[Rcpp-devel] Advice on installing CHOLMOD/Suitesparse

Rodney Sparapani rsparapa at mcw.edu
Thu Aug 30 22:24:06 CEST 2012

On 08/30/2012 02:24 PM, Douglas Bates wrote:
> But the RcppEigen package should not access Eigen 3.1.1 headers other
> than the ones that it provides.  Yes, in a sane world we would be able
> to install Debian packages of libraries like Eigen 3.1.1, Suitesparse,
> etc. and access the code from an R package.  However doing so in a
> portable way is quite nontrivial.  The Rcpp and RcppEigen packages
> provide their own header files in the inst/include subdirectory of the
> source package which becomes the include  subdirectory of the
> installed package.  Packages that use these headers should have
> "LinkingTo: Rcpp, RcppEigen" in their DESCRIPTION file so that these
> header files are found.
> So RcppEigen should be completely separate from any Eigen or
> Suitesparse packages that you have installed on your machine.  If your
> code is accessing the system Eigen or Suitesparse libraries it will
> all blow up, in the way you have described.  Your code should have the
> line
> #include<RcppEigen.h>
> and nothing else related to Eigen or Suitesparse.
> This is all assuming that I haven't accidentally left a line referring
> to cholmod.h in the RcppEigen include files.

Dear Doug:

I think I understand all that.  But, I am not intentionally co-mingling
sources.  For example, this is what I see when I try to install
RcppEigen from source ...

# R CMD INSTALL RcppEigen_0.3.1.tar.gz
* installing to library '/opt/local/lib64/R/library'
* installing *source* package 'RcppEigen' ...
** package 'RcppEigen' successfully unpacked and MD5 sums checked
** libs
g++ -I/opt/local/lib64/R/include  -I/opt/local/include 
-I"/opt/local/lib64/R/library/Rcpp/include"  -I../inst/include -fpic  -g 
-c RcppEigen.cpp -o RcppEigen.o
In file included from ../inst/include/RcppEigenForward.h:31,
                  from ../inst/include/RcppEigen.h:25,
                  from RcppEigen.cpp:22:
/opt/local/include/Eigen/CholmodSupport:9:23: error: cholmod.h: No such 
file or directory

Something is pulling in the Eigen header file

Rodney Sparapani, PhD  Center for Patient Care and Outcomes Research
Sr. Biostatistician               http://www.mcw.edu/pcor
4 wheels good, 2 wheels better!   Medical College of Wisconsin (MCW)
WWLD?:  What Would Lombardi Do?   Milwaukee, WI, USA

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