More revising of INSTALL and README files

INSTALL

@@ -7,54 +7,12 @@ Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,
 This file is free documentation; the Free Software Foundation gives
 unlimited permission to copy, distribute and modify it.
 
-Important Notes Specific to GTSAM
-==================
-
-1)
-GTSAM uses CCOLAMD to find good variable elimination orders.  You can download
-it from Tim Davis's website:  http://www.cise.ufl.edu/research/sparse/ccolamd/
-Then, pass the following arguments (paths are just examples) to ./configure:
---with-ccolamd-inc=/usr/local/include
---with-ccolamd-lib=/usr/local/lib
-
-2)
-GTSAM makes extensive use of debug assertions, even for checking input of
-the functions you will call.  These assertions are disabled when NDEBUG is
-defined.  Thus, we strongly recommend compiling GTSAM and your own code without
-this symbol during debugging.
-
-After debugging, GTSAM will run much faster when compiled with NDEBUG defined,
-so that debug checks are disabled.
-
-Another useful debugging symbol is _GLIBCXX_DEBUG, which enables debug checks
-and safe containers in the standard C++ library.  We suggest testing your code
-with this symbol defined, as it will make problems much easier to find.
-NOTE:  The native Snow Leopard g++ compiler/library contains a bug that makes
-it impossible to use this symbol.  The MacPorts g++ compilers work fine with it
-though.
-
-3)
-Putting the above together, here are some sample ./configure commands for
-compiling gtsam:
-
-For Debugging (native Snow Leopard g++ compiler):
-./configure CXXFLAGS="-fno-inline -g -Wall" \
-    LDFLAGS="-fno-inline -g -Wall" --enable-blas --enable-lapack \
-    --with-toolbox=$HOME/toolbox/
-
-For Debugging (Linux or MacPorts g++ compilers):
-./configure CXXFLAGS="-fno-inline -g -Wall -D_GLIBCXX_DEBUG" \
-    LDFLAGS="-fno-inline -g -Wall" --enable-blas --enable-lapack \
-    --with-toolbox=$HOME/toolbox/
-
-For Performance:
-../configure CXXFLAGS="-DNDEBUG -O3" LDFLAGS="-O3" --enable-blas \
-    --enable-lapack --with-toolbox=$HOME/toolbox/
-
-
 Basic Installation
 ==================
 
+IMPORTANT NOTE:  GTSAM has some special compilation requirements, see
+the README file.
+
 Briefly, the shell commands `./configure; make; make install' should
 configure, build, and install this package.  The following
 more-detailed instructions are generic; see the `README' file for

README

@@ -39,54 +39,63 @@ Finally, there are some local libraries built needed in the rest of the code:
   doc					documentation
   m4					local M4 macros
 
-Boost Dependencies:
-------------------
-The GTSAM library is based on the 'Boost C++ Libraries' which can be
-found here: http://www.boost.org/. 
-Donwload the lates version and extract Boost in any place. To this
-place the compiler will be linking. 
 
-- On Linux BOOST can also be installed with a packaged manager.
+Important Installation Notes Specific to GTSAM
-- On Mac OS Mac Ports can be used.
+----------------------------------------------
 
-For example the Boost path could be '/opt/local/include/' on a typical
+1)
-Mac system, where you should be able to find one of the header files:
+GTSAM requires the following libraries to be installed on your system:
-/opt/local/include/boost/config.hpp 
+ - BOOST version 1.40 or greater (install through Linux repositories or MacPorts)
+ - BLAS, ATLAS, and LAPACK (libblas, libatlas, and liblapack in Debian/Ubuntu
+                            repositories, on Mac these should already installed
+                            with the OS)
 
-If your boost files are in a different place change the path according
+2)
-to your path.
+GTSAM uses CCOLAMD to find good variable elimination orders.  You can download
+it from Tim Davis's website:  http://www.cise.ufl.edu/research/sparse/ccolamd/
+Then, pass the following arguments (paths are just examples) to ./configure:
+--with-ccolamd-inc=/usr/local/include
+--with-ccolamd-lib=/usr/local/lib
 
-The path to the Boost files can be set as an environmental variable in
+3)
-the startup script. For a Bash shell the startup file is ~/.bashrc
+GTSAM makes extensive use of debug assertions, even for checking input of
-put the following command in this file:
+the functions you will call.  These assertions are disabled when NDEBUG is
-export BOOST_DIR=/opt/local/include/ 
+defined.  Thus, we strongly recommend compiling GTSAM and your own code without
+this symbol during debugging.
 
