This package depends on Open Babel 2.3.2 or greater. On linux and mac it can be compiled 
and run against the standard shared library version of Open Babel. On windows, the distributed
binary has been compiled agains a static version of Open Babel 2.3.2. This was done because the 
version downloadable from the Open Babel website was compiled with MSVC and is not 
compatible with GNU based toolchain used by BioConductor. This means that on  windows
there is no need to install Open Babel seperataly, but also that Open Babel cannot be 
updated outside of the ChemmineOB package. If you need to compile ChemmineOB from source
on windows you can follow the instructions below.

Compling with OpenBabel in a non-standard location
---------------------------------------------------
If the OpenBabel include and/or library files are not in one of the default
search paths (e.g., /usr/lib,/usr/include, /usr/local/lib,/usr/local/include), then you must set the
following environment variables before installing the ChemmineOB package:

OPEN_BABEL_INCDIR = path to header files
OPEN_BABEL_LIBDIR = path to shared (.so) library file

These values can also be set through command line switches to the configure scripts:

R CMD INSTALL --configure-args='--with-openbabel-include=... --with-openbabel-lib=...' ChemmineOB.tgz

where the '...' are replaced by the relevant paths.

Compiling on Windows
---------------------

Set up directory structure like this:

C:\openbabel\src
    \i386
     \x64

c:\openbabel\bin
     \i386
      \x64

c:\openbabel\build
     \i386
     \x64

Download the openbabel source and copy it into both c:\openbabel\src\i386 and
c:\openbabel\src\x64.
Download and install RTools and Cmake.

Set up the following global environment variables: in control panel/system:

  OPEN_BABEL_SRC = c:/openbabel/src

  OPEN_BABEL_BIN = c:/openbabel/bin

Install the zlibbioc package. In R, do this:

  source("http://bioconductor.org/biocLite.R")
  biocLite("zlibbioc")

Get the location of the zlib includes as follows (in R):

  > library(zlibbioc)
  > pkgconfig("PKG_CFLAGS")

That will print out something like:

  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include"

Get rid of the -I and the quotes and there is your ZLIB_INCLUDE_DIR

Then get the location of the zlib library as follows:

  > pkgconfig("PKG_LIBS_shared")

That will print out something like:

  -L"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/i386" -lzlib1bioc>

Get rid of the -L, the quotes, and the -lzlibbioc> and append /zlib1bioc.dll
and now you have ZLIB_LIBRARY

For i386 builds:
-----------------
Make sure "c:/Rtools/mingw_32/bin" in the system PATH.
Move into c:\openbabel\build\i386

Run: 

 cmake -G "Unix Makefiles" -DCMAKE_C_FLAGS=-m32 -DCMAKE_CXX_FLAGS=-m32  -DCMAKE_RC_COMPILER=c:/Rtools/mingw_32/bin/gcc.exe -DBUILD_SHARED=OFF -DCMAKE_INSTALL_PREFIX=c:\openbabel\bin\i386 -DZLIB_INCLUDE_DIR=C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include -DZLIB_LIBRARY=C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/i386/zlib1bioc.dll C:/openbabel/src/i386

Replace the value of ZLIB_INCLUDE_DIR and ZLIB_LIBRARY with the values you
found above.

Then run:

  make
  make install

Copy openbabel config header file into place:

  copy c:\openbabel\bin\i386\include\openbabel-2.0\openbabel\babelconfig.h c:\openbabel\src\i386\include\openbabel\babelconfig.h

For x64 builds:
------------------
Make sure "c:/Rtools/mingw_64/bin" in the system PATH and make sure that "c:/Rtools/mingw_32/bin" IS NOT IN the system PATH, 
otherwise cmake will choose the 32 bit version over the 64 bit version
Move into c:\openbabel_build\x64

Run: 

  cmake -G "Unix Makefiles" -DCMAKE_C_FLAGS=-m64 -DCMAKE_CXX_FLAGS=-m64  -DCMAKE_RC_COMPILER=c:/Rtools/mingw_64/bin/gcc.exe -DBUILD_SHARED=OFF -DCMAKE_INSTALL_PREFIX=c:/openbabel/bin/x64 -DZLIB_INCLUDE_DIR=C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include -DZLIB_LIBRARY=C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/x64/zlib1bioc.dll c:/openbabel/src/x64

Replace the value of ZLIB_INCLUDE_DIR and ZLIB_LIBRARY with the values you
found above.

Then run:

  make
  make install

Copy openbabel config header file into place:

  copy c:\openbabel\bin\x64\include\openbabel-2.0\openbabel\babelconfig.h c:\openbabel\src\x64\include\openbabel\babelconfig.h

Remember to add c:/Rtools/mingw_32/bin back into the system PATH if you
temporarily took it away.


Then for all architectures:
------------------------------

Set environment variables:

  OPEN_BABEL_BIN = c:/openbabel/bin
  OPEN_BABEL_SRC = c:/openbabel/src

Build ChemmineOB:

  R CMD build --no-build-vignettes ChemmineOB
  R CMD INSTALL --merge-multiarch ChemmineOB_1.13.0.tar.gz   #(replace version with whatever version you have)