Installing HMSC
Breckie opened this issue · comments
Hello,
I am having trouble installing HMSC through Rstudio (Version 1.0.136).
Initially, just using install.packages(), I receive the error "Warning in install.packages :
package ‘HMSC’ is not available (for R version 3.3.2)".
My standard workaround for this, is to install directly from github, which is how I found your repository:
library(devtools)
install_github("guiblanchet/HMSC")
This installs for quite a while, but ends with the error:
"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: *** [HMSC.so] Error 1
ERROR: compilation failed for package ‘HMSC’
- removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/HMSC’
Error: Command failed (1)
When looking into this error, I also tried installing "Rcpp" and "RcppArmadillo" before installing via "guiblanchet/HMSC", with the same result.
Then I found this article http://thecoatlessprofessor.com/programming/rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error/
which seemed promising, but neither running
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
...through Terminal, nor following this help comment:
"Could you close out all R sessions (including RStudio), open Terminal and type:
xcode-select --install
This ensures that you have development command line tools (e. g. gcc, git, et cetera) on your system.
Please run:
git --version
To make sure the license agreements have been approved.
From there, I'd like you to try to install the gfortran binaries by again repeating:
curl -O http://r.research.att.com/l...
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
...got me any closer. I apologize for bothering you with such a mundane issue, but I believe I have a great data set to use with this package and I am excited to try it out.
Thanks!
Sorry it took me so long to answer you, I have been trying to solve the problem you presented here.
From your message, I gather that you are working under Mac OS X and that your problem is mainly a compiler problem related to Rcpp and RcppArmadillo.
I put up a readme on GitHub file that, hopefully, will be helpful for you and allow you to install the HMSC package.
Thanks, the readme and Rcpp FAQ document were helpful. I think I am getting closer but still not quite there. Rcpp and RcppArmadillo appear to be working fine. I think now the problem lies in trying to get R to be able to locate gfortran. I am going to spend a little more time exploring this path:
I will let you know when I come up with a solution!
I don't exactly how, or why, but on my third try, this worked!
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
-run the above text through Terminal, when prompted, enter your password
-restart R
-and then try and install HMSC
library(devtools)
install_github("guiblanchet/HMSC")
library(HMSC)
via: Homebrew/legacy-homebrew#43290 (I ignored the part where someone commented "please do not install the r.research.att.com compilers.", and am going to run with it for now!)