-Installation:
+After debugging, GTSAM will run much faster when compiled with NDEBUG defined,
--------------
+so that debug checks are disabled.
-To finally install the library go into the directory where you unpacked the 
-GTSAM library. We recommend you do an out-of-source build, as described in the
-next section. However, this is not required:
 
-Standard Build:
+Another useful debugging symbol is _GLIBCXX_DEBUG, which enables debug checks
----------------
+and safe containers in the standard C++ library.  We suggest testing your code
+with this symbol defined, as it will make problems much easier to find.
+NOTE:  The native Snow Leopard g++ compiler/library contains a bug that makes
+it impossible to use this symbol.  The MacPorts g++ compilers work fine with it
+though.
 
-run the command below to configure the library:
+4)
+Putting the above together, here are some sample ./configure commands for
+compiling gtsam:
 
-$] ./configure --with-toolbox=$HOME/toolbox/ 
+For Debugging (native Snow Leopard g++ compiler):
+./configure CXXFLAGS="-fno-inline -g -Wall" \
+    LDFLAGS="-fno-inline -g -Wall" --enable-blas --enable-lapack \
+    --with-toolbox=$HOME/toolbox/
 
-where the path after --with-toolbox should point to the directory you want to have the gtsam
+For Debugging (Linux or MacPorts g++ compilers):
-matlab scripts installed in. You have to set it to an existing directory. 
+./configure CXXFLAGS="-fno-inline -g -Wall -D_GLIBCXX_DEBUG" \
-After successful installation there will be a gtsam directory with all Matlab GTSAM Toolbox files.
+    LDFLAGS="-fno-inline -g -Wall" --enable-blas --enable-lapack \
+    --with-toolbox=$HOME/toolbox/
 
-The configure script will attempt to find the Boost C++ library on your system. If you installed
+For Performance:
- Boost in a non-standard place, you have to to specify an additional flag to the configure script:
+./configure CXXFLAGS="-DNDEBUG -O3" LDFLAGS="-O3" --enable-blas \
+    --enable-lapack --with-toolbox=$HOME/toolbox/
 
-$] ./configure --with-toolbox=$HOME/toolbox/ --with-boost=/path/to/boost/include/
+After that (this would be for an in-source build, see next for out-of-source):
+$ make
+$ make check (optional, runs unit tests)
+$ make install
 
-After configuring your makefile you have to compile the library
-Type:
-$] make
-$] make install
 
 Out-of-source build:
 --------------------
@@ -97,16 +106,18 @@ run it in sub-directory of choice, e.g., starting out in the main GTSAM folder:
 
 $] mkdir build
 $] cd build
-$] ../configure --with-toolbox=$HOME/toolbox/
+$] ../configure ..... (command as above)
 $] make install
 
+
 Built-in Unit Tests:
-----------------
+--------------------
 There is one more optional step in which you can invoke the unit tests included in the gtsam libraries. 
 $] make check
 By verifying all the test results are positive, you can make sure that the functionalities of the GTSAM
 libraries are correct.
 
+
 Compile Matlab Toolbox:
 -----------------------
 1) Start Matlab
@@ -115,6 +126,7 @@ Compile Matlab Toolbox:
 3) Change your current directory to the GTSAM Matlab Toolbox
 4) Type 'make_gtsam' at the Command Window
 
+
 Run Matlab Unit Tests:
 -----------------------
 In the matlab command window, change directory to $gtsam/matlab and then type 'run_tests', which will