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

[Jon Clayden]

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