Linking against RNAlib

In order to use our implemented algorithms you simply need to link your program to our RNAlib C-library that usually comes along with the ViennaRNA Package installation. If you’ve installed the ViennaRNA Package as a pre-build binary package, you probably need the corresponding development package, e.g. viennarna-devel, or viennarna-dev. The only thing that is left is to include the ViennaRNA header files into your source code, e.g.:

#include <ViennaRNA/mfe.h>

and start using our fast and efficient algorithm implementations.

Compiler and Linker flags

Of course, simply adding the ViennaRNA header files into your source code is usually not enough. You probably need to tell your compiler where to find the header files, and sometimes add additional pre-processor directives. Whenever your installation of RNAlib was build with default settings and the header files were installed into their default location, a simple:

-I/usr/include

pre-processor/compile flag should suffice. It can even be omitted in this case, since your compiler should search this directory by default anyway. You only need to change the path from /usr/include to the correct location whenever the header files have been installed into a non-standard directory.

If you’ve compiled RNAlib with some non-default settings then you probably need to define some additional pre-processor macros:

VRNA_DISABLE_C11_FEATURES … Disable C11/C++11 features.

Warning

Add this directive to your pre-processor/compile flags only if RNAlib was build with the --disable-c11 configure option.

See also…

Disable C11/C++11 features and vrna_C11_features()
VRNA_WARN_DEPRECATED … Enable warnings for using deprecated symbols.

Note

Adding this directive enables compiler warnings whenever you use symbols in RNAlib that are marked deprecated.

See also…

Deprecated symbols and Deprecated List
USE_FLOAT_PF … Use single precision floating point operations instead of double precision in partition function computations.

Warning

Define this macro only if RNAlib was build with the --enable-floatpf configure option!

See also…

Single precision

For instance, you might want to add the following definition(s) to your pre-processor/compile flags:

-DVRNA_DISABLE_C11_FEATURES

Finally, linking against RNAlib is achieved by adding the following linker flag:

-L/usr/lib -lRNA -flto -fopenmp

Again, the path to the library, /usr/lib, may be omitted if this path is searched for libraries by default. The second flag tells the linker to include libRNA.a, and the remaining two flags activate Link Time Optimization and OpenMP support, respectively.

Note

Depending on your linker, the last two flags may differ.

Depending on your configure time decisions, you can drop one or both of the last flags.

In case you’ve compiled RNAlib with LTO support (See Link Time Optimization) and you are using a different compiler for your third-party project that links against our library, you may add the -fno-lto flag to disable Link Time Optimization.

The pkg-config tool

Instead of hard-coding the required compiler and linker flags, you can also let the pkg-config tool automatically determine the required flags. This tool is usually packaged for any Linux distribution and should be available for MacOS X and MinGW as well. We ship a file RNAlib2.pc which is installed along with the static libRNA.a C-library and populated with all required compiler and linker flags that correspond to your configure time decisions.

The compiler flags required for properly building your code that uses RNAlib can be easily obtained via:

pkg-config --cflags RNAlib2

You get the corresponding linker flags using:

pkg-config --libs RNAlib2

With this widely accepted standard it is also very easy to integrate RNAlib in your autotools project, just have a look at the PKG_CHECK_MODULES macro.