[Rcpp-devel] [RcppArmadillo] Install problem

[Alan Coppola]

Dirk,
Thanks for the quick reply.
I had found
http://grokbase.com/t/r/r-help/109fvxeb44/r-lapack-in-r-2-11-1-ubuntu-10-04-1/oldest
and did what it recommended, with your r-base-dev add-on, along with 
reading the FAQ.

sudo apt-get update
sudo apt-get remove r-base
sudo apt-get remove r-base-dev
sudo apt-get autoremove
sudo apt-get install r-base
sudo apt-get install r-base-dev

I still have the same problem after all that, so am starting to believe 
that my system has problems filling in the path vars

LAPACK_LIBS, BLAS_LIBS, and FLIBS

where liblapack.so and libquadmath.so live for some arcane reason.

On my system, they live in:
/usr/lib/liblapack.so -> 
/etc/alternatives/liblapack.so->/usr/lib/lapack/liblapack.so
/var/lib/dpkg/alternatives/liblapack.so
and
/usr/lib/gcc/x86_64-linux-gnu/4.6/libquadmath.so -> 
../../../x86_64-linux-gnu/libquadmath.so.0

Thanks for any insights...I realize that it is hard to debug system 
problems from afar.
alan




On 01/11/2013 12:16 PM, Dirk Eddelbuettel wrote:
> On 11 January 2013 at 12:04, Alan Coppola wrote:
> | I've been using Rcpp for a while now, through Rstudio, and like it.
> | I now have the need to use RcppArmadillo, and have been trying to
> | install it through Rstudio.
> | Somehow, LAPACK_LIBS, BLAS_LIBS, and FLIBS from the Makevars file are
> | not getting filled in properly.
>
> You misunderstood a clear error message. See below:
>
> | I don't understand enough about installing R packages to know what was
> | supposed fill in thos variables.
> |
> | Everything is up to date, and I uninstalled/reinstalled R-base and
> | R-dev, as was mentioned
> | in a problem report similar to mine from a year ago...any ideas?
> | alan
> |
> | -------------- lsb_release -a output----
> | Distributor ID: Ubuntu
> | Description: Ubuntu 11.10
> | Release: 11.10
> | Codename: oneiric
> |
> |
> |
> |
> | ------------------Rstudio output-----------------------
> |  > install.packages("RcppArmadillo")
> | Installing package(s) into ‘/home/enacor/R/x86_64-pc-linux-gnu-library/2.15’
> | (as ‘lib’ is unspecified)
> | trying URL 'http://cran.fhcrc.org/src/contrib/RcppArmadillo_0.3.6.1.tar.gz'
> | Content type 'application/x-gzip' length 753168 bytes (735 Kb)
> | opened URL
> | ==================================================
> | downloaded 735 Kb
> |
> | * installing *source* package ‘RcppArmadillo’ ...
> | ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
> | ** libs
> | g++ -I/usr/share/R/include -DNDEBUG
> | -I"/home/enacor/R/x86_64-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/enacor/R/x86_64-pc-linux-gnu-library/2.15/Rcpp/include"
> | -I../inst/include -fpic -O3 -pipe -g -c fastLm.cpp -o fastLm.o
> | g++ -shared -o RcppArmadillo.so RcppArmadillo.o fastLm.o
> | -L/home/enacor/R/x86_64-pc-linux-gnu-library/2.15/Rcpp/lib -lRcpp
> | -Wl,-rpath,/home/enacor/R/x86_64-pc-linux-gnu-library/2.15/Rcpp/lib
> | -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
> | /usr/bin/ld: cannot find -lgfortran
> | /usr/bin/ld: cannot find -lquadmath
>
> The linker complains.
>
> Do 'sudo apt-get install r-base-dev' which should take care of it.
>
> It's a FAQ, and googling for the string of the error message is often much
> quicker than posting here.
>
> Dirk
>
>
> | collect2: ld returned 1 exit status
> | make: *** [RcppArmadillo.so] Error 1
> | ERROR: compilation failed for package ‘RcppArmadillo’
> | * removing ‘/home/enacor/R/x86_64-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/Rtmp5YjUpn/downloaded_packages’
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