Rcpp warning: “directory not found for option '-L/usr/local/Cellar/gfortran/4.8.2/gfortran'”

Question

This question relates to some others out there, like RccpArmadillo or element-wise-multiplication.

However, my settings are such that I do not know what I have to ed

Answer 1

Short Answer

Just put the path to libgfortran into FLIBS, e.g.

FLIBS=-L/opt/local/lib/gcc48/

Or, symlink the files within to /usr/local/lib/, if you're comfortable with that. This solution is, however, quite brittle as it's easy to forget to update this path if you update gfortran, or move it to a different directory.

Slightly Longer Answer

You can query gfortran for the path to libgfortran.dylib as e.g.

gfortran -print-file-name=libgfortran.dylib

You can just execute this directly in your Makevars file; e.g.

FLIBS = -L`gfortran -print-file-name=libgfortran.dylib | xargs dirname`

---

Obsolete Long Answer

Try parsing an appropriate FLIBS directly from gfortran output.

First, some background. The /usr/local/Cellar directory is the default path used by homebrew, a package manager for OS X. Think of it as an alternative to macports.

Homebrew now provides gfortran and its associated libraries as part of the gcc package, and so the paths where it installs FORTRAN libraries has now changed. However, these can (in general) be discovered using gfortran -print-search-dirs. For example, on my system,

gfortran -print-search-dirs

will give me

install: /usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/
programs: =/usr/local/Cellar/gcc/4.9.2_1/libexec/gcc/x86_64-apple-darwin14.0.0/4.9.2/:/usr/local/Cellar/gcc/4.9.2_1/libexec/gcc/x86_64-apple-darwin14.0.0/4.9.2/:/usr/local/Cellar/gcc/4.9.2_1/libexec/gcc/x86_64-apple-darwin14.0.0/:/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/:/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/:/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../../../../x86_64-apple-darwin14.0.0/bin/x86_64-apple-darwin14.0.0/4.9.2/:/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../../../../x86_64-apple-darwin14.0.0/bin/
libraries: =/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/:/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../../../../x86_64-apple-darwin14.0.0/lib/x86_64-apple-darwin14.0.0/4.9.2/:/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../../../../x86_64-apple-darwin14.0.0/lib/:/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../x86_64-apple-darwin14.0.0/4.9.2/:/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../:/lib/x86_64-apple-darwin14.0.0/4.9.2/:/lib/:/usr/lib/x86_64-apple-darwin14.0.0/4.9.2/:/usr/lib/

Split, and printed with R, I see:

[[1]]
[1] "/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/"

[[2]]
[1] "/usr/local/Cellar/gcc/4.9.2_1/libexec/gcc/x86_64-apple-darwin14.0.0/4.9.2/"                                                                                    
[2] "/usr/local/Cellar/gcc/4.9.2_1/libexec/gcc/x86_64-apple-darwin14.0.0/4.9.2/"                                                                                    
[3] "/usr/local/Cellar/gcc/4.9.2_1/libexec/gcc/x86_64-apple-darwin14.0.0/"                                                                                          
[4] "/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/"                                                                                
[5] "/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/"                                                                                      
[6] "/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../../../../x86_64-apple-darwin14.0.0/bin/x86_64-apple-darwin14.0.0/4.9.2/"
[7] "/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../../../../x86_64-apple-darwin14.0.0/bin/"                                

[[3]]
[1] "/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/"                                                                                
[2] "/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../../../../x86_64-apple-darwin14.0.0/lib/x86_64-apple-darwin14.0.0/4.9.2/"
[3] "/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../../../../x86_64-apple-darwin14.0.0/lib/"                                
[4] "/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../x86_64-apple-darwin14.0.0/4.9.2/"                                       
[5] "/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../"                                                                       
[6] "/lib/x86_64-apple-darwin14.0.0/4.9.2/"                                                                                                                         
[7] "/lib/"                                                                                                                                                         
[8] "/usr/lib/x86_64-apple-darwin14.0.0/4.9.2/"                                                                                                                     
[9] "/usr/lib/"  

In my case, libgfortran actually lives here:

/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../

And so this is the path we want to pass to FLIBS. But, pulling that out is kind of a pain, so let's just tell FLIBS to use whatever paths are normally used by gfortran:

gfortran -print-search-dirs | grep ^libraries: | sed 's|libraries: =||'

This is nice, but we want the library paths in a format suitable for the compiler; ie, with -L prepended. Let's do that with sed:

gfortran -print-search-dirs | grep ^libraries: | sed 's|libraries: =||' | sed 's|:| -L|g' | sed 's|^|-L|'

This outputs (split for readability)

-L/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/
-L/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../../../../x86_64-apple-darwin14.0.0/lib/x86_64-apple-darwin14.0.0/4.9.2/
-L/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../../../../x86_64-apple-darwin14.0.0/lib/
-L/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../x86_64-apple-darwin14.0.0/4.9.2/
-L/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9/gcc/x86_64-apple-darwin14.0.0/4.9.2/../../../
-L/lib/x86_64-apple-darwin14.0.0/4.9.2/
-L/lib/
-L/usr/lib/x86_64-apple-darwin14.0.0/4.9.2/
-L/usr/lib/

All together, this implies that the following should work for you, at least on OS X, but should (in general) work on any platform with gfortran (as long as it's on the PATH):

FLIBS=`gfortran -print-search-dirs | grep ^libraries: | sed 's|libraries: =||' | sed 's|:| -L|g' | sed 's|^|-L|'`

This isn't perfect, e.g. it will fail if you have spaces in your paths -- if you do, 1) you deserve what you get and 2) it should also be a 'relatively' easy fix.

Answer 2

A small tweak to the answer from @kevin-ushey (that at least I needed; I use Prezto) was adding single quotes to grep '^libraries:', resulting in:

FLIBS=`gfortran -print-search-dirs | grep '^libraries:' | sed 's|libraries: =||' | sed 's|:| -L|g' | sed 's|^|-L|'`

Adding that line to my ~/.R/Makevars file did the trick!