#include "Mdefines.h"
#include "cholmod-common.h"

Macros
#define	MKMS(_FORMAT_, ...) mkString(Matrix_sprintf(_FORMAT_, __VA_ARGS__))

#define	FREE_THEN(_EXPR_)

#define	FREE_THEN(_EXPR_)

#define	FREE_THEN(_EXPR_)

#define	FREE_THEN(_EXPR_)

#define	SET_FRAME_FROM_MEMBER(_MEMBER_, _KIND_)

#define	GET_MEMBER_FROM_FRAME(_MEMBER_, _KIND_)

Functions
SEXP	checkpi (SEXP p, SEXP i, int m, int n)

cholmod_factor *	sexp_as_cholmod_factor (cholmod_factor *L, SEXP from)
	Coerce from CHMfactor to (cholmod_factor *)

cholmod_sparse *	sexp_as_cholmod_sparse (cholmod_sparse *A, SEXP from, Rboolean checkUnit, Rboolean sortInPlace)
	Coerce from CsparseMatrix to (cholmod_sparse *)

cholmod_triplet *	sexp_as_cholmod_triplet (cholmod_triplet *A, SEXP from, Rboolean checkUnit)
	Coerce from TsparseMatrix to (cholmod_triplet *)

cholmod_dense *	sexp_as_cholmod_dense (cholmod_dense *A, SEXP from)
	Coerce from [nlidz]geMatrix or vector to (cholmod_dense *)

cholmod_dense *	numeric_as_cholmod_dense (cholmod_dense A, double data, int nrow, int ncol)
	Coerce from (double ) to (cholmod_dense ) with given dimensions.

SEXP	cholmod_factor_as_sexp (cholmod_factor *L, int doFree)
	Coerce from (cholmod_factor *) to CHMfactor.

SEXP	cholmod_sparse_as_sexp (cholmod_sparse A, int doFree, int ttype, int doLogic, const char diagString, SEXP dimnames)
	Coerce from (cholmod_sparse *) to CsparseMatrix.

SEXP	cholmod_triplet_as_sexp (cholmod_triplet A, int doFree, int ttype, int doLogic, const char diagString, SEXP dimnames)
	Coerce from (cholmod_triplet *) to TsparseMatrix.

SEXP	cholmod_dense_as_sexp (cholmod_dense *A, int doFree)
	Coerce from (cholmod_dense *) to [dz]geMatrix.

double	cholmod_factor_ldetA (cholmod_factor *L)
	Log determinant from Cholesky factorization.

cholmod_factor *	cholmod_factor_update (cholmod_factor L, cholmod_sparse A, double beta)
	Update a Cholesky factorization.

static void	R_cholmod_error_handler (int status, const char file, int line, const char message)

int	R_cholmod_start (cholmod_common *Common)

int	R_cholmod_finish (cholmod_common *Common)

SEXP	R_cholmod_common_envini (SEXP rho)

void	R_cholmod_common_envset (void)

void	R_cholmod_common_envget (void)

Variables
SEXP	cholmod_common_env

static SEXP	dboundSym

static SEXP	grow0Sym

static SEXP	grow1Sym

static SEXP	grow2Sym

static SEXP	maxrankSym

static SEXP	supernodal_switchSym

static SEXP	supernodalSym

static SEXP	final_asisSym

static SEXP	final_superSym

static SEXP	final_llSym

static SEXP	final_packSym

static SEXP	final_monotonicSym

static SEXP	final_resymbolSym

static SEXP	prefer_zomplexSym

static SEXP	prefer_upperSym

static SEXP	quick_return_if_not_posdefSym

static SEXP	nmethodsSym

static SEXP	postorderSym

static SEXP	m0_ordSym

Macro Definition Documentation

◆ FREE_THEN [1/4]

#define FREE_THEN ( _EXPR_ )

Value:

    do { \
        if (doFree != 0) { \
            if (doFree < 0) \
                R_Free(L); \
            else if (L->itype == CHOLMOD_INT) \
                cholmod_free_factor(&L, &c); \
            else \
                cholmod_l_free_factor(&L, &cl); \
            _EXPR_; \
        } \
    } while (0)

◆ FREE_THEN [2/4]

#define FREE_THEN ( _EXPR_ )

Value:

    do { \
        if (doFree != 0) { \
            if (doFree < 0) \
                R_Free(A_); \
            else if (A_->itype == CHOLMOD_INT) \
                cholmod_free_sparse(&A_, &c); \
            else \
                cholmod_l_free_sparse(&A_, &cl); \
            _EXPR_; \
        } \
    } while (0)

