Every once in a while, I’ll import an R or Python library and I’ll get an error telling me that it can’t find some scary fortran library. This happened in R:

library(lme4)
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Users/your_username/Rlibs/minqa/libs/minqa.so':
  dlopen(/Users/your_username/Rlibs/minqa/libs/minqa.so, 6):
   Library not loaded: /usr/local/lib/gcc/4.9/libgfortran.3.dylib
  Referenced from: /Users/your_username/Rlibs/minqa/libs/minqa.so
  Reason: image not found

If I really needed that library I would either cry and/or try to uninstall and install everything again, hoping things would get solved. I eventually learned the proper fix, so I though I’d share it with you. I use a Mac, but I’m guessing very similar (if not the same) steps apply for Linux.

The usual problem is that you have the dynamic library (dylib) but the compiled .so file is looking at it in the wrong place.

For this example, let’s look at minqa.so, which is trying to find libgfortran.3.dylib in gcc/4.9/.

To check the references of minqa.so, we run on the terminal:

otool -L minqa.so

which printed:

minqa.so:
	minqa.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/local/lib/gcc/4.9/libgfortran.3.dylib (compatibility version 4.0.0, current version 4.0.0)
	/usr/local/lib/gcc/4.9/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)

Ok. I looked at my lib/gcc folder and realized I had version 5, not 4.9. The libgfortran3.dylib was there in the 5 folder. How can I communicate the good news to minqa.so?

install_name_tool -change /usr/local/lib/gcc/4.9/libgfortran.3.dylib
   /usr/local/lib/gcc/5/libgfortran.3.dylib minqa.so

You might need to put sudo before that command. In general the syntax is

install_name_tool -change old_location new_location file_you_wanna_change.so

If you don’t know where the dylib library is, you can search for it with Spotlight or with locate on the command line.

Also, sometimes the dylib won’t even have a location and the otool step will output only libgfortran.3.dylib. The same steps above apply, but the old_location will just be the name of the dynamic library.

You can read more about this issue in this stackoverflow question