[R-SIG-Mac] RcppArmadillo errors

[David Winsemius]

> On Aug 27, 2016, at 5:35 AM, Oskar Knapik <oknapik at gmail.com> wrote:
> 
> Dear all
> 
> I am having some problems with your package.
> 
> It looks that I can't load it on my Mac computer (OS X El Capitan 10.11.6)
> 
> I got the following errors:
> Error in dyn.load(file, DLLpath = DLLpath, ...) : 
> can't load shared object
> '/Users/oknapik/Library/R/3.3/library/RcppArmadillo/libs/RcppArmadillo.so':
>  dlopen(/Users/oknapik/Library/R/3.3/library/RcppArmadillo/libs/RcppArmadillo.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libRlapack.dylib
>  Referenced from: /Users/oknapik/Library/R/3.3/library/RcppArmadillo/libs/RcppArmadillo.so
>  Reason: image not found
> 
> The newest OS X doesn't support X11 (I am not sure if you use it)

XQuartz is the X11 for the Mac:

https://www.xquartz.org/

This error can be found on SO and I think the second answer (to just (re-?) install XQuartz) is the correct one.

http://stackoverflow.com/questions/26489928/cant-load-x11-in-r-after-os-x-yosemite-upgrade

-- 
David.
> 
> I am also trying to install the package on Microsoft R
> https://mran.microsoft.com <https://mran.microsoft.com/>
> 
> 
> Below the errors from the installation:
> 
> install.packages("RcppArmadillo", verbose=T)
> Installing package into ‘/Users/oknapik/Library/R/3.3/library’
> (as ‘lib’ is unspecified)
> system (cmd0): /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL
> trying URL 'https://mran.revolutionanalytics.com/snapshot/2016-07-01/src/contrib/RcppArmadillo_0.7.100.3.1.tar.gz <https://mran.revolutionanalytics.com/snapshot/2016-07-01/src/contrib/RcppArmadillo_0.7.100.3.1.tar.gz>'
> Content type 'application/octet-stream' length 1055712 bytes (1.0 MB)
> ==================================================
> downloaded 1.0 MB
> 
> foundpkgs: RcppArmadillo, /var/folders/mr/_t437jvd5v5fty4z3pypn_yc0000gn/T//RtmpPj3WB7/downloaded_packages/RcppArmadillo_0.7.100.3.1.tar.gz
> files: /var/folders/mr/_t437jvd5v5fty4z3pypn_yc0000gn/T//RtmpPj3WB7/downloaded_packages/RcppArmadillo_0.7.100.3.1.tar.gz
> Warning
> In command 'doTryCatch(return(expr), name, parentenv, handler)':
>  can't load the shared object  '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
>  dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Symbol not found: _CGBitmapContextCreate
>  Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so
>  Expected in: flat namespace
> in /Library/Frameworks/R.framework/Resources/modules//R_X11.so
> * installing *source* package ‘RcppArmadillo’ ...
> ** package ‘RcppArmadillo’ has been sucessuflly unpacked and  MD5 soms were checked
> checking whether the C++ compiler works... yes
> checking for C++ compiler default output file name... a.out
> checking for suffix of executables... 
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C++ compiler... yes
> checking whether clang++ accepts -g... yes
> checking how to run the C++ preprocessor... clang++ -E
> checking whether we are using the GNU C++ compiler... (cached) yes
> checking whether clang++ accepts -g... (cached) yes
> checking whether g++ version is sufficient... checking LAPACK_LIBS... system LAPACK found
> configure: creating ./config.status
> config.status: creating inst/include/RcppArmadilloLapack.h
> ** libs
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include -I"/Users/oknapik/Library/R/3.3/library/Rcpp/include"  -I../inst/include -fPIC  -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include -DU_STATIC_IMPLEMENTATIN -Wall -mtune=core2 -g -O2 -I/opt/X11/include -framework CoreFoundation -framework CoreGraphics -framework CoreText  -c RcppArmadillo.cpp -o RcppArmadillo.o
> clang: warning: -framework CoreFoundation: 'linker' input unused
> clang: warning: -framework CoreGraphics: 'linker' input unused
> clang: warning: -framework CoreText: 'linker' input unused
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include -I"/Users/oknapik/Library/R/3.3/library/Rcpp/include"  -I../inst/include -fPIC  -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include -DU_STATIC_IMPLEMENTATIN -Wall -mtune=core2 -g -O2 -I/opt/X11/include -framework CoreFoundation -framework CoreGraphics -framework CoreText  -c RcppExports.cpp -o RcppExports.o
> clang: warning: -framework CoreFoundation: 'linker' input unused
> clang: warning: -framework CoreGraphics: 'linker' input unused
> clang: warning: -framework CoreText: 'linker' input unused
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include -I"/Users/oknapik/Library/R/3.3/library/Rcpp/include"  -I../inst/include -fPIC  -I/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/include -DU_STATIC_IMPLEMENTATIN -Wall -mtune=core2 -g -O2 -I/opt/X11/include -framework CoreFoundation -framework CoreGraphics -framework CoreText  -c fastLm.cpp -o fastLm.o
> clang: warning: -framework CoreFoundation: 'linker' input unused
> clang: warning: -framework CoreGraphics: 'linker' input unused
> clang: warning: -framework CoreText: 'linker' input unused
> clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/lib -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -framework Accelerate -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -L/usr/local/lib -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
> ld: warning: directory not found for option '-L/private/var/root/jenkins/workspace/External-R-3.3.1/vendor/build/lib'
> ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64'
> ld: warning: directory not found for option '-L/usr/local/lib/x86_64'
> ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3'
> 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 ‘/Users/oknapik/Library/R/3.3/library/RcppArmadillo’
> * restoring previous ‘/Users/oknapik/Library/R/3.3/library/RcppArmadillo’
> Warning in install.packages :
>  installation of package ‘RcppArmadillo’ had non-zero exit status
> 
> 
> 
> I would be very grateful for help.
> 
> Best,
> Oskar
> 	[[alternative HTML version deleted]]
> 
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David Winsemius
Alameda, CA, USA