#include < Rcpp.h >
#include < RcppEigen.h >
#include <Eigen/Dense>
#include <iostream>
#include <string>
using Eigen::MatrixXd;
using namespace std;
using namespace Rcpp;
using namespace RcppEigen;
using namespace Eigen;

RcppExport SEXP MatOp(SEXP Xr, SEXP Yr, SEXP Kr)
{
  MatrixXd X = RcppEigen::as<MatrixXd>(Xr);
  MatrixXd Y = RcppEigen::as<MatrixXd>(Yr);
  string K = Rcpp::as<string>(Kr);

  int n=X.rows();
  int p=X.cols();
  int nY=Y.cols();
  MatrixXd I(n,n);
  I.setIdentity(n,n);
  double SSE=(Y.transpose()*(I-X*(X.transpose()*X).inverse()*X.transpose())*Y).determinant();

  if(Criteria=="k1")
    return (wrap(n*log(SSE/n)+log(n)*p));
  if(Criteria=="k2")
    return (wrap(n*log(SSE/n)+(2*p*nY*n+nY*(nY+1))/n-2/n+n+2));
}

CRT_R <- function(Xr,Yr,criteriar) {
  .Call('CRTRCppEigen',Xr,Yr,criteriar,PACKAGE = 'CRTRCppEigen')
}

Rcmd INSTALL --build CRTRCppEigen

PAUSE

Rcmd build CRTRCppEigen

pause

Rcmd INSTALL CRTRCppEigen

PAUSE

Rcmd check CRTRCppEigen

PAUSE

C:Windowssystem32;C:Windows;C:WindowsSystem32Wbem;C:WindowsSystem32WindowsPowerShellv1.0;c:Program Files (x86)Hewlett-PackardHP ProtectTools Security ManagerBin;c:Program FilesIntelDMIX;C:Program Files (x86)IntelServicesIPT;C:Program FilesSASHomeSecure;C:Program FilesSASHomex86Secure;C:OptMiKTeX2.9miktexbinx64;C:OptMiKTeX2.9miktexbinx64;C:Rtoolsbin;C:Rtoolsgcc-4.6.3bin;C:RR-3.1.1binx64;C:RR-3.1.1bini386;

* installing *source* package 'CRTRCppEigen' ...
    ** libs

    *** arch - i386
    cygwin warning:
      MS-DOS style path detected: C:/R/R-31~1.1/etc/i386/Makeconf
      Preferred POSIX equivalent is: /cygdrive/c/R/R-31~1.1/etc/i386/Makeconf
      CYGWIN environment variable option "nodosfilewarning" turns off this warning.
      Consult the user's guide for more details about POSIX paths:
        http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
    g++ -m32 -I"C:/R/R-31~1.1/include" -DNDEBUG    -I"C:/Users/LJH/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/LJH/Documents/R/win-library/3.1/RcppEigen/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c CRTRCppEigen.cpp -o CRTRCppEigen.o
    CRTRCppEigen.cpp:3:20: fatal error:  Rcpp.h : No such file or directory
    compilation terminated.
    make: *** [CRTRCppEigen.o] Error 1
    Warning: running command 'make -f "Makevars.win" -f "C:/R/R-31~1.1/etc/i386/Makeconf" -f "C:/R/R-31~1.1/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="CRTRCppEigen.dll" OBJECTS="CRTRCppEigen.o RcppExports.o rcppeigen_hello_world.o"' had status 2
    cygwin warning:
      MS-DOS style path detected: C:/R/R-31~1.1/etc/i386/Makeconf
      Preferred POSIX equivalent is: /cygdrive/c/R/R-31~1.1/etc/i386/Makeconf
      CYGWIN environment variable option "nodosfilewarning" turns off this warning.
      Consult the user's guide for more details about POSIX paths:
        http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
    g++ -m32 -I"C:/R/R-31~1.1/include" -DNDEBUG    -I"C:/Users/LJH/Documents/R/win-library/3.1/Rcpp/include" -I"C:/Users/LJH/Documents/R/win-library/3.1/RcppEigen/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c CRTRCppEigen.cpp -o CRTRCppEigen.o
    CRTRCppEigen.cpp:3:20: fatal error:  Rcpp.h : No such file or directory
    compilation terminated.
    make: *** [CRTRCppEigen.o] Error 1
    Warning: running command 'make -f "Makevars.win" -f "C:/R/R-31~1.1/etc/i386/Makeconf" -f "C:/R/R-31~1.1/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="CRTRCppEigen.dll" OBJECTS="CRTRCppEigen.o RcppExports.o rcppeigen_hello_world.o" symbols.rds' had status 2
    ERROR: compilation failed for package 'CRTRCppEigen'
    * removing 'C:/Users/LJH/Documents/CRTRCppEigen.Rcheck/CRTRCppEigen'