I have recently installed Bioconductor (version 2.13) on Rstudio (R version 3.0.2). I use Linux Mint 17.2 Cinnamon 64bit. I have been trying to install the "genefo" package, which has a dependency on the Rcpp package. However, the installation of Rcpp stalls with the error -
(Unable to insert the code from the beginning)
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -O3 -pipe -g -c Date.cpp -o Date.o
In file included from ../inst/include/RcppCommon.h:122:0,
from ../inst/include/Rcpp.h:27,
from Date.cpp:31:
../inst/include/Rcpp/exceptions.h:267:23: error: expected initializer before ‘stop’
inline void NORET stop(const std::string& message) {
^
../inst/include/Rcpp/exceptions.h:272:23: error: expected initializer before ‘stop’
inline void NORET stop(const char* fmt, const T1& arg1) {
^
../inst/include/Rcpp/exceptions.h:277:23: error: expected initializer before ‘stop’
inline void NORET stop(const char* fmt, const T1& arg1, const T2& arg2) {
^
../inst/include/Rcpp/exceptions.h:282:23: error: expected initializer before ‘stop’
inline void NORET stop(const char* fmt, const T1& arg1, const T2& arg2, const T3& arg3) {
^
../inst/include/Rcpp/exceptions.h:287:23: error: expected initializer before ‘stop’
inline void NORET stop(const char* fmt, const T1& arg1, const T2& arg2, const T3& arg3, const T4& arg4) {
^
../inst/include/Rcpp/exceptions.h:292:23: error: expected initializer before ‘stop’
inline void NORET stop(const char* fmt, const T1& arg1, const T2& arg2, const T3& arg3, const T4& arg4, const T5& arg5) {
^
../inst/include/Rcpp/exceptions.h:297:23: error: expected initializer before ‘stop’
inline void NORET stop(const char* fmt, const T1& arg1, const T2& arg2, const T3& arg3, const T4& arg4, const T5& arg5, const T6& arg6) {
^
../inst/include/Rcpp/exceptions.h:302:23: error: expected initializer before ‘stop’
inline void NORET stop(const char* fmt, const T1& arg1, const T2& arg2, const T3& arg3, const T4& arg4, const T5& arg5, const T6& arg6, const T7& arg7) {
^
../inst/include/Rcpp/exceptions.h:307:23: error: expected initializer before ‘stop’
inline void NORET stop(const char* fmt, const T1& arg1, const T2& arg2, const T3& arg3, const T4& arg4, const T5& arg5, const T6& arg6, const T7& arg7, const T8& arg8) {
^
../inst/include/Rcpp/exceptions.h:312:23: error: expected initializer before ‘stop’
inline void NORET stop(const char* fmt, const T1& arg1, const T2& arg2, const T3& arg3, const T4& arg4, const T5& arg5, const T6& arg6, const T7& arg7, const T8& arg8, const T9& arg9) {
^
../inst/include/Rcpp/exceptions.h:317:23: error: expected initializer before ‘stop’
inline void NORET stop(const char* fmt, const T1& arg1, const T2& arg2, const T3& arg3, const T4& arg4, const T5& arg5, const T6& arg6, const T7& arg7, const T8& arg8, const T9& arg9, const T10& arg10) {
^
In file included from ../inst/include/Rcpp/Vector.h:56:0,
from ../inst/include/Rcpp.h:38,
from Date.cpp:31:
../inst/include/Rcpp/vector/DimNameProxy.h: In member function ‘Rcpp::internal::DimNameProxy& Rcpp::internal::DimNameProxy::assign(SEXP)’:
../inst/include/Rcpp/vector/DimNameProxy.h:43:121: error: too many arguments to function ‘void Rcpp::stop(const string&)’
stop("dimension extent is '%d' while length of names is '%d'", INTEGER(dims)[dim_], Rf_length(other));
^
In file included from ../inst/include/RcppCommon.h:70:0,
from ../inst/include/Rcpp.h:27,
from Date.cpp:31:
../inst/include/Rcpp/utils/tinyformat.h:127:10: note: declared here
void stop(const std::string& message);
^
In file included from ../inst/include/Rcpp.h:47:0,
from Date.cpp:31:
../inst/include/Rcpp/Function.h: In constructor ‘Rcpp::Function_Impl<StoragePolicy>::Function_Impl(const string&, const string&)’:
../inst/include/Rcpp/Function.h:72:63: error: too many arguments to function ‘void Rcpp::stop(const string&)’
stop("there is no namespace called \"%s\"", ns);
^
In file included from ../inst/include/RcppCommon.h:70:0,
from ../inst/include/Rcpp.h:27,
from Date.cpp:31:
../inst/include/Rcpp/utils/tinyformat.h:127:10: note: declared here
void stop(const std::string& message);
^
make: *** [Date.o] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/home/anjali/R/x86_64-pc-linux-gnu-library/3.0/Rcpp’
The downloaded source packages are in
‘/tmp/RtmpCt7qAW/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘Rcpp’ had non-zero exit status
Please help me. I am new to Linux and Bioconductor.
Please EDIT your question to provide the output of
sessionInfo()
, and also from the command lineg++ --version
. Please also consider asking for support about Rcpp on the Rcpp mailing list.You're using rather outdated versions of R and (therefore) bioconductor. Please upgrade R to the latest version (v3.3.1) and try to install your packages again into a "clean" library -- ie. do not copy your old R packages over to your new installation.