GCC in error when compiling R package on Cloudera CDH4

Question

I am trying to install RHadoop on Cloudera's CDH4 Hadoop VM. RHadoop is a framework for using Hadoop via an R programming interface. One of the prerequisites to installing the RHadoop R package "rmr" is another R package called Rcpp, which is for calling C++ code from R. When I attempt to install the package, I get the following error. I contacted both the Rcpp and RHadoop communities and both say its a GCC problem. When I try to update or reinstall GCC, I get "Package gcc-4.4.6-4.e16.x86_64 already installed and latest version, nothing to do." Any suggestions?

Here is the error (from the R command line).

> install.packages("Rcpp")
Installing package(s) into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
 trying URL 'http://cran.csdb.cn/src/contrib/Rcpp_0.9.15.tar.gz'
Content type 'application/x-gzip' length 2119769 bytes (2.0 Mb)
opened URL
 ==============================
====================
downloaded 2.0 Mb

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c Date.cpp -o Date.o
 g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c DateVector.cpp -o DateVector.o
 g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c Datetime.cpp -o Datetime.o
 g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c DatetimeVector.cpp -o DatetimeVector.o
 g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c Dimension.cpp -o Dimension.o
 g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c DottedPair.cpp -o DottedPair.o
 g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c Environment.cpp -o Environment.o
 g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c Evaluator.cpp -o Evaluator.o
 g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c Formula.cpp -o Formula.o
 g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c Function.cpp -o Function.o
 g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c Language.cpp -o Language.o
 g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  -c Module.cpp -o Module.o
 {standard input}: Assembler messages:
{standard input}:10671: Warning: end of file not at end of a line; newline inserted
{standard input}:11544: Error: bad register name `%'
{standard input}:11544: Error: open CFI at the end of file; missing .cfi_endproc directive
 g++: Internal error: Killed (program cc1plus)
Please submit a full bug report.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
make: *** [Module.o] Error 1
 ERROR: compilation failed for package ‘Rcpp’
* removing ‘/usr/lib64/R/library/Rcpp’

The downloaded source packages are in
    ‘/tmp/RtmpGdXO9h/downloaded_packages’
Updating HTML index of packages in '.Library'
 Making packages.html  ... done
Warning message:
In install.packages("Rcpp") :
  installation of package ‘Rcpp’ had non-zero exit status

Answer 1

As one of the Rcpp authors, I can assure that the error is probably at your end and with either gcc (unlikely) or CDH. Rcpp gets built and rebuild a bazillion times both on CRAN (and yes there are pages summarizing the builds on CRAN and also on Debian. The package does not normally kill the compiler.

Could you be running out of ram on the box?