Hello,
I am new to R and I having some issues installing packages. I am trying to install DESeq2 and I am getting and error when installing the dependency 'RcppArmadillo':
install.packages("RcppArmadillo")
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [RcppArmadillo.so] Error 1
ERROR: compilation failed for package 'RcppArmadillo'
- removing '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RcppArmadillo'
Could you please help me?
Some info: I use OSX el Capitan 10.11.
R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
Platform: x86_64-apple-darwin13.4.0 (64-bit)
R Studio Version 0.99.489
Thanks a lot,
Isabel
I am also having the same problem with DESeq2 (returning a non-zero exit status), even though I use biocLite. I have also tried to install RcppArmadillo independently from R (on the command line), but I get an error message that says I need to use a different compiler.
Many of the suggestions that I have seen, including the reply above this one, suggest using sudo; however, I do not have root privileges. I do have a work around. I could use my current institute's server, but the project is for my previous institute. It would just be nice to understand why I'm having such troubles.
Thank you.