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and four MAJOR releases each, out of date.
| 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
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’
| | _______________________________________________
| | Rcpp-devel mailing list
| | Rcpp-devel@lists.r-forge.r-project.org
| | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
|
|
|
--
Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com
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