Building and installing libSBML

This section explains how to build libSBML from the source distribution.

Table of contents

1. Building libSBML under Linux, Mac OS X, FreeBSD, Solaris and Cygwin 1.1 Configuring using CMake 1.2 Configuring using GNU make 1.2.a Basic configuration for Linux, Mac OS X, Solaris, and Cygwin 1.2.b Interfaces for C#, Java, JavaScript, MATLAB, Octave, Perl, Python, R and Ruby 1.2.c Creating 32- and/or 64-bit binaries 1.2.d Creating universal binaries on Mac OS X 1.2.e Configuring for SWIG 1.2.f Configuring support for compression 1.2.g Configuring for generating documentation 1.2.h Configuring for software unit testing 1.3 Compiling and installing 1.3.a Using CMake 1.3.b Using GNU make 1.3.c Debugging build problems 1.4 Advanced configuration options

2. Building libSBML under Windows 2.1 Configuring using CMake 2.2 Compiling and installing using MSVC

3. Files installed by libSBML, and their locations

4. What to do if problems arise

1. Procedures for Linux, Mac OS X, FreeBSD, Solaris and Cygwin

LibSBML supports two build systems: CMake, and GNU autoconf plus GNU make. CMake is preferred and is the only one supported for building SBML Level 3 package extensions; the use of GNU autoconf and GNU make is deprecated but is currently still used to build the documentation. In all cases below, you will need to download the libSBML source code archive from the download area on GitHub then unpack the archive somewhere on your computer.

1.1 Configuring using CMake

CMake is a cross-platform build configuration system that can be used to generate makefiles as well as project files for common development environments such as Visual Studio, Eclipse, Xcode and CodeBlocks. If you do not already have CMake installed on your system, please make sure to download and install a copy of CMake 3.10 or later from cmake.org on your computer system.

Next, start up the CMake graphical user interface (GUI). This is a configuration tool that allows you to select options for configuring your libSBML build and then generate makefiles for running the actual build. The GUI will look something similar to the following screenshot:

Screenshot of CMake when it first starts up. Shown here is the Mac OS X version of CMake; it will look similar but not identical on other operating systems.

In the CMake GUI interface, first click on the Browse Source... button and navigate to the directory where you unpacked the libSBML source code archive on your file system. Next, check the value of the field Where to build the binaries. We use so-called “out-of-source builds” for libSBML, meaning that CMake will place compiled binary files in a separate build directory, not intermixed with the source files. If the field for the build directory in the CMake GUI is blank, or CMake filled it with a different value than what you prefer, click on the Browse Build... button to change the directory.

After filling in the fields at the top of the interface, click on the Configure button. If this is the first time you have executed CMake's Configure command in the libSBML source directory, you may see a dialog such as the following, asking you whether it can create a subdirectory where it will compile libSBML. Click on the "Yes" button if the directory location is acceptable.

Dialog presented by CMake before it creates the subdirectory that it will use to compile libSBML.

After the dialog above, CMake should then display a dialog similar to the next one.

Screenshot of the Configure screen under Mac OS X.

Unless you have special requirements, select the default choices of "Unix Makefiles" and "Use default native compilers", then click the Done button. This will close the selection dialog, whereupon CMake will read the libSBML configuration files and populate the options area in the CMake GUI with various options for controlling how libSBML is built. These new options are displayed in red, as illustrated in the following screenshot.

Screenshot of the CMake interface after the configuration step.

In this panel, you can set values for various libSBML configuration/build options. To find out the meaning of a particular option, hover your mouse/pointer over the item for a few seconds until a tooltip appears—it will provide a short description of the option under the cursor. There are numerous options available; below, we point out just a few that are especially popular for customization:

• CMAKE_INSTALL_PREFIX: the location into which the compiled libSBML libraries. After clicking on this field, you can type a directory path directly into the field or click on the square ... icon to invoke a file/open dialog.
• WITH_JAVA, WITH_PYTHON, etc.: toggle whether to build the language bindings for programming languages supported by libSBML, such as C#, Java, JavaScript, MATLAB, Octave, Perl, Python, R, Ruby, and possibly others. If you need to indicate an explicit path to the interpreter (e.g., for Python), click the "Advanced" checkbox in the upper part of the CMake GUI to gain access to additional configuration options. (For Python, they are PYTHON_EXECUTABLE, PYTHON_INCLUDE_DIR and PYTHON_LIBRARY.)
• ENABLE_COMP, ENABLE_QUAL, etc.: toggle whether support for various SBML Level 3 packages is included. The names following the ENABLE_ part are the package nicknames: “comp” for the Hierarchical Model Composition package, “qual” for the Qualitative Models package, and so on.
• WITH_EXPAT, WITH_XERCES: by default, libSBML will use the libxml2 XML library. If you prefer to use Expat (version 1.95.8 or greater) or Xerces (version 2.7.0 or greater), select one of these options instead, and set WITH_LIBXML to false.