◆ FREE_THEN [3/4]

#define FREE_THEN ( _EXPR_ )

Value:

    do { \
        if (doFree != 0) { \
            if (doFree < 0) \
                R_Free(A); \
            else if (A->itype == CHOLMOD_INT) \
                cholmod_free_triplet(&A, &c); \
            else \
                cholmod_l_free_triplet(&A, &cl); \
            _EXPR_; \
        } \
    } while (0)

◆ FREE_THEN [4/4]

#define FREE_THEN ( _EXPR_ )

Value:

    do { \
        if (doFree != 0) { \
            if (doFree < 0) \
                R_Free(A); \
            else \
                cholmod_free_dense(&A, &c); \
            _EXPR_; \
        } \
    } while (0)

◆ GET_MEMBER_FROM_FRAME

#define GET_MEMBER_FROM_FRAME	(	_MEMBER_,
		_KIND_
	)

Value:

    do { \
        PROTECT(tmp = findVarInFrame(rho, _MEMBER_ ## Sym)); \
        c. _MEMBER_ = as ## _KIND_(tmp); \
        UNPROTECT(1); \
    } while (0)

◆ MKMS

#define MKMS	(	_FORMAT_,
		...
	)	mkString(Matrix_sprintf(_FORMAT_, __VA_ARGS__))

◆ SET_FRAME_FROM_MEMBER

#define SET_FRAME_FROM_MEMBER	(	_MEMBER_,
		_KIND_
	)

Value:

    do { \
        PROTECT(tmp = Scalar ## _KIND_(c. _MEMBER_)); \
        defineVar(_MEMBER_ ## Sym, tmp, rho); \
        UNPROTECT(1); \
    } while (0)

Function Documentation

◆ checkpi()

SEXP checkpi	(	SEXP	p,
		SEXP	i,
		int	m,
		int	n
	)

Definition at line 5 of file cholmod-common.c.

References _, and MKMS.

Referenced by CsparseMatrix_validate_maybe_sorting(), and sexp_as_cholmod_sparse().

◆ cholmod_dense_as_sexp()

SEXP cholmod_dense_as_sexp	(	cholmod_dense *	A,
		int	doFree
	)

Coerce from (cholmod_dense *) to [dz]geMatrix.

Allocates an S4 object of class [dz]geMatrix and copies into the slots from members of a pointed-to cholmod_dense struct. The specific class of the result is determined by struct member xtype.

Parameters

A	a pointer to a cholmod_dense struct.
doFree	a flag indicating if and how to free A before returning. (0) don't free, (>0) free with cholmod_free_dense, (<0) free with R_Free.

Returns: A [dz]geMatrix.

Definition at line 954 of file cholmod-common.c.

References _, FREE_THEN, GET_SLOT, Matrix_DimSym, Matrix_xSym, newObject(), and SET_SLOT.

Referenced by R_init_Matrix().

◆ cholmod_factor_as_sexp()

SEXP cholmod_factor_as_sexp	(	cholmod_factor *	L,
		int	doFree
	)

Coerce from (cholmod_factor *) to CHMfactor.

Allocates an S4 object inheriting from virtual class CHMfactor and copies into the slots from members of a pointed-to cholmod_factor struct. The specific class of the result is determined by struct members xtype and is_super.

Parameters

L	a pointer to a cholmod_factor struct.
doFree	a flag indicating if and how to free L before returning. (0) don't free, (>0) free with cholmod_free_factor, (<0) free with R_Free.

Returns: A CHMfactor.

Definition at line 584 of file cholmod-common.c.

References _, FREE_THEN, GET_SLOT, Matrix_DimSym, Matrix_iSym, Matrix_permSym, Matrix_pSym, Matrix_xSym, newObject(), and SET_SLOT.

Referenced by R_init_Matrix().

◆ cholmod_factor_ldetA()

double cholmod_factor_ldetA ( cholmod_factor * L )

Log determinant from Cholesky factorization.

Computes log(det(A)) given the Cholesky factorization of A as P1 * A * P1' = L1 * D * L1' = L * L', L = L1 * sqrt(D). The result is computed as sum(log(diag(D))) or 2*sum(log(diag(L))), depending on members is_super and is_ll of the supplied struct. Note that CHOLMOD does not require diag(D) to be positive and that this routine does not check (FIXME).

Parameters

L	a pointer to a cholmod_factor struct. It is assumed that L->xtype=CHOLMOD_REAL.