[Rcpp-devel] Advice on installing CHOLMOD/Suitesparse

Douglas Bates bates at stat.wisc.edu
Fri Aug 31 00:53:42 CEST 2012

On Thu, Aug 30, 2012 at 4:29 PM, Rodney Sparapani <rsparapa at mcw.edu> wrote:
> On 08/30/2012 04:14 PM, Douglas Bates wrote:
>> It is quite possible that you would have gotten a buggy version if you
>> checked out a copy of the SVN archive at some random time.  Making
>> such a change is something I would tend to forget until tests started
>> failing.
> I can confirm that it is not a buggy version.  What it is happening is
> that the pre-processor is seeing my Eigen 3.1.1 installation at
> /opt/local/include/Eigen
> instead of the RcppEigen 0.3.1 at
> /opt/local/lib64/R/library/RcppEigen/include/Eigen
> This must be happening because of the order of the -I switches...
> # 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 ...
> Shouldn't -I../inst/include be first?  In src/Makevars,
> there is just PKG_CXXFLAGS=-I../inst/include.  So, I guess that
> should have been prepended to the CXXFLAGS rather than
> appended.  Am I making sense?

You're right.  I didn't see that -I/opt/local/include was in the
compiler call.  If you look at $RHOME/etc/Make.conf you will probably
see that


(in my case /usr/local/include) for reasons that are somewhat
mysterious to me.  It seems like the sort of thing that a prominent
member of R-core would yell and scream about if he had not put that
there himself.

It happens that the Ubuntu package for eigen3 installs the Eigen
header files in /usr/include/eigen3 so I don't get bitten by that.

It seems that you options are 1) Change R's default CPPFLAGS, which
seems unlikely to happen or 2) change the location of the Eigen header

> --
> 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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