Note that selecting options and configuring libSBML using the GUI actually involves a two-step process:

1. Select options in the panel.
2. Click on CMake's Configure button. This causes CMake to process the configuration options, and if the chosen options require additional information, CMake will update the list in the window and highlight some items in red. This indicates that CMake requests you to make additional choices, provide additional information or resolve conflicting choices.

You may need to iterate in between the two steps above, setting options and clicking the Configure button, until there are no options left in red and the Generate button becomes enabled.

Once you are satisfied with the options selected and there are no more red items the dialog box, click on the Generate button. This will cause CMake to create configuration files for the compilation environment you selected in the beginning (e.g., Visual Studio under Windows, or regular Unix makefiles under Mac OS or Linux, and so on). The files will be placed in the "build" directory you indicated in the second line of the CMake GUI.

Now please proceed to Section 1.3, Compiling and installing LibSBML.

1.2 Configuring using GNU Make

Warning: the use of GNU autoconf and GNU make is deprecated. It cannot be used to properly build the libSBML packages, and it has only been retained to build the libSBML documentation. Please use the CMake-based build system unless you are attempting to build the documentation.

First, in a shell (terminal), cd into the directory where you unpacked the libSBML source code archive. (It will have a name such as libSBML-5.20.4-Source.)

1.2.a Basic configuration for Linux, Mac OS X, Solaris, and Cygwin

If you only want to build the C and C++ interfaces and install libSBML into /usr/local (the default), then configuring libSBML is simply a matter of executing the following command:

./configure

LibSBML requires a separate XML library for low-level XML tokenizing and Unicode support. It will by default attempt to use the libxml2 XML library; if you do not have libxml2 version 2.6.16 or later on your system, the configure program will terminate with an error explaining it cannot find libxml2. (Important: libSBML needs the development libraries for libxml2, not only the runtime library, which on systems such as Linux means that you need to have installed both the basic libxml2 distribution and the -dev distribution. These distributions typically have the root names libxml2 and libxml2-dev, often followed by a version number.)

Instead of using libxml2, you can inform the configure program to use the Expat or Xerces libraries. Many Linux and other UNIX-like systems provide one or more of these libraries either as part of their standard distribution or as an optional RPM, Debian, Mandrake or other package distributions. To use Expat, run the libSBML configuration program as follows:

./configure --with-expat

And for Xerces, use

./configure --with-xerces

Compatibility warning: The default XML parser library used by libSBML is libxml2. If you chose to use another XML parser library instead, beware there is a known bug in Xerces 2.6.0 that cannot be worked around at this time and causes errors in software using it. Xerces versions 2.2 – 2.5, and 2.7.0 and above, are known to work properly, and all Expat versions above 1.95.8 are also known to work.

If your copy of libxml2, Expat, or Xerces is installed in a non-standard location on your computer system (e.g., a private home directory), configure may not be able to find it by itself. In this case, configure needs to be told explicitly where to find the libraries. Use the following forms:

./configure --with-libxml="DIR"

or

./configure --with-xerces="DIR"

or

./configure --with-expat="DIR"

where DIR is the parent directory of where the include and lib directories of Xerces, Expat or libxml2 (whichever one you are trying to use) is located. For example, on Mac OS X, if you used Fink to install Expat in Fink's default software tree, you would configure libSBML using the following command:

./configure --with-expat="/sw"

By default, during the installation phase (i.e., when running make install, discussed below), the libSBML installation commands will copy header files to /usr/local/include/sbml, the shared and static library files to /usr/local/lib, and documentation files to /usr/local/share/doc/libsbml-VERSION (where VERSION is the version number of libSBML). To specify a different installation location instead of the default, use the --prefix argument to the configure program. For example,

./configure --prefix="/my/favorite/path"

Of course, you can combine the flags to configure, giving both --prefix and --with-expat or --with-xerces or --with-libxml to set both options.

