                       INSTALLATION INSTRUCTIONS

To install LNKnet, gunzip and untar the provided gzipped tar file
using the following commands:
gunzip -c lnknet_5_2_1_src.tgz | tar xvf -
cd lnknet
./runConfig
gmake install

Set the environment variable LNKHOME to the directory where you
unpacked lnknet, for example /u/kukolich/lnknet.

Add $LNKHOME/bin to your path and $LNKHOME/man to your MANPATH.

LNKnet uses the GNU configure scripts for configuration of Makefiles
and certain header files prior to compilation. The GNU gcc compiler is
assumed to be your compiler and the Makefiles that are generated work
best with GNU's gmake.

			LNKNET DOCUMENTATION
The document "quickref.pdf" in the $LNKHOME/doc directory describes
how a simple experiment can be performed to verify that LNKnet is
installed correctly. The document "usersguide.pdf" in the same directory
provides a complete description of LNKnet capabilities and use. These
files can be viewed using Adobe Acrobat Reader which is available for
free from http://www.adobe.com/acrobat/

                       LNKNET SRC DIRECTORIES

$LNKHOME/src/lib
	Code for nnlib.a, our basic library of shared functions
for the algorithms and plotting programs. There are also a couple
small programs here including a modified copy of the Unix tee program.

$LNKHOME/src/lippic
	Code for lnkplot, the plot display program and xlippic, the
library used by plot programs to communicate with lnkplot. Also code
for conversion programs, plot2ps and plot2mif.

$LNKHOME/src/algorithm
	The pattern classification and clustering programs. Each
algorithm has its own subdirectory.

$LNKHOME/src/plot
	Programs which generate plot files which are displayed by
lnkplot.

$LNKHOME/src/mclass
	The Motif based graphical user interface for generating and
running classification experiment shell scripts.

$LNKHOME/src/analysis
	Perl code for some results analysis programs.

$LNKHOME/src/gclass, gmap, gseq
	Older Xview based GUIs. They haven't been updated or compiled
in a while.

$LNKHOME/src/xgobi
	A copy of xgobi, a public domain data exploration tool which
we have found useful. LNK2gobi can be used to translate lnknet style
data files to xgobi style data files for data exploration.

                       RECOMPILING LNKNET

LNKnet uses the GNU configure scripts for configuration of Makefiles
and certain header files prior to compilation. The GNU gcc compiler is
assumed to be your compiler and the Makefiles that are generated work
best with GNU's gmake.

cd src
./runConfig
gmake install

Libraries configure checks for:
-lm -lXm -lXt -lX11 -lSM -lICE -lsocket

Under Linux and Cygwin, we use LessTif, a Motif replacement. In the
runConfig file there is a commented out line that sets the library
path to look in the Lesstif directory for the Xm library.

The algorithm programs should just need the math library, -lm. This is
the library required for the sin() function, for example.

The plot display program, lnkplot, can be compiled several different
ways. There is a straight Xlib version (xplot), an Xt version using
the Athena widget set (awxplot) or a Motif version (mtfxplot). Which
additional X libraries you require to compile the plot display program
depend on which version of the program you compile.
Whichever version of the plot program you want should be
installed in $LNKHOME/bin under the name lnkplot.

The plotting programs need BSD style sockets to connect to the
plot display program, on which it also depends.

The graphical user interface is written using the X-Motif libraries.
You will need a development copy of these libraries to recompile the
user interface. Basically, this means that you need a copy of the
Motif include files that matches the Motif library files you have. In
the past, I have faked it by copying another machine's include files
onto a "user" installation of the Motif libraries. It seems to have
worked fine. However, this shouldn't be necessary in the future, since
I believe MOTIF has become fully public domain. On Suns, CDE versions
of the Motif libraries seem to work, although I use the OPENWINHOME
versions. On Linux, lesstif also works.

		NOTE ON COMPILING WITHOUT GMAKE AND GCC

FIXING THE MAKEFILES:

In lnknet/src run the perl script un_gmake.pl. This will remove some
gmake dependent lines in the Makefile.in files.

Then, make the gcc vs cc changes below. Then run runConfig and make install.

USING CC INSTEAD OF GCC:

If configure gives you trouble for missing or having a bad gcc, add
"CC=cc" to the configure call at the bottom of the runConfig
script. Also change the CFLAGS line to something like
setenv CFLAGS "-g"
since the -Wall will probably give your cc fits.
