Merge pull request #12 from ralmond/Netica-607

Netica 607

.gitignore

@@ -0,0 +1,23 @@
+#*#
+*.o
+*~
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+src/*.o
+src/*.so
+src/*.dll
+
+autom4te.cache
+config.log
+config.status
+
+Makevars
+
+aclocal.m4
+./
+config.h
+#DESCRIPTION#
+.Rbuildignore
+symbols.rds

ChangeLog

@@ -1,3 +1,15 @@
+2020-04-16  Russell Almond  <ralmond@pei>
+
+	* src/Makevars.in (PKG_CFLAGS): Added -DNETICA_VERSION here.  I still don't understand autoconf.
+
+	* src/Experience.c (NewLearner_rn): Added switch for Ascent/descent
+
+2020-04-16  Russell Almond  <ralmond@Cherry>
+
+	* configure.ac: Changed compile procedure to (a) use pkg-config
+	when available and (b) use a NETICA_VERSION flag, as NETICA
+	doesn't seem to supply this.
+
 2020-03-09  Russell Almond  <ralmond@Cherry>
 
 	* R/Networks.R ("NetworkName<-"): Same problem, different place.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RNetica
 Version: 0.8-2
-Date: 2020/03/09
+Date: 2020/04/16
 Title: R interface to Netica(R) Bayesian Network Engine 
 Author: Russell Almond
 Maintainer: Russell Almond <ralmond@fsu.edu>

INSTALLATION

@@ -3,25 +3,81 @@ rather than the object version of RNetica.
 
 The current version does not automatically download the Netica API,
 you need to download and unzip it yourself.  You also need to point
-the installation at the place where it is located.  
+the installation at the place where it is located.
+
+The current latest versions are:
+Linux:  https://norsys.com/downloads/NeticaAPI_Linux_607.zip
+Windows: https://norsys.com/downloads/NeticaAPI_Win_510.zip
+MacOS: https://norsys.com/downloads/NeticaAPI_Mac.zip
+or https://norsys.com/downloads/NeticaJ_MacOSX10.7_504.zip
+
+
+Linux and MacOS X.  The appropriate libnetica.so file from the Netica
+tarball needs to be copied into a directory where R can find it when
+loading.  Under Ubuntu 18.04, the choices seem to be /usr/lib,
+/usr/share/lib, and ${R_HOME}/lib.
+
+=====================================
+
+As of 2020, Norsys is making available a version 6.07 of the API,
+currenlty only out for Linux, but probably available soon for MacOS
+and Windows.  There are some slight difference in the header files and
+shared library locations between the two, so it is necessary for the
+configuration file to pickup which version you are using.
+
+The best way to do this is using the pkg-config mechanism.  This works
+on all three platforms, but may need to be installed.
+
+I have included a netica.pc config file, this should be (a) edited so
+the first line points to where the Netica API lives (in my case in a
+directory under my home directory) and then (b) moved to somewhere
+where pkg-config can find it.  (If pkg-config is configured correctly,
+then `pkg-config -variable pc_path pkg-config` should reveal the
+localtion of the pkg-config packages.
+
+The file netica504.pc is for the older version of the API (still most
+recent for MacOS and Windows).  If you are using that version, then
+rename the files (so it will be easy to replace when you upgrade).
+Netica_5.04 is not recommended because of the bug in the absorb nodes
+function, but it is still necesary until Norsys releases new
+versions of the DLL/shared library for Windows/MacOS.
+
+================================================================
+
+These describe the older mechanism, now replaced by pkg-config.
 
 On Linux and Unix (including Mac OS X) distributions you do that with
 the "--with-netica" switch to configure.  Thus I compile with
 
-R CMD INSTALL RNetica --configure-args='--with-netica=/home/ralmond/software/Netica_API_607'
+R CMD INSTALL RNetica --configure-args='--with-netica=/home/ralmond/software/Netica_API_504'
 
 To check I run with
 
-R CMD check RNetica --install-args="--configure-args='--with-netica=/home/ralmond/software/Netica_API_607'"
+R CMD check RNetica --install-args="--configure-args='--with-netica=/home/ralmond/software/Netica_API_504'"
 
 For Windows installations, set an environmental variable NETICA_HOME
 with the path in which you unpacked the Netica API.  R will give a
 warning about manual configuration, this is the necessary manual
 configuration. 
 
+===================================================
+
+
 If you have obtained a valid Netica API license key from Norsys, you
 can insert it in the variable NeticaLicenseKey in the main workspace.
 RNetica will then consult this value when loading the Netica DLL.  All
 of the functions in the man pages work in the unlicensed version, so R
 CMD check RNetica does not require a license key.
 
+As of version 0.6, the startup mechanism now requires the program to
+explicitly call:
+sess <- NeticaSession()
+startSession(sess)
+
+In particular, this exposes the session object which contains
+references to all available networks.  The licence key can be passed
+as an optional argument to NeticaSession:
+sess <- NeticaSession(LicenseKey=NeticaLicenceKey).
+
+I've been keeping the license key in a file NeticaLicense.R in my home
+directory, which I source at the begining of each session.

RNetica.Rproj

@@ -1,17 +1,20 @@
-Version: 1.0
-
-RestoreWorkspace: Default
-SaveWorkspace: Default
-AlwaysSaveHistory: Default
-
-EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
-Encoding: UTF-8
-
-RnwWeave: Sweave
-LaTeX: pdfLaTeX
-
-BuildType: Package
-PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source  --configure-args='--with-netica=/home/ralmond/software/Netica_API_607'
+PackageBuildArgs: --configure-args='--with-netica=/home/ralmond/software/Netica_API_607'
+PackageBuildBinaryArgs: --configure-args='--with-netica=/home/ralmond/software/Netica_API_607'
+PackageCheckArgs: --install-args="--configure-args='--with-netica=/home/ralmond/software/Netica_API_607'"

cleanup

@@ -1,3 +1,3 @@
 #!/bin/sh
 
-rm -f *~ src/*~ src/*.o src/*.so src/symbols.rds man/*~ R/*~ config.* src/Makevars 
+rm -f *~ src/*~ src/*.o src/*.so src/symbols.rds man/*~ R/*~ config.* src/Makevars src/config.h