1.2.b Interfaces for C#, Java, JavaScript, MATLAB, Octave, Perl, Python, R and Ruby

LibSBML's core is written in C and C++, but libSBML comes with APIs for other languages as well. To enable the library extensions for C#, Java, JavaScript, MATLAB, Octave, Perl, Python, R and/or Ruby, you need to supply additional options to configure. These options are --with-csharp, --with-java, --with-javascript, --with-matlab, --with-octave, --with-perl, --with-python, --with-r, and --with-ruby, respectively. As with other configure options discussed above, all of these accept an optional prefix argument; for example, on a Mac OS X 10.5 Intel-based system with MATLAB version R2010a installed in its default location of /Applications/MATLAB_R2010a.app, the proper argument would be

./configure --with-matlab=/Applications/MATLAB_R2010a.app

If you want to build multiple language bindings for libSBML, combine multiple flags together as in the following example:

./configure --with-java --with-python

Some of the language interfaces provide additional configuration options besides the basic --with-language option. In particular, for Python and C#, there are options allowing you to specify the language interpreter that should be used, which is important for systems that have multiple versions installed. For example, to indicate that you want to use the Apple-supplied version of Python 2.6 on a Mac OS X 10.7 system (which has versions 2.5, 2.6 and 2.7 located in /usr/bin), you could use the following options:

./configure --with-python --with-python-interpreter=/usr/bin/python2.6

Please run configure --help to obtain a list of the possible options offered by configure.

The libSBML distribution ships with certain interface files provided, so that you do not need to have the software necessary to recreate them. However, if you obtained the libSBML distribution from the project repository on GitHub, or you want to recreate the files deliberately, you may need to configure libSBML to use SWIG to regenerate the libSBML language interfaces. Please see the section below on using SWIG.

Finally, note that these additional language bindings are implemented via foreign function interfaces in the respective languages; in all cases, the core C/C++ libSBML library still must be compiled and installed. The language binding files are not standalone implementations. For instance, the Java language API files consist of a file named libsbmlj.jar and a native object library file named (depending on the operating system) libsbmlj.jnilib (Mac OS X), libsbml.so (Linux), or sbmlj.dll (Windows); both of these must be installed and shipped with applications along with the core libSBML library file. Please refer to section Files installed by libSBML, and their locations) for an explanation of the name and location of the libSBML library file under different operating systems.

A warning about Java versions: we have been unable to successfully compile the libSBML Java interface using the GNU Compiler for Java (gcj), at least in the case of gcj version 4.4.3 under Ubuntu Linux version 10.10. We do not recommend using gcj with libSBML for this reason.

1.2.c Creating 32- and/or 64-bit binaries

On some hardware and operating system combinations, it is possible to compile 64-bit as well as 32-bit versions of programs. Normally, the most sensible default will be chosen by the systems' compilers automatically, but when you download third-party software or compile your own, sometimes it becomes necessary to select specific versions. LibSBML is no exception. To make it easier to build libSBML explicitly in a 32-bit or 64-bit version, configure offers the two optional arguments --enable-m32 and --enable-m64, respectively.

Whether you need to do this depends very much on your hardware, operating system, and the format of other libraries and programs on your system. Currently, the most common situation where this issue arises is on 64-bit systems where not all libraries (e.g., the XML parser libraries) are available in 64-bit format. Then, libSBML needs to be configured to be built as a 32-bit binary:

./configure --enable-m32

The two options --enable-m32 and --enable-m64 cannot be used together; if they are both given, then the 32-bit option is silently ignored. On Mac OS X systems, where it is in fact possible to build so-called universal (or "fat") binaries containing both 32-bit and 64-bit executable code, a separate option is available for configure and is discussed in the next section.

1.2.d Creating universal binaries on Mac OS X

Apple Macintosh operating systems versions 10.4–10.6 provide the option of building binaries that can run natively on either PowerPC or x86 (Intel) architectures, as well as in either 32-bit or 64-bit versions. Compiling a library to be a so-called universal binary containing multiple versions of the object code requires the use of special options at compilation time. To configure libSBML to be built as a universal binary, specify the optional argument --enable-universal-binary to configure. The following example illustrates how to do this:

./configure --enable-universal-binary

By default, on Mac OS 10.5, the libSBML option above will construct a universal binary containing 32-bit PowerPC and 32-bit Intel x86 binaries; on Mac OS 10.6, this becomes 32-bit PowerPC, 32-bit x86, and 64-bit x86 binaries. If you want to build universal binaries with a different combination of CPU architectures, then you can specify it as an optional argument to the --enable-universal-binary option. For example, universal binaries will be built with i386, ppc, x86_64 and ppc64 architectures in the following example:

./configure --enable-universal-binary="-arch i386 -arch ppc -arch x86_64 -arch ppc64"

Beware that building with this option turn on results in the creation of larger libSBML binary files, because the files contain essentially two copies of the same code (one for each architecture).

