[Rcpp-devel] Advice on installing CHOLMOD/Suitesparse

[Douglas Bates]

On Wed, Aug 29, 2012 at 4:42 PM, Douglas Bates <bates at stat.wisc.edu> wrote:
> On Wed, Aug 29, 2012 at 4:32 PM, Rodney Sparapani <rsparapa at mcw.edu> wrote:
>> Hi Gang:
>>
>> I have been using CHOLMOD/Suitesparse, but I'm having an issue
>> coaxing RcppEigen to see it.  I have Matrix, inline, Rcpp and
>> RcppEigen installed as well as Suitesparse.  But, when I run

You should not need to have Suitesparse installed.  All the
Suitesparse code that is used in RcppEigen is included in the Matrix
package.

>> this simple program (that works with Rcpp alone)...
>>
>> require(inline)
>> require(Rcpp)
>> require(RcppEigen)
>>
>> N <- 100
>> p <- 3
>> q <- 10
>>
>> data <- list(X=matrix(NA, N, p), Z=matrix(NA, N, q),
>>              t=double(N), y=double(N), v1=integer(N), v2=integer(N),
>>              c=integer(N))
>>
>> par.info <- list(beta=list(init=0., prior=list(mean=0., prec=0.001)),
>>                   mu=list(init=c(0., 0.),
>>                     prior=list(mean=c(0., 0.), prec=diag(0.001, 2))),
>>                   theta=list(init=c(rep(0., ncol(data$X)),
>>                                rep(1., ncol(data$Z)),
>>                                rep(0., ncol(data$X))),
>>                     prior=list(mean=rep(0., ncol(data$Z)+2*ncol(data$X)),
>>                            prec=diag(0.001, ncol(data$Z)+2*ncol(data$X))))
>>                   )
>>
>> src <- '
>> List list(arg1), beta=list["beta"], mu=list["mu"],
>> theta=list["theta"];
>>
>> return theta["init"];
>> '
>>
>> check1 <- cxxfunction(signature(arg1="list"), src, #plugin="Rcpp")
>>                       plugin="RcppEigen")
>>
>> I get...
>> In file included from
>> /opt/local/lib64/R/library/RcppEigen/include/RcppEigenForward.h:31,
>>                  from
>> /opt/local/lib64/R/library/RcppEigen/include/RcppEigen.h:25,
>>                  from file7289313ed735.cpp:3:
>> /opt/local/include/Eigen/CholmodSupport:9:23: error: cholmod.h: No such file or directory
>
> Perhaps you have an out-of-date version of the RcppEigen package (or
> maybe the Mac version hasn't been built or ...).  In any case
> RcppEigenForward should include RcppEigenCholmod.h, not cholmod.h and
> the correct version would be at
> /opt/local/lib64/R/library/RcppEigen/include/RcppEigenCholmod.h
>
>> make: *** [file7289313ed735.o] Error 1
>>
>> ERROR(s) during compilation: source code errors or compiler configuration
>> errors!
>>
>> Program source:
>>   1:
>>   2: // includes from the plugin
>>   3: #include <RcppEigen.h>
>>   4: #include <Rcpp.h>
>>   5:
>>   6:
>>   7: #ifndef BEGIN_RCPP
>>   8: #define BEGIN_RCPP
>>   9: #endif
>>  10:
>>  11: #ifndef END_RCPP
>>  12: #define END_RCPP
>>  13: #endif
>>  14:
>>  15: using namespace Rcpp;
>>  16:
>>  17:
>>  18: // user includes
>>  19:
>>  20:
>>  21: // declarations
>>  22: extern "C" {
>>  23: SEXP file7289313ed735( SEXP arg1) ;
>>  24: }
>>  25:
>>  26: // definition
>>  27:
>>  28: SEXP file7289313ed735( SEXP arg1 ){
>>  29: BEGIN_RCPP
>>  30:
>>  31: List list(arg1), beta=list["beta"], mu=list["mu"],
>>  32: theta=list["theta"];
>>  33:
>>  34: return theta["init"];
>>  35:
>>  36: END_RCPP
>>  37: }
>>  38:
>>  39:
>> Error in compileCode(f, code, language = language, verbose = verbose) :
>>   Compilation ERROR, function(s)/method(s) not created! In file included
>> from /opt/local/lib64/R/library/RcppEigen/include/RcppEigenForward.h:31,
>>                  from
>> /opt/local/lib64/R/library/RcppEigen/include/RcppEigen.h:25,
>>                  from file7289313ed735.cpp:3:
>> /opt/local/include/Eigen/CholmodSupport:9:23: error: cholmod.h: No such file
>> or directory
>> make: *** [file7289313ed735.o] Error 1
>> In addition: Warning message:
>> running command '/opt/local/lib64/R/bin/R CMD SHLIB file7289313ed735.cpp 2>
>> file7289313ed735.cpp.err.txt' had status 1
>>
>> So, I'm wondering...  Where does RcppEigen expect to see cholmod.h?
>> Perhaps, I should re-install RcppEigen from source rather than from
>> CRAN.  Or possibly install Suitesparse from source in either
>> /usr/local, or preferably, /opt/local?  What works for other?  Thanks
>>
>> Compiler Settings:
>> CC="gcc"
>> CFLAGS="-g"
>> CXX="g++"
>> CXXFLAGS="-g"
>> CPP=""
>> CPPFLAGS="-I/opt/local/include"
>> LDFLAGS="-L/opt/local/lib64 -Wl,-rpath -Wl,/opt/local/lib64"
>> LIBS=""
>> PKG_CONFIG_PATH="/opt/local/lib64/pkgconfig"
>> F77="gfortran"
>> FFLAGS="-g -ff2c"
>> FC="gfortran"
>> FCFLAGS=""
>>
>> sessionInfo()
>> R version 2.14.2 (2012-02-29)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>>  [1] LC_CTYPE=en_US.ISO8859-1       LC_NUMERIC=C
>>  [3] LC_TIME=en_US.ISO8859-1        LC_COLLATE=en_US.ISO8859-1
>>  [5] LC_MONETARY=en_US.ISO8859-1    LC_MESSAGES=en_US.ISO8859-1
>>  [7] LC_PAPER=C                     LC_NAME=C
>>  [9] LC_ADDRESS=C                   LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.ISO8859-1 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] RcppEigen_0.2.0 Rcpp_0.9.10     inline_0.3.8
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_2.14.2 grid_2.14.2     lattice_0.20-6  Matrix_1.0-5
>> [5] tools_2.14.2
>>
>> yum install suitesparse
>> Loaded plugins: auto-update-debuginfo, refresh-packagekit, rhnplugin
>> Setting up Install Process
>> Package suitesparse-3.4.0-2.el6.x86_64 already installed and latest version
>> Nothing to do
>>
>> --
>> 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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