I am trying to use the igraph package, my functions run just fine under R, but when I add igraph to Jamovi, after many lines of successful build commands, is see this error:
ld: warning: directory not found for option '-L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.5'
ld: warning: directory not found for option '-L/opt/local/lib/gcc48'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [igraph.so] Error 1
ERROR: compilation failed for package ‘igraph’
* removing '.../casnet-jmvMAC/build/R/igraph’
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync.
Falling back to library file for linking. installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/igraph/libs
oh yup. at the moment we're maintain compatibility with macOS mavericks ... (but probably not for too much longer). so you'll need a version of gfortran compatible with mavericks. i'm using 4.8.2
so the R we ship with the macOS version of jamovi is 3.3, where as proxy requires R >= 3.4
in these situations, it's easiest to modify proxy, remove the >= 3.4, install it locally using a matching version of R (3.3.0 for mavericks), then copy the built package to build/R
i appreciate this is a bit of a pain. we will update the R version with ship with macOS at some point, but you wouldn't believe how painful it is to modify R (on macOS) so it can be bundled with an application!
(won't be an issue on windows, we ship 3.4 for that, and 3.5 for linux.)
I found an alternative for proxy so it is not urgent, though at some point I'll want to use it again.
Then the easiest solution will be to install R as if it were the good old Mavericks days , with gfortran 4.8.2
Could be useful to have an 'R setup recommendation' for developers , and if such a thing already exists & I missed it, I will go hide in shame and stop asking for help (for a while )