- Last changes: 9.3.2019
This Readme file provides information on how to compile BayesX from source code.
If you do not have the source code avalailable already, it can be obtained in two different ways:
- The download website on www.bayesx.org offers a zip-archive with the current stable release of BayesX (sourcecode.zip).
- There is an anonymous (read-only) SVN access to the current development version of BayesX via https://svn.gwdg.de/svn/bayesx/. This is not considered a stable distribution and may comprise development versions that may fail for several reasons.
For compiling the source code, we provide support for two different versions:
- Customized make support via the cmake functionality (http://www.cmake.org/).
- A basic makefile that has to be adapted manually to your OS.
The advantage of cmake is that it provides automated support for adapting the makefile to your local computing environment (automatic detection of some required components) across a variety of platforms. The ordinary makefile makes less requirement for your system but may require more manual adujstments.
Comments / additions / corrections to the information in this file should be submitted to bayesx@gwdg.de.
The basic idea of cmake is to generate a makefile for BayesX adapted to your local working environment. In its somplest form, this should work as follows:
cd <location of the source code>
cmake .
This will generate the Makefile so that you can call
make
and this should finally yield the compiled BayesX versions (more details on the two versions are given below). Unfortunately, this basic version will most probably only work on platforms with a good preset of tools (e.g. most linux distributions) but in most cases some additional arguments will be required (see below).
The cmake specifications are made in CMakeLists.txt which comprise a specification of the sources included and additional information on required libraries etc. Usually, you should not have to make any changes to these files.
Calling cmake will create a make file that builds the BayesX executable, such that
bayesx
starts the software. Note that BayesX has to be executable. Under linux systems, the call sometimes has to be changed to
./bayesx
To be able to use cmake to generate a customized Makefile, you will need the following components:
- the cmake (>= version 2.8.10) facility (available from www.cmake.org).
- C and C++ compiler such as gcc and g++ (available for windows via www.mingw.org).
- when working in a unix-type environment (linux, Mac OS), you will need the readline library. This is not required for windows platforms.
The directories containing cmake as well as the C and C++ compiler have to be in your search path when executing the cmake command. For windows systems, you can temporarily add a directory to the path by specifying for example
PATH c:\rtools\MinGW64\bin;c:\rtools\mingw\bin;%PATH%
which adds "c:\rtools\MinGW64\bin" and "c:\rtools\mingw\bin" (the locations of 32bit and 64bit MinGW executables) to the current path. The command
echo %PATH%
displays the current path.
Note that paths including the directory of the r-tools binaries (such as c:\rtools\bin) will conflict with cmake and should therefore be excluded from the path variable.
In most cases (at least under windows OS), additional options will have to be parsed to cmake. Useful options from our experience are the following:
To explicitly specify the make facility that will be used for compiling BayesX,
set the -G <GENERATOR> option. For example, to use mingw32-make, you will have to
specify -G "MinGW Makefiles" as an option, i.e. the call will be
cmake -G "MinGW Makefiles" .
Calling cmake without options will give you a list of supported make facilities.
The C and C++ compiler that will be used by make can be specified by
-D CMAKE_C_COMPILER=<C COMPILER> abd -D CMAKE_CXX_COMPILER=<C++ Compiler>
For example to specify 64bit MinGW compilers, the cmake call may look as follows:
cmake -D CMAKE_C_COMPILER=x86_64-w64-mingw32-gcc -D CMAKE_CXX_COMPILER=x86_64-w64-mingw32-g++ .
Of course, all options can be combined.
-
cmake conflicts with r-tools: If you have installed r-tools and included r-tools binaries in your search path, this will conflict with cmake. You will have to delete r-tools from the path (see "Requirements" above).
-
If cmake failes, it sometimes helps to delete the cmake cache file CMakeCache.txt
-
When checking out BayesX via SVN, you may conflict with an older makefile already contained in the SVN directory. This old file is lower case (makefile) while the makefile generated by cmake is upper case (Makefile). If your system is case specific, the call to make may use either of the two. You may either delete the lower case makefile or specify explicitly that Makefile shall be used by
make -f Makefile
We assume that we start with a "clean" path that does not contain cmake, the compilers, the make facility and no r-tools. Then we proceed as follows:
Add cmake to the path:
PATH C:\Program Files (x86)\cmake 2.8\bin;%PATH%
Add mingw (obtained as a part of the CodeBlocks compiler suite) to the path to make mingw32-make available:
PATH c:\Program Files (x86)\CodeBlocks\MinGW\bin;%PATH%
Call cmake with explicit compiler specification for 64bit comilation and requesting MinGW makefiles:
cmake -G "MinGW Makefiles" -D CMAKE_C_COMPILER=x86_64-w64-mingw32-gcc -D CMAKE_CXX_COMPILER=x86_64-w64-mingw32-g++ .
The compiler specification will be stored in the cmake cache. Therefore, once you have successfully called cmake once, the call
cmake -G "MinGW Makefiles" .
will be sufficient since the required compiler info is extracted from the cache.
Now call make
mingw32-make
If you are working in an environment with multiple kernels, the no. of kernels to be used by make can be specified by the -j option. Four example, four kernels will be used with
mingw32-make -j4
BayesX can now be invoked by
BayesX
We assume that we start with a "clean" path that does not contain cmake, the compilers, the make facility and no r-tools. Then we proceed as follows:
Add cmake to the path:
PATH C:\Programme\cmake 2.8\bin;%PATH%
Add mingw (obtained as a part of the CodeBlocks compiler suite) to the path to make gcc/g++ available:
PATH c:\Programme\CodeBlocks\MinGW\bin;%PATH%
Call cmake with explicit compiler specification and requesting MinGW makefiles:
cmake -G "MinGW Makefiles" -D CMAKE_C_COMPILER=gcc -D CMAKE_CXX_COMPILER=g++ .
The compiler specification will be stored in the cmake cache. Therefore, once you have successfully called cmake once, the call
cmake -G "MinGW Makefiles" .
will be sufficient since the required compiler info is extracted from the cache.
Add r-tools to make mingw32-make available:
PATH c:\rtools\bin;C:\Rtools\MinGW\bin;C:\Rtools\MinGW64\bin;%PATH%
and call make (with no. of kernels defined by -j):
mingw32-make -j2
BayesX can now be invoked by
BayesX
A basic makefile for BayesX is provided in makefile.orig. If you want to use this makefile without relying on the cmake facility, either rename makefile.orig to makefile and invoke
make BayesX
or call
make -f makefile.orig BayesX
This should compile an executable BayesX in the current working directory that can be started by
BayesX
Note that BayesX has to be executable. Under linux systems, the call sometimes has to be changed to
./BayesX