[Rcpp-devel] [RcppArmadillo] Install problem

Fri Jan 11 22:40:30 CET 2013

On 11 January 2013 at 13:23, Alan Coppola wrote:
| 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/

With all due respect that implies an R and Ubuntu version that is two years,
and four MAJOR releases each, out of date.  

Why?  I never suggested that.

| 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.

I respectfully disagree. I happen to be the R maintainer Debian; LAPACK_LIBS
etc are _hardcoded_ at built time.

| 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.

Not at all. 

I work on Ubuntu everyday, and Rcpp is used by myself and many other people
on Ubuntu.  This is really not an Rcpp issue.  

What is your R version?  Where is your R version from? Ie what does 'apt-cache
policy r-base-core' show?

If you have basic R-on-Ubuntu usage and upgrade issues, try the r-sig-debian
list (which covers Ubuntu).

Dirk

| 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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| 
| 
| 

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com  