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
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
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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