Question

I have a problem to compile RcppArmadillo. This is the result when I try to install the package:

 > install.packages("RcppArmadillo")
Installing package(s) into ‘/home/*****/R/i686-pc-linux-gnu-library/2.15’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/RcppArmadillo_0.3.4.4.tar.gz'
Content type 'application/x-gzip' length 742125 bytes (724 Kb)
opened URL
==================================================
downloaded 724 Kb

Loading required package: survival
Loading required package: stats
Loading required package: utils
Loading required package: graphics
Loading required package: splines
Hmisc library by Frank E Harrell Jr

Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview')
to see overall documentation.

NOTE:Hmisc no longer redefines [.factor to drop unused levels when
subsetting.  To get the old behavior of Hmisc type dropUnusedLevels().


Attaching package: ‘Hmisc’

The following object(s) are masked from ‘package:survival’:

    untangle.specials

The following object(s) are masked from ‘package:base’:

    format.pval, round.POSIXt, trunc.POSIXt, units


    Welcome at Sun Dec  2 18:54:49 2012 
    * installing *source* package ‘RcppArmadillo’ ...
    ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
    ** libs
    g++ -I/usr/share/R/include -DNDEBUG   -I"/home/******/R/i686-pc-linux-gnu-library/2.15/Rcpp/include"  -I../inst/include -fpic  -O3 -pipe  -g  -c RcppArmadillo.cpp -o RcppArmadillo.o
    g++ -I/usr/share/R/include -DNDEBUG   -I"/home/******/R/i686-pc-linux-gnu-library/2.15/Rcpp/include"  -I../inst/include -fpic  -O3 -pipe  -g  -c fastLm.cpp -o fastLm.o
    Loading required package: survival
    Loading required package: stats
    Loading required package: utils
    Loading required package: graphics
    Loading required package: splines
    Hmisc library by Frank E Harrell Jr

    Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview')
    to see overall documentation.

    NOTE:Hmisc no longer redefines [.factor to drop unused levels when
    subsetting.  To get the old behavior of Hmisc type dropUnusedLevels().


    Attaching package: ‘Hmisc’

    The following object(s) are masked from ‘package:survival’:

        untangle.specials

    The following object(s) are masked from ‘package:base’:

        format.pval, round.POSIXt, trunc.POSIXt, units

    g++ -shared -o RcppArmadillo.so RcppArmadillo.o fastLm.o Welcome at Sun Dec 2 18:55:06 2012
-L/home/******/R/i686-pc-linux-gnu-library/2.15/Rcpp/lib -lRcpp -Wl,-rpath,/home/******/R/i686-pc-linux-gnu-library/2.15/Rcpp/lib -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
    Loading required package: survival
    Loading required package: stats
    Loading required package: utils
    Loading required package: graphics
    Loading required package: splines
    Hmisc library by Frank E Harrell Jr

    Type library(help='Hmisc'), ?Overview, or ?Hmisc.Overview')
    to see overall documentation.

    NOTE:Hmisc no longer redefines [.factor to drop unused levels when
    subsetting.  To get the old behavior of Hmisc type dropUnusedLevels().


    Attaching package: ‘Hmisc’

    The following object(s) are masked from ‘package:survival’:

        untangle.specials

    The following object(s) are masked from ‘package:base’:

        format.pval, round.POSIXt, trunc.POSIXt, units
        g++: error: Welcome: No such file or directory
        g++: error: at: No such file or directory
        g++: error: Sun: No such file or directory
        g++: error: Dec: No such file or directory
        g++: error: 2: No such file or directory
        g++: error: 18:55:08: No such file or directory
        g++: error: 2012: No such file or directory
        make: *** [RcppArmadillo.so] Error 1
        ERROR: compilation failed for package ‘RcppArmadillo’
        * removing ‘/home/****/R/i686-pc-linux-gnu-library/2.15/RcppArmadillo’
        Warning in install.packages :
          installation of package ‘RcppArmadillo’ had non-zero exit status

        The downloaded source packages are in
            ‘/tmp/RtmpDAngtR/downloaded_packages

’

I am using R version 2.15.2 on Ubuntu 12.04.
First I thought that some dependencies are missing, but I have installed Armadillo (libarmadillo2 v2.4.2) via the synaptic package manager, also g++ is installed (v4.6.3). I am not familiar with c++, so I don’t know if I might need some additional packages. However, installing Rcpp works perfectly fine.

I would be really glad if somebody could help me.

Answer 1

install.packages and R CMD INSTALL will (re)start R and read your .Rprofile. Therefore, you should consider wrapping if (interactive()) { } around code in your .Rprofile file that you only want run in interactive sessions (e.g. library or require calls).

Otherwise, you need to start R with the --vanilla flag before using install.packages(), or use R --vanilla CMD INSTALL from bash.