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README
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changelog
version 0.99.4
- vignette updates
This package depends on Open Babel 2.3.0 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
\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.
Set up the following global environment variables: in control panel/system:
D:\sandbox\ChemmineOB\src>echo %OPEN_BABEL_SRC%
c:/openbabel_src
D:\sandbox\ChemmineOB\src>echo %OPEN_BABEL_BIN%
c:/openbabel
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"D:/biocbld/bbs-2.13-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"D:/biocbld/bbs-2.13-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
Then compile with cmake:
cmake -G "Unix Makefiles" -DBUILD_SHARED=OFF -DCMAKE_INSTALL_PREFIX=c:/openbabel/i386 -DZLIB_INCLUDE_DIR=D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include -DZLIB_LIBRARY=D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/libs/i386/zlib1bioc.dll c:/openbabel_src/i386
You can run this from c:/openbabel_build/i386
Then:
make
make install