutorial/Lesson1/Makefile.am

@@ -0,0 +1,16 @@
+
+bin_PROGRAMS		= FirstBitGA FirstRealGA exercise1.3
+
+FirstBitGA_SOURCES	= FirstBitGA.cpp
+
+FirstRealGA_SOURCES	= FirstRealGA.cpp
+
+exercise1_3_SOURCES	= exercise1.3.cpp
+
+
+LDADD			= -L$(top_builddir)/src -L$(top_builddir)/src/ga -L$(top_builddir)/src/utils
+
+LIBS			=  -lga -leoutils -leo
+
+INCLUDES		= -I$(top_srcdir)/src
+

eo/tutorial/Lesson2/.cvsignore

@@ -0,0 +1 @@
+Makefile.in

eo/tutorial/Lesson2/Makefile.am

@@ -0,0 +1,23 @@
+
+bin_PROGRAMS		= FirstBitEA FirstRealEA exercise2.3
+
+
+FirstBitEA_SOURCES	= FirstBitEA.cpp
+
+FirstRealEA_SOURCES	= FirstRealEA.cpp
+
+exercise2_3_SOURCES	= exercise2.3.cpp
+
+
+noinst_HEADERS		= binary_value.h \
+			real_value.h
+
+extra_DIST		= Makefile.simple
+
+
+LDADD			= -L$(top_builddir)/src -L$(top_builddir)/src/ga -L$(top_builddir)/src/utils
+
+LIBS			=  -lga -leoutils -leo
+
+INCLUDES		= -I$(top_srcdir)/src
+

eo/tutorial/Lesson3/.cvsignore

@@ -0,0 +1 @@
+Makefile.in

eo/tutorial/Lesson3/Makefile.am

@@ -0,0 +1,26 @@
+
+bin_PROGRAMS		= SecondBitEA SecondRealEA exercise3.1
+
+
+SecondBitEA_SOURCES	= SecondBitEA.cpp
+
+SecondRealEA_SOURCES	= SecondRealEA.cpp
+
+exercise3_1_SOURCES	= exercise3.1.cpp
+
+
+noinst_HEADERS		= binary_value.h \
+			real_value.h
+
+extra_DIST		= Makefile.simple
+
+
+LDADD			= -L$(top_builddir)/src -L$(top_builddir)/src/ga -L$(top_builddir)/src/utils
+
+LIBS			=  -lga -leoutils -leo
+
+INCLUDES		= -I$(top_srcdir)/src
+
+
+clean-local: 
+	@/bin/rm $(ALL) *.o *.sav *.xg *.status *~

eo/tutorial/Lesson4/.cvsignore

@@ -0,0 +1 @@
+Makefile.in

eo/tutorial/Lesson4/Makefile.am

@@ -0,0 +1,27 @@
+
+bin_PROGRAMS		= BitEA RealEA ESEA
+
+
+BitEA_SOURCES		= BitEA.cpp
+
+RealEA_SOURCES		= RealEA.cpp
+
+ESEA_SOURCES		= ESEA.cpp
+
+
+noinst_HEADERS		= binary_value.h \
+			real_value.h
+
+extra_DIST		= Makefile.simple
+
+
+LDADD			= -L$(top_builddir)/src -L$(top_builddir)/src/es \
+			-L$(top_builddir)/src/ga -L$(top_builddir)/src/utils
+
+LIBS			=  -lga -les -leoutils -leo
+
+INCLUDES		= -I$(top_srcdir)/src
+
+
+clean-local: 
+	@/bin/rm $(ALL) *.o *.sav *.xg *.status *~

eo/tutorial/Lesson5/.cvsignore

@@ -0,0 +1 @@
+Makefile.in

eo/tutorial/Lesson5/Makefile.am

@@ -0,0 +1,25 @@
+
+bin_PROGRAMS		= OneMaxEA OneMaxLibEA
+
+OneMaxEA_SOURCES	= OneMaxEA.cpp
+
+OneMaxLibEA_SOURCES	= OneMaxLibEA.cpp make_OneMax.cpp
+
+
+noinst_HEADERS		= eoOneMax.h \
+			eoOneMaxEvalFunc.h \
+			eoOneMaxInit.h \
+			eoOneMaxMutation.h \
+			eoOneMaxQuadCrossover.h \
+			make_genotype_OneMax.h \
+			make_op_OneMax.h
+
+extra_DIST		= Makefile.simple
+
+
+LDADD			= -L$(top_builddir)/src -L$(top_builddir)/src/ga -L$(top_builddir)/src/utils
+
+LIBS			=  -lga -leoutils -leo
+
+INCLUDES		= -I$(top_srcdir)/src
+

eo/tutorial/Makefile.am

@@ -0,0 +1 @@
+SUBDIRS = Lesson1 Lesson2 Lesson3 Lesson4 Lesson5