Merge pull request #131 from jaganmn/rcppeigen_cholmod

Header clean-up to fix lme4/lme4#745

Author: eddelbuettel

DESCRIPTION

@@ -24,7 +24,7 @@ License: GPL (>= 2) | file LICENSE
 LazyLoad: yes
 Depends: R (>= 3.6.0)
 LinkingTo: Rcpp
-Imports: Matrix (>= 1.1-0), Rcpp (>= 0.11.0), stats, utils
-Suggests: inline, tinytest, pkgKitten, microbenchmark
+Imports: Rcpp (>= 0.11.0), stats, utils
+Suggests: Matrix, inline, microbenchmark, pkgKitten, tinytest
 URL: https://github.com/RcppCore/RcppEigen, https://dirk.eddelbuettel.com/code/rcpp.eigen.html
 BugReports: https://github.com/RcppCore/RcppEigen/issues

NAMESPACE

@@ -1,6 +1,5 @@
 useDynLib("RcppEigen", .registration=TRUE)
 
-importClassesFrom("Matrix", "dgCMatrix", "dgeMatrix", "dsCMatrix", "dtCMatrix")
 importFrom("Rcpp", "evalCpp")
 importFrom("utils", "packageDescription", "package.skeleton")
 importFrom("stats", "model.frame", "model.matrix", "model.response", "fitted", "coef", "printCoefmat", "pt")

inst/include/Eigen/CholmodSupport

@@ -12,10 +12,6 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-extern "C" {
-  #include <RcppEigenCholmod.h>
-}
-
 /** \ingroup Support_modules
   * \defgroup CholmodSupport_Module CholmodSupport module
   *

inst/include/Eigen/src/CholmodSupport/CholmodSupport.h

@@ -10,6 +10,10 @@
 #ifndef EIGEN_CHOLMODSUPPORT_H
 #define EIGEN_CHOLMODSUPPORT_H
 
+#ifndef R_MATRIX_CHOLMOD
+# define R_MATRIX_CHOLMOD(_NAME_) cholmod_ ## _NAME_
+#endif
+
 namespace Eigen { 
 
 namespace internal {
@@ -195,23 +199,23 @@ class CholmodBase : public SparseSolverBase<Derived>
     {
       EIGEN_STATIC_ASSERT((internal::is_same<double,RealScalar>::value), CHOLMOD_SUPPORTS_DOUBLE_PRECISION_ONLY);
       m_shiftOffset[0] = m_shiftOffset[1] = 0.0;
-      cholmod_start(&m_cholmod);
+      R_MATRIX_CHOLMOD(start)(&m_cholmod);
     }
 
     explicit CholmodBase(const MatrixType& matrix)
       : m_cholmodFactor(0), m_info(Success), m_factorizationIsOk(false), m_analysisIsOk(false)
     {
       EIGEN_STATIC_ASSERT((internal::is_same<double,RealScalar>::value), CHOLMOD_SUPPORTS_DOUBLE_PRECISION_ONLY);
       m_shiftOffset[0] = m_shiftOffset[1] = 0.0;
-      cholmod_start(&m_cholmod);
+      R_MATRIX_CHOLMOD(start)(&m_cholmod);
       compute(matrix);
     }
 
     ~CholmodBase()
     {
       if(m_cholmodFactor)
-        cholmod_free_factor(&m_cholmodFactor, &m_cholmod);
-      cholmod_finish(&m_cholmod);
+        R_MATRIX_CHOLMOD(free_factor)(&m_cholmodFactor, &m_cholmod);
+      R_MATRIX_CHOLMOD(finish)(&m_cholmod);
     }
 
     inline StorageIndex cols() const { return internal::convert_index<StorageIndex, Index>(m_cholmodFactor->n); }
@@ -246,11 +250,11 @@ class CholmodBase : public SparseSolverBase<Derived>
     {
       if(m_cholmodFactor)
       {
-        cholmod_free_factor(&m_cholmodFactor, &m_cholmod);
+        R_MATRIX_CHOLMOD(free_factor)(&m_cholmodFactor, &m_cholmod);
         m_cholmodFactor = 0;
       }
       cholmod_sparse A = viewAsCholmod(matrix.template selfadjointView<UpLo>());
-      m_cholmodFactor = cholmod_analyze(&A, &m_cholmod);
+      m_cholmodFactor = R_MATRIX_CHOLMOD(analyze)(&A, &m_cholmod);
 
       this->m_isInitialized = true;
       this->m_info = Success;
@@ -268,7 +272,7 @@ class CholmodBase : public SparseSolverBase<Derived>
     {
       eigen_assert(m_analysisIsOk && "You must first call analyzePattern()");
       cholmod_sparse A = viewAsCholmod(matrix.template selfadjointView<UpLo>());
-      cholmod_factorize_p(&A, m_shiftOffset, 0, 0, m_cholmodFactor, &m_cholmod);
+      R_MATRIX_CHOLMOD(factorize_p)(&A, m_shiftOffset, 0, 0, m_cholmodFactor, &m_cholmod);
 
       // If the factorization failed, minor is the column at which it did. On success minor == n.
       this->m_info = (m_cholmodFactor->minor == m_cholmodFactor->n ? Success : NumericalIssue);
@@ -293,15 +297,15 @@ class CholmodBase : public SparseSolverBase<Derived>
       Ref<const Matrix<typename Rhs::Scalar,Dynamic,Dynamic,ColMajor> > b_ref(b.derived());
 
       cholmod_dense b_cd = viewAsCholmod(b_ref);
-      cholmod_dense* x_cd = cholmod_solve(CHOLMOD_A, m_cholmodFactor, &b_cd, &m_cholmod);
+      cholmod_dense* x_cd = R_MATRIX_CHOLMOD(solve)(CHOLMOD_A, m_cholmodFactor, &b_cd, &m_cholmod);
       if(!x_cd)
       {
         this->m_info = NumericalIssue;
         return;
       }
       // TODO optimize this copy by swapping when possible (be careful with alignment, etc.)
       dest = Matrix<Scalar,Dest::RowsAtCompileTime,Dest::ColsAtCompileTime>::Map(reinterpret_cast<Scalar*>(x_cd->x),b.rows(),b.cols());
-      cholmod_free_dense(&x_cd, &m_cholmod);
+      R_MATRIX_CHOLMOD(free_dense)(&x_cd, &m_cholmod);
     }
 
     /** \internal */
@@ -316,15 +320,15 @@ class CholmodBase : public SparseSolverBase<Derived>
       // note: cs stands for Cholmod Sparse
       Ref<SparseMatrix<typename RhsDerived::Scalar,ColMajor,typename RhsDerived::StorageIndex> > b_ref(b.const_cast_derived());
       cholmod_sparse b_cs = viewAsCholmod(b_ref);
-      cholmod_sparse* x_cs = cholmod_spsolve(CHOLMOD_A, m_cholmodFactor, &b_cs, &m_cholmod);
+      cholmod_sparse* x_cs = R_MATRIX_CHOLMOD(spsolve)(CHOLMOD_A, m_cholmodFactor, &b_cs, &m_cholmod);
       if(!x_cs)
       {
         this->m_info = NumericalIssue;
         return;
       }
       // TODO optimize this copy by swapping when possible (be careful with alignment, etc.)
       dest.derived() = viewAsEigen<typename DestDerived::Scalar,ColMajor,typename DestDerived::StorageIndex>(*x_cs);
-      cholmod_free_sparse(&x_cs, &m_cholmod);
+      R_MATRIX_CHOLMOD(free_sparse)(&x_cs, &m_cholmod);
     }
     #endif // EIGEN_PARSED_BY_DOXYGEN