Finally, if both --enable-universal-binary and either --enable-m32 or --enable-m64 are given, the latter two options are ignored and the option for universal binaries takes precedence. This is justified because, on Mac OS X, the optional argument to --enable-universal-binary can be used to accomplish the same goals as the two other individual options.

1.2.e Configuring for SWIG

Important: libSBML is known to work with SWIG version 2.0.0 or later; earlier versions are known not to work. You must use version 2.0.0 or later.

SWIG is the Simplified Wrapper and Interface Generator and in libSBML it is used to create the bindings for C#, Java, JavaScript, Python, and other programming languages. To configure libSBML to use SWIG, use the --with-swig option to configure. If your copy of SWIG is installed in a location where configure cannot find it on its own, you can specify it as an optional argument to the --with-swig option as in the following example:

./configure --with-swig="DIR"

1.2.f Configuring support for compression

LibSBML provides built-in support for reading and writing compressed SBML files. This facility works transparently: if a given SBML filename ends with one of the suffixes recognized for a compressed file (namely, .gz, .zip, or .bz2), the libSBML readSBML() method will automatically decompress the file upon reading it and the writeSBML() method will compress the file upon writing it. (Files whose names have no extensions are read and written in uncompressed form.)

These features are enabled by default if the required libraries can be found on your system. The libraries are the zlib library (for the gzip and zip formats) and the bzip2 library (for the bzip2 format). If the libSBML configure program cannot find the libraries in the locations where it searches by default, you can inform the configure program where to look by adding the flag --with-zlib=DIR where DIR is the parent directory of the lib directory where the zlib library is located, and/or the flag --with-bzip2=DIR where DIR is the parent directory of the lib directory where the bzip2 library is located.

To selectively disable specific library checks and format support, add the option --with-zlib=no and/or --with-bzip2=no to the configure program invocation. Or, to completely disable compression support and checking for both libraries, add the --enable-compression=no option to configure:

./configure --enable-compression=no

1.2.g Configuring for generating documentation

LibSBML comes with extensive documentation, and the document you are currently reading is part of it. Because the documentation is large and regenerating it requires the use of software tools that not all users may have, the authors of libSBML supply a separate downloadable archive containing only the documentation. The documentation archive file has a name of the form libsbml-VERSION-docs.zip, where VERSION is the version of libSBML. After you download it, you can simply unzip the file in the same location as your libSBML source directory (or alternatively, in any other location that suits you). We recommend downloading the ready-made documentation archive as the easiest way to get the libSBML documentation.

The same documentation files should also be available online at http://sbml.org/Software/libSBML/, although this online copy normally corresponds to the last stable release of libSBML and may not be up-to-date with the latest development version of libSBML in the SVN repository on SourceForge.

If you would like to generate the documentation yourself, you will need the following software tools in addition to a Unix-like environment (or Cygwin under Windows):

• For the C, C++ and Python API documentation: You will need Doxygen version 1.8.4 or later and a reasonably complete installation of LaTeX. You will also need to configure libSBML to use Doxygen by supplying the option --with-doxygen to the configure program. Tip for Macintosh users: if you are on a Mac OS X system and you installed the binary distribution of Doxygen from the .dmg image provided by Doxygen's author, you will need to point configure to the doxygen executable inside the package for Doxygen:

  ./configure --with-doxygen=/Applications/Doxygen.app/Contents/Resources
  

• For the Java API documentation: You will need Javadoc version 1.5 (also known as version 5.0, confusingly enough), which should have come supplied with your installation of Java 1.5 or later. No additional configuration of libSBML is needed beyond supplying the --with-java option to configure.

Once libSBML is configured as above, you can generate the documentation files by running make docs from the top level of the libSBML source directory to regenerate all the documentation files. Alternatively, you can moving to the docs/src subdirectory and execute

make java-manual           # Note: use 'gmake java-manual' on FreeBSD

to recreate just the Java documentation, or

make cpp-manual            # Note: use 'gmake cpp-manual' on FreeBSD

to recreate just the C++ documentation, or

make c-manual              # Note: use 'gmake c-manual' on FreeBSD

to recreate just the C documentation, or

make python-manual         # Note: use 'gmake python-manual' on FreeBSD

to recreate just the Python documentation.

