error with install from devtools

[brooksandrew]

Hi there - read your paper. Interesting stuff. Would like to play around with your package, but I'm getting an install error on my mac using devtools. Have you encountered this?

devtools::install_github('zmjones/edarf')

Downloading github repo zmjones/edarf@master Installing edarf Installing dependencies for edarf: RcppArmadillo % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 10 1239k 10 130k 0 0 168k 0 0:00:07 --:--:-- 0:00:07 168k100 1239k 100 1239k 0 0 1356k 0 --:--:-- --:--:-- --:--:-- 1356k

The downloaded binary packages are in /var/folders/29/dj4wm1714q7flrdgvg7src8h0000gn/T//RtmpxEpsRy/downloaded_packages '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL \ '/private/var/folders/29/dj4wm1714q7flrdgvg7src8h0000gn/T/RtmpxEpsRy/devtoolsa4220b25ed7/zmjones-edarf-e39a4c5' \ --library='/Library/Frameworks/R.framework/Versions/3.1/Resources/library' --install-tests

• installing source package ‘edarf’ ... \ libs clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -fPIC -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -fPIC -Wall -mtune=core2 -g -O2 -c edarf.cpp -o edarf.o clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o edarf.so RcppExports.o edarf.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation 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: *\ [edarf.so] Error 1 ERROR: compilation failed for package ‘edarf’
• removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/edarf’ Error: Command failed (1)

[zmjones]

No I haven't seen this one and wasn't able to replicate it. Compiler errors are no fun. Did Rcpp and RcppArmadillo install correctly and load w/o error?

You have Clang installed via Xcode I presume? Are you using the R binary? How is gfortran installed on your system? For reference I use the version of gfortran that is supplied in GCC which is installed (along with R) from source by homebrew.

Since I am waiting on packages/forks not on CRAN I can't get them to generate a binary but if you know of a way that would be helpful.

[zmjones]

did you figure this out?

[brooksandrew]

sorry for delay. I'm not super familiar with the some of the software/installations you mentioned and haven't had to check on them pulling packages from GitHub before with devtools.

RcppAramadillo and Rcpp are load properly with library() in R. Just reinstalled to most recent version to be sure

clang specs:

Andrews-MacBook-Pro:~ ajb$ clang --version Apple LLVM version 7.0.0 (clang-700.0.72) Target: x86_64-apple-darwin14.5.0 Thread model: posix

R specs:

sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.5 (Yosemite)

Tried again today with install_github('zmjones/edarf') Here are the warnings & 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: *\ [edarf.so] Error 1
ERROR: compilation failed for package ‘edarf’

• removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/edarf’
  Error: Command failed (1)

[zmjones]

So it looks like gfortran is not in the place that it is expected or is missing altogether. I know the build works fine on a clean linux system from scratch and it works on my Mac so I think this is particular to your system.

Are you using the R binary (i.e. R is installed using a .dmg file)? If so install this. If you are using homebrew or another package manager you can install it manually.

Please let me know if that works.

[brooksandrew]

hmmm. yeah, R was installed from R-3.2.2.pkg. Installed gfortran from your link. No luck. This time error with lquadmath

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 -lquadmath clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *\ [edarf.so] Error 1 ERROR: compilation failed for package ‘edarf’

• removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/edarf’ Error: Command failed (1)

[zmjones]

did you restart R after doing so?

if that doesn't work try manual installation.

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 /

[brooksandrew]

manual install works. thanks! could this be bundled into the install, perhaps?

[zmjones]

No that is a system requirement. I think that would not pass R CMD check. This will be solved in a way though, when/if this eventually ends up on CRAN and there is a binary which doesn't require you to compile things. This is just an OSX specific thing that has to do with how the fortran compiler is packaged.

[zmjones]

Also if you plan on using more packages compiled from source I would recommend using homebrew. I have a post on doing all this on as well.

Hope the package works for you!