12 Installation Help

Below are some common errors you may run into when attempting to install or run vcfdist.

If you encounter any problems not listed below, please open a new issue.

Failure to compile on Mac

On Mac devices, g++ is aliased to clang, which is not supported (in versions prior to v2.4.0). Please install g++ through homebrew.

Errors with libstdc++fs

Older versions of vcfdist (prior to v2.4.0) use libstdc++fs. Although std::filesystem is officially part of the C++17 standard library, g++ < 9.1 and llvm < 9.0 require linking to -lstdc++fs during compilation. If you're using g++ < 9.1, please add -lstdc++fs to LDFLAGS in src/Makefile before running make.

Errors while loading shared libraries

You may encounter the following error while trying to run vcfdist:

vcfdist: error while loading shared libraries: libhts.so.2to3part12: cannot open shared object file: No such file or directory

This occurs because the HTSlib library cannot be found. If you have installed HTSlib in /usr/local, add /usr/local/lib to your linker's library path:

export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

Optionally, you can add this export to your .bashrc file so that HTSlib is always discoverable:

echo "export LD_LIBRARY_PATH=/usr/local/lib:\$LD_LIBRARY_PATH" >> ~/.bashrc

Please note the escape \ character before $, and use of >> to append to your .bashrc (NOT >, which will overwrite the file).