1.2.h Configuring for software unit testing

libSBML provides built-in facilities for testing itself. To run the unit tests, a second library is required, libcheck (version 0.9.2 or higher). Check is a very lightweight C unit test framework based on the xUnit framework popularized by Kent Beck and eXtreme Programming. Check is quite small and once installed, it consists of only two files: libcheck.a and check.h. To install Check, you may first want to examine whether it is easily available via a software package manager for your system (e.g., Synaptic under Ubuntu Linux, MacPorts or Fink under Mac OS X, etc.); if not, you can also download Check from http://check.sf.net/.

(Note: If you are using g++ version 3.3, you will need to avoid using Check version 0.9.5, and instead use version 0.9.2. The problem is an incompatibility between Check 0.9.5 and earlier versions of g++. It appears that the compatibility problems in Check 0.9.5 disappear with versions of g++ after 3.3.)

To enable the unit testing facilities in libSBML, add the --with-check flag to the configure command:

./configure --with-check

Following this, you must build libSBML and then you can run the tests:

make                   # Note: use 'gmake' on FreeBSD
make check             # Note: use 'gmake check' on FreeBSD

The make check step is optional and will build and run an extensive suite of unit tests to verify all facets of the library. These tests are meant primarily for developers of libSBML and running them is not required for the library to function properly. All tests should pass with no failures or errors. If for some reason this is not the case on your system, please submit a bug report using the mechanisms described in the section titled "Bug Reports, Mailing Lists, and Related Topics" elsewhere in this manual.

1.3 Compiling and installing libSBML

After the configuration step (and if you are using CMake, the generation of the makefiles), the final steps are to run the compilation process followed by a command to install libSBML on your system.

1.3.a Using CMake

If you are using CMake, then in a terminal/shell window, first cd into the "build" directory that you indicated to CMake in the second line of the CMake GUI during the configuration step described in Section 1.1, Configuring using CMake above. For instance, if your "build" directory is simply named build and you placed it in a subdirectory of the libSBML source directory (let SRC stand for that directory), you would simply do the following:

cd SRC/build

Next, execute the following command to compile libSBML:

make                # Note: use 'gmake' on FreeBSD

If all went well and libSBML compiled without errors, you can use the following command to install libSBML on your computer:

sudo make install   # Note: use 'sudo gmake install' on FreeBSD

Once the libSBML files are installed as described above, you may need to perform additional steps so that software can find the libSBML library files at run time. Please see the instructions in the section on making libSBML accessible to your software, provided elsewhere in this documentation.

1.3.b Using GNU make

Important: parallel GNU make builds of libSBML are not supported at this time. Attempting to use the -j option with make will not work properly and will not complete, but will also not produce diagnostics that indicate the cause of the failure (thus making it difficult to understand what went wrong). Do not use the -j option with GNU make.

If you are using GNU make and not using CMake, in a terminal/shell window, cd to the top level of the libSBML source directory. In the following example, let SRC stand for that directory:

cd SRC

Next, execute the following commands to compile libSBML:

make                # Note: use 'gmake' on FreeBSD

If all went well and libSBML compiled without errors, you can use the following command to install libSBML on your computer:

sudo make install   # Note: use 'sudo gmake install' on FreeBSD

Once the libSBML files are installed as described in the sections above, you may need to perform additional steps so that software can find the libSBML library files at run time. Please see the separate section on making libSBML accessible to your software provided elsewhere in this documentation.

1.3.c Debugging build problems

If something went wrong during the build step and the compilation of libSBML stopped with an error, it may be useful to get more information in order to debug the process.

• If you use CMake: When building libSBML with CMake, you can easily run the build with verbose debugging output by giving the argument VERBOSE=1 in the make step:

  make VERBOSE=1
  

• If you use GNU make: When building libSBML with GNU make, you can use the argument --debug=b to get additional debugging information without the overwhelming amount of output produced by make -d. In other words, you can use the following command:

  make --debug=b
  

If you need to contact the libSBML Team for help with debugging a failing libSBML build, it will greatly help us to get a record of the debugging output from a clean build. On Linux, Mac OS X and Cygwin, you can use the convenient script command to record input and output in a terminal shell, and then email us the output.

• If you use CMake:

  make clean          # Clean everything to get a fresh build
  script              # Start recording everything in the shell
  make VERBOSE=1      # Build with debugging on
  exit                # Stop recording the script
  

• If you use GNU make:

  make clean          # Clean everything to get a fresh build
  script              # Start recording everything in the shell
  make --debug=b      # Build with debugging on
  exit                # Stop recording the script
  

Don't forget to type exit!

Once you type exit, the script command will stop and leave a file named "typescript" in the current directory. Please include the "typescript" when contacting the libSBML Team with questions about build failures.

