[R-SIG-Mac] RcppArmadillo compilation failure (OS X 10.10)

[Jon Clayden]

Apologies - this seems to have been down to an issue with the
developer tools on my install. I've managed to fix it now.

All the best,
Jon

On 13 November 2014 14:03, Jon Clayden <jon.clayden at gmail.com> wrote:
> Dear all,
>
> After recently updating to OS X 10.10, "Yosemite", and recompiling R
> 3.1.2, I'm reinstalling various packages, but running into trouble
> with RcppArmadillo.
>
> I configured R with
>
> ./configure --with-blas="-framework Accelerate" --with-lapack
> --enable-memory-profiling --with-system-zlib --without-internal-tzcode
> CC=clang CXX=clang++ OBJC=clang F77=gfortran-4.9 FC=gfortran-4.9
> CFLAGS="-mtune=native -g -O2" CXXFLAGS="-mtune=native -g -O2"
> FFLAGS="-mtune=native -g -O2" FCFLAGS="-mtune=native -g -O2"
>
> The output from trying to install Rcpp and RcppArmadillo is at the
> bottom of this email.
>
> My only thought is that it might be an issue with Accelerate on
> Yosemite, but I'm not sure where the "_wrapper_ddot_" symbol is
> expected to be found. Ideas welcome.
>
> (I first posted this question to Rcpp-devel, but am now trying here as
> suggested by Dirk. Apparently the issue has not been reported before.)
>
> Thanks,
> Jon
>
> --
>
>> install.packages(c("Rcpp","RcppArmadillo"))
>
> Installing packages into
> ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library’
>
> (as ‘lib’ is unspecified)
>
> trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.11.3.tar.gz'
>
> Content type 'application/x-gzip' length 2169583 bytes (2.1 Mb)
>
> opened URL
>
> ==================================================
>
> downloaded 2.1 Mb
>
>
> trying URL 'http://cran.rstudio.com/src/contrib/RcppArmadillo_0.4.500.0.tar.gz'
>
> Content type 'application/x-gzip' length 934902 bytes (912 Kb)
>
> opened URL
>
> ==================================================
>
> downloaded 912 Kb
>
>
> * installing *source* package ‘Rcpp’ ...
>
> ** package ‘Rcpp’ successfully unpacked and MD5 sums checked
>
> ** libs
>
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I../inst/include/ -I/usr/local/include    -fPIC  -mtune=native -g -O2
>  -c Date.cpp -o Date.o
>
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I../inst/include/ -I/usr/local/include    -fPIC  -mtune=native -g -O2
>  -c Module.cpp -o Module.o
>
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I../inst/include/ -I/usr/local/include    -fPIC  -mtune=native -g -O2
>  -c Rcpp_init.cpp -o Rcpp_init.o
>
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I../inst/include/ -I/usr/local/include    -fPIC  -mtune=native -g -O2
>  -c api.cpp -o api.o
>
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I../inst/include/ -I/usr/local/include    -fPIC  -mtune=native -g -O2
>  -c attributes.cpp -o attributes.o
>
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I../inst/include/ -I/usr/local/include    -fPIC  -mtune=native -g -O2
>  -c barrier.cpp -o barrier.o
>
> clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined
> dynamic_lookup -single_module -multiply_defined suppress
> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
> Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
>
> installing to /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/libs
>
> ** R
>
> ** inst
>
> ** preparing package for lazy loading
>
> ** help
>
> *** installing help indices
>
> ** building package indices
>
> ** installing vignettes
>
> ** testing if installed package can be loaded
>
> * DONE (Rcpp)
>
> * installing *source* package ‘RcppArmadillo’ ...
>
> ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
>
> * checking LAPACK_LIBS: divide-and-conquer complex SVD available via
> system LAPACK
>
> ** libs
>
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"
>  -I../inst/include -fPIC  -mtune=native -g -O2  -c RcppArmadillo.cpp
> -o RcppArmadillo.o
>
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"
>  -I../inst/include -fPIC  -mtune=native -g -O2  -c RcppExports.cpp -o
> RcppExports.o
>
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"
>  -I../inst/include -fPIC  -mtune=native -g -O2  -c fastLm.cpp -o
> fastLm.o
>
> clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined
> dynamic_lookup -single_module -multiply_defined suppress
> -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
> RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -framework
> Accelerate -L/usr/local/Cellar/gcc/4.9.2/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2
> -L/usr/local/Cellar/gcc/4.9.2/lib
> -L/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib
> -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/..
> -framework R -Wl,-framework -Wl,CoreFoundation
>
> installing to /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/libs
>
> ** R
>
> ** inst
>
> ** preparing package for lazy loading
>
> ** help
>
> *** installing help indices
>
> ** building package indices
>
> ** installing vignettes
>
> ** testing if installed package can be loaded
>
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>
>   unable to load shared object
> '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/libs/RcppArmadillo.so':
>
>   dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/libs/RcppArmadillo.so,
> 6): Symbol not found: _wrapper_ddot_
>
>   Referenced from:
> /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/libs/RcppArmadillo.so
>
>   Expected in: flat namespace
>
>  in /Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/libs/RcppArmadillo.so
>
> Error: loading failed
>
> Execution halted
>
> ERROR: loading failed
>
> * removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo’
>
> * restoring previous
> ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo’
>
>
> The downloaded source packages are in
>
> ‘/private/var/folders/1n/6tq3nkqs6rb5t1zfts5wr5c80000gp/T/Rtmp29p0uh/downloaded_packages’
>
> Warning message:
>
> In install.packages(c("Rcpp", "RcppArmadillo")) :
>
>   installation of package ‘RcppArmadillo’ had non-zero exit status