Dealing with dependency without sudo like a dummy (again)

The more I work with Linux, the more I encounter dependency issues. This is of course not too big a surprise, but it can be painful especially when you aren’t sudo, so the most obvious solution does not work for you.

Don’t misunderstand me. sudo is definitely not something to play with when we don’t know what we are doing, and access control does a terrific job preventing me from shooting my own foot (or worse, other’s foot) from time to time. It is just that it also prevents me from shooting something that ought to be shot.

In terms of dependency, my usual workaround is to install things locally in $HOME/.local. I think this is also the default place R and Python turn to when installing packages locally. This should work just fine if I remember to add $HOME/.local/bin to my $PATH. Unfortunately, if you not only use something but also have to compile it from time to time, there’s more things to worry about.

Generally, my compilation fails when there are some shared library is missing, and as someone who is totally green in this, some files that are often missing are shared object (.so) files and header files (.h). They would usually be mentioned in the error messages when your compilation fails. In some cases, package configuration files (.pc) would also be gone.

The following suggestions might work if you have actually installed the required library but make failed to find it:

  • If a .so file is missing, try:
    ./configure LDFLAGS="-L [where your library is]" (Example path: $HOME/.local/lib)
  • If a .h file is missing, try:
    CPPFLAGS=”-I [where your library is]” (Example path: $HOME/.local/include)
PhD Student

A graduate student interested in developmental biology, neurobiology and bioinformatics.