1.4 Advanced configuration options

Whether you use CMake or GNU make, there are some additional advanced options that are uncommonly used, but still worth explaining. We list the options below using their names as they appear in the CMake configuration screen; the alternative configure approach uses slightly different command-line flag names, but still similar to the names below.

• LIBSBML_SHARED_VERSION: This flag controls whether the version number should be written into the libSBML shared library.
• LIBSBML_USE_STRICT_INCLUDES: This flag is intended for libSBML developers; it permits faster recompilation of libSBML by reducing the files that are #include'd in certain ways, such that changing a single libSBML class does not cause as many dependencies to be triggered. This option makes no difference to compilation except when you make changes to libSBML class definitions and recompile libSBML, so there is no advantage for regular user code to enable this option.

2. Procedures for Windows

There are two ways to compile libSBML under Windows: using the native Windows compilation tools from Microsoft, and using the Cygwin environment. In this section, we focus on using the native Windows environment because this appears to be the more popular approach used by Windows-based users of libSBML. Cygwin users can follow essentially the same instructions as for other Unix environments given above.

2.1 Configuring using CMake

To create configurations suitable for compiling libSBML using the native Windows build tools, we recommend using CMake to generate them. (If you do not already have CMake installed on your system, please begin by downloading a copy of CMake version 2.8.4 or later from cmake.org.) Once you have CMake installed, also download and unzip the libSBML source code archive from the download area on GitHub.net and save the archive somewhere on your file system, then unpack it.

Before going further, an issue on Windows concerns the dependency libraries on which libSBML depends. CMake will try to find all the dependencies for the default options, which leads to problems if they do not exist. We recommend Windows users download the dependencies we have prepackaged at the following download location:

https://sourceforge.net/projects/sbml/files/libsbml/win-dependencies

Download and extract this file into the same folder where you unpacked the libSBML source distribution. CMake will look for these dependencies in a folder called dependencies directly below the libSBML root folder.

Once you have the libSBML sources and the dependency libraries unpacked on your system, start up the CMake graphical user interface (GUI). It will look something like the following screenshot:

Screenshot of CMake when it first starts up.

Click on the Browse Source... button and navigate to the directory where you unpacked the libSBML source code archive on your file system. CMake should automatically fill in the next line, Where to build the binaries, using a subdirectory named build within the directory where your source code is located. (If it does not, fill in the field in the CMake interface yourself.) Then, click on the Configure button. CMake should display a dialog similar to the following.

Screenshot of the Configure screen under Microsoft Windows 7. Choose the settings appropriate for the build environment you are using and click the Finish button.

After you close the configuration screen, CMake will populate the options area with various options it reads from the libSBML configuration files. These new options are displayed in red, as illustrated in the following screenshot.

Screenshot of the CMake interface after the configuration step.

In this panel, you can set values for various libSBML configuration/build options. For example, you can set the location into which the compiled libSBML libraries will be installed by clicking on the line for CMAKE_INSTALL_PREFIX and replacing the default value with a value of your choosing. To find out the meaning of a particular option, hover your mouse/pointer over the item for a few seconds until the tooltip text appears.

Select the options with which you wish to build libSBML. All the options for configuring libSBML, including language bindings and SBML Level 3 packages, are listed here and may be selected/deselected as required. For instance, to include the Java language bindings, click the check-box for WITH_JAVA. Once you are done configuring, click on CMake's Configure button. CMake will process the configuration, and if it lacks any information, it will highlight the options in red. You may need to iterate between setting options and clicking the Configure button until there are no options left in red and the Generate button becomes enabled.

Next, click on the Generate button. This will cause CMake to create project configuration files ("Solutions") for the compilation environment you selected in the beginning (e.g., Visual Studio 2010).

2.2 Compiling and installing using MSVC

The MSVC Solution will contain a number of projects files, depending on the configuration selected. The following screenshot illustrates what you should see when you use the Solution Explorer in MSVC, and some of the most important targets that you will find there:

Screenshot of MSVC's Solution Explorer when viewing the MSVC Solution files generated using CMake.

• ALL_BUILD: This target builds all the libSBML project files; that is, all projects except the ones that involve installation, packaging or testing.
• INSTALL: This target will install the compiled binaries to the directory specified for the CMAKE_INSTALL_PREFIX option of the CMake configuration step.
• ZERO_CHECK: This target is merely a verification project; it is used to check whether there have been any changes to the configuration since the last time it was run. It is invoked automatically whenever any other target is being built.
• PACKAGE: This target creates binary installers for libSBML. If the Nullsoft scriptable installation system, NSIS (http://nsis.sf.net) is available, an installer is created for the current platform. Most users will not need to use this build target/Solution.
• RUN_TESTS: This target can be used to test all the libraries built. It is only available if the WITH_CHECK option is selected during the CMake configuration step. (Note: the libcheck library upon which this facility depends is incompatible with MSVC 7, so you will need to use a newer version of MSVC if you want to try RUN_TESTS.) The checks will fail if Windows is unable to locate the dynamic libraries, or for each language binding if it is unable to locate both the binding library and the libSBML native library.

