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Header clean-up to fix lme4/lme4#745 #131

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merged 4 commits into from
Nov 1, 2023
Merged

Header clean-up to fix lme4/lme4#745 #131

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eeaba38
first try (no rev. dep. checked yet)
jaganmn Oct 6, 2023
2849344
Suggests: Matrix { and sort Suggests }
jaganmn Oct 6, 2023
c3cd732
less (apparently useless) copying from lme4
jaganmn Oct 6, 2023
451678f
fallback prefix matching original prefix
jaganmn Oct 8, 2023
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Expand Up @@ -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
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Just a side comment and not a request to change: When I modify code (particular "other people's code" I try to be minimal. Adding Matrix was needed on the Suggests:, doing it at the front is fine, reordering the four remaining words just puts cognitive load here that we do not need. (Again, no need to change, just a comment.)

URL: https://github.com/RcppCore/RcppEigen, https://dirk.eddelbuettel.com/code/rcpp.eigen.html
BugReports: https://github.com/RcppCore/RcppEigen/issues
1 change: 0 additions & 1 deletion NAMESPACE
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@@ -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")
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4 changes: 0 additions & 4 deletions inst/include/Eigen/CholmodSupport
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Expand Up @@ -12,10 +12,6 @@

#include "src/Core/util/DisableStupidWarnings.h"

extern "C" {
#include <RcppEigenCholmod.h>
}

/** \ingroup Support_modules
* \defgroup CholmodSupport_Module CholmodSupport module
*
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22 changes: 11 additions & 11 deletions inst/include/Eigen/src/CholmodSupport/CholmodSupport.h
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Expand Up @@ -195,23 +195,23 @@ 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); }
Expand Down Expand Up @@ -246,11 +246,11 @@ 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;
Expand All @@ -268,7 +268,7 @@ 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);
Expand All @@ -293,15 +293,15 @@ 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 */
Expand All @@ -316,15 +316,15 @@ 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

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