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Cant install packages bfast, RcppArmadillo in Microsoft R Open 3.2.5 RRS feed

  • Question

  •  in Centos 6.7

    In install.packages("bfast") :

    Error: unexpected symbol in "In install.packages"
     installation of package RcppArmadillo had non-zero exit status

    install.packages("RcppArmadillo")
      % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                     Dload  Upload   Total   Spent    Left  Speed
    100  979k  100  979k    0     0   128k      0  0:00:07  0:00:07 --:--:--  482k
    * installing *source* package \u2018RcppArmadillo\u2019 ...
    ** package \u2018RcppArmadillo\u2019 successfully unpacked and MD5 sums checked
    * checking LAPACK_LIBS: R-supplied partial LAPACK found
    * some operations may not be available
    ** libs
    g++ -I/usr/lib64/MRO-3.2.5/R-3.2.5/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/usr/lib64/MRO-3.2.5/R-3.2.5/lib64/R/library/Rcpp/include"  -I../inst/include -fpic  -g -O2  -c RcppArmadillo.cpp -o RcppArmadillo.o
    In file included from ../inst/include/armadillo:107,
                     from ../inst/include/RcppArmadilloForward.h:46,
                     from ../inst/include/RcppArmadillo.h:31,
                     from RcppArmadillo.cpp:22:
    ../inst/include/armadillo_bits/traits.hpp: In instantiation of \u2018const bool arma::is_arma_type<std::__traitor<std::__is_integer<int>, std::__is_floating<int> >::<anonymous enum> >::value\u2019:
    ../inst/include/armadillo_bits/op_logmat_meat.hpp:289:   instantiated from here
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<int>, std::__is_floating<int> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_subview_elem2\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<int>, std::__is_floating<int> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_subview_elem1\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<int>, std::__is_floating<int> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_subview_col\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<int>, std::__is_floating<int> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_subview_row\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<int>, std::__is_floating<int> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_subview\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<int>, std::__is_floating<int> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_diagview\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<int>, std::__is_floating<int> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_mtGlue\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<int>, std::__is_floating<int> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_mtOp\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<int>, std::__is_floating<int> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_eGlue\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<int>, std::__is_floating<int> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_eOp\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<int>, std::__is_floating<int> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_Glue\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<int>, std::__is_floating<int> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_Op\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<int>, std::__is_floating<int> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_Gen\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<int>, std::__is_floating<int> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_Mat\u2019
    ../inst/include/armadillo_bits/traits.hpp: In instantiation of \u2018const bool arma::is_arma_type<std::__traitor<std::__is_integer<double>, std::__is_floating<double> >::<anonymous enum> >::value\u2019:
    ../inst/include/armadillo_bits/op_logmat_meat.hpp:289:   instantiated from here
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<double>, std::__is_floating<double> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_subview_elem2\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<double>, std::__is_floating<double> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_subview_elem1\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<double>, std::__is_floating<double> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_subview_col\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<double>, std::__is_floating<double> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_subview_row\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<double>, std::__is_floating<double> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_subview\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<double>, std::__is_floating<double> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_diagview\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<double>, std::__is_floating<double> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_mtGlue\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<double>, std::__is_floating<double> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_mtOp\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<double>, std::__is_floating<double> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_eGlue\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<double>, std::__is_floating<double> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_eOp\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<double>, std::__is_floating<double> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_Glue\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<double>, std::__is_floating<double> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_Op\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<double>, std::__is_floating<double> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_Gen\u2019
    ../inst/include/armadillo_bits/traits.hpp:642: error: \u2018std::__traitor<std::__is_integer<double>, std::__is_floating<double> >::<anonymous enum>\u2019 is/uses anonymous type
    ../inst/include/armadillo_bits/traits.hpp:642: error:   trying to instantiate \u2018template<class T> struct arma::is_Mat\u2019
    make: *** [RcppArmadillo.o] Error 1
    ERROR: compilation failed for package \u2018RcppArmadillo\u2019
    * removing \u2018/usr/lib64/MRO-3.2.5/R-3.2.5/lib64/R/library/RcppArmadillo\u2019

    The downloaded source packages are in
    \u2018/tmp/Rtmpnjf0eB/downloaded_packages\u2019
    Updating HTML index of packages in '.Library'
    Making 'packages.html' ... done
    Warning message:
    In install.packages("RcppArmadillo") :
      installation of package \u2018RcppArmadillo\u2019 had non-zero exit status


    Friday, May 20, 2016 12:27 PM

All replies

  • I believe the most recent RcppArmadillo requires c++11 compiler (http://dirk.eddelbuettel.com/blog/2016/05/28#rcpparmadillo_0.7.100.3.0) which Centos 6.x does not provide. Either build newer gcc yourself or use something like Nix (http://nixos.org/nix) to install it.
    Tuesday, June 14, 2016 5:35 PM