Other projects generated by the libSBML CMake configuration system and listed in the MSVC Solution explorer are named to indicate the intended target. Some examples include the following:

• binding_python_lib: builds the Python language bindings _libsbml.pyd file.
• binding_java_classes: builds the Java language bindings class JAR file.
• example_c_convertSBML: builds the convertSBML example program in C.
• example_java_addCVTerms: builds the addCVTerms example program in Java.
• test_sbml_math: builds the tests in the libSBML src/math subdirectory.

A typical procedure for building libSBML using MSVC consistes of performing the following steps:

1. Select and run the ALL_BUILD target. After a successful build, MSVC will put the libSBML library files and DLL into the Release subdirectory of the location specified using CMake. This includes the language bindings, which will be placed in a subdirectory of the Release directory. For example, C# files will appear in Release/csharp.
2. Select and run the INSTALL target. This will install the compiled libSBML library and associated files into the directory determined by the CMAKE_INSTALL_PREFIX CMake configuration variable.

Once the libSBML files are installed as described in the sections above, you may need to perform additional steps so that software can find the libSBML library files at run time. Please see the instructions on Making libSBML accessible to your software provided on a separate page of this documentation.

3. Files installed by libSBML, and their locations

If all went as it should, the libSBML object files should end up compiled and installed on your system, in either the default location (/usr/local/) or in the location you indicated during the configuration step as explained above. The core libSBML library object files will have slightly different names depending on the operating system in use. The following table summarizes the possibilities:

	Names of core libSBML object files
Type of file	Linux/Unix-based OS	Mac OS X	Windows
Dynamically-linked	libsbml.so.5	libsbml.5.dylib	libsbml.dll
Statically-linked	libsbml.a	libsbml.a	libsbml.lib
Libtool control file	libsbml.la	libsbml.la	N/A

If you have compiled additional language extensions with libSBML, these files will be installed as well, but their names and locations depend on the particular language extension. The following two tables summarize the possibilities. The first table lists the names of the files, while the second table below lists the pathnames where those files will be installed.

Legend: N/A = not available.

		Names of language extension object files
Language		Linux/Unix-based OS	Mac OS X	Windows
C#	(unmanaged C++ DLL) (managed C# DLL)	libsbmlcs.so libsbmlcsP.dll	libsbmlcs.so libsbmlcsP.dll	libsbmlcs.dll libsbmlcsP.dll
Java	(native C++ library) (Java JAR file)	libsbmlj.so libsbmlj.jar	libsbmlj.jnilib libsbmlj.jar	sbmlj.dll libsbmlj.jar
JavaScript	(Node.js module)	sbml.node	sbml.node	sbml.node
MATLAB	(Intel 32-bit)	TranslateSBML.mexglx OutputSBML.mexglx	TranslateSBML.mexmaci OutputSBML.mexmaci	TranslateSBML.mexw32 OutputSBML.mexw32
	(Intel 64-bit)	TranslateSBML.mexa64 OutputSBML.mexa64	TranslateSBML.mexmaci64 OutputSBML.mexmaci64	TranslateSBML.mexw64 OutputSBML.mexw64
	(PPC)	N/A	TranslateSBML.mexmac OutputSBML.mexmac	N/A
	(Additional files)	CheckAndConvert.m Contents.m ConvertFormulaToMathML.m isSBML_Model.m isoctave.m	CheckAndConvert.m Contents.m ConvertFormulaToMathML.m isSBML_Model.m isoctave.m	CheckAndConvert.m Contents.m ConvertFormulaToMathML.m isSBML_Model.m isoctave.m
Octave		TranslateSBML.mex OutputSBML.mex CheckAndConvert.m Contents.m ConvertFormulaToMathML.m isSBML_Model.m isoctave.m	TranslateSBML.mex OutputSBML.mex CheckAndConvert.m Contents.m ConvertFormulaToMathML.m isSBML_Model.m isoctave.m	TranslateSBML.mex OutputSBML.mex CheckAndConvert.m Contents.m ConvertFormulaToMathML.m isSBML_Model.m isoctave.m
Perl	(native C++ library) (Perl module file) (Other files)	LibSBML.so LibSBML.pm LibSBML.pod .packlist	LibSBML.bundle LibSBML.pm LibSBML.pod .packlist	LibSBML.dll LibSBML.pm LibSBML.pod .packlist
Python 2.3–2.4	(native C++ library) (Python module file) (Compiled module file) (Path configuration file)	_libsbml.so libsbml.py libsbml.pyc libsbml.pth	_libsbml.so libsbml.py libsbml.pyc libsbml.pth	_libsbml.dll libsbml.py libsbml.pyc libsbml.pth
Python 2.5–2.7	(native C++ library) (Python module file) (Compiled module file) (Path configuration file)	_libsbml.so libsbml.py libsbml.pyc libsbml.pth	_libsbml.so libsbml.py libsbml.pyc libsbml.pth	_libsbml.pyd libsbml.py libsbml.pyc libsbml.pth
R		libSBML.rdb libSBML.rdx libSBML	libSBML.rdb libSBML.rdx libSBML.so	libSBML.rdb libSBML.rdx libSBML.dll
Ruby		libSBML.so	libSBML.bundle	libSBML.dll

The next table gives the locations of the files listed in the table above for Linux/Unix-based operating systems. The pathnames shown here are relative to the prefix directory used in configuring libSBML (meaning the value DIR given to the --prefix=DIR option to the configure program discussed above).

Legend: The placeholder platform stands for a platform-specific directory name; the exact string depends on the combination of your operating system, machine architecture, programming language, and the versions of all of these. The placeholder perl-version refers to the version number of the Perl executable against which libSBML was configured. The placeholder python-version refers to the version number of the Python executable against which libSBML was configured. The placeholder ruby-version refers to the version number of the Ruby executable against which libSBML was configured. Note that none of these values are actually under the control of libSBML; they are set by the operating system and programming language package conventions.

Additional notes:
(1) The Octave installation directory actually depends on how Octave was configured at build time. If your installation of Octave came as a precompiled binary, the package directory may in fact be different from what is shown here.
(2) The directory component lib may be replaced by lib64 on some 64-bit operating systems (e.g., CentOS 5.2 x86-64).

Language		Directories	Notes
C#	(unmanaged C++ DLL) (managed C# DLL)	DIR/lib/mono/libsbmlcsP/ DIR/lib/mono/libsbmlcsP/
Java	(native C++ library) (Java JAR file)	DIR/lib/ DIR/share/java/
JavaScript		DIR/lib/node/
MATLAB		DIR/lib/
Octave		DIR/lib/octave/site/oct/platform/	(1)
Perl	(native C++ library) (Perl module file) (Other files)	DIR/lib/perl5/site_perl/perl-version/platform/auto/libSBML/ DIR/lib/perl5/site_perl/perl-version/platform/ DIR/lib/perl5/site_perl/perl-version/platform/	(2)
Python (Ubuntu)	(native C++ library) (Python module file) (Compiled module file) (Path configuration file)	DIR/lib/python-version/dist-packages/libsbml/ DIR/lib/python-version/dist-packages/libsbml/ DIR/lib/python-version/dist-packages/libsbml/ DIR/lib/python-version/dist-packages/
Python (Other Linux distributions)	(native C++ library) (Python module file) (Compiled module file) (Path configuration file)	DIR/lib/python-version/site-packages/libsbml/ DIR/lib/python-version/site-packages/libsbml/ DIR/lib/python-version/site-packages/libsbml/ DIR/lib/python-version/site-packages/	(2)
R		DIR/lib/R/site-library/libSBML/
Ruby		DIR/lib/ruby/site_ruby/ruby-version/platform/

4. What to do if problems arise

Given the large number of variables that are involved in installing libSBML (e.g., operating systems versions, library versions, etc.), it is not impossible that issues arise when you try to get libSBML working. We offer the following tips for what to do if you encounter problems:

1. Check the list of known issues elsewhere in this manual. There, we try to describe the known problems, limitations and possible pitfalls in using libSBML.
2. Ask for help on the libSBML and SBML mailing lists.
3. Contact the developers directly by sending email to libsbml-team@googlegroups.com. Please make sure to include the following information:
   • The version of libSBML you are using,
   • The operating system, and operating system version, that you are using,
   • The programming language you are using,
   • A description of what you are trying to do, and
   • A copy of any error messages or other diagnostic messages printed by libSBML or your compiler or any other software involved in the problem. If the problem occurs while compiling libSBML, please follow the instructions in section 1.3.c Debugging build problems on how to produce a record of the output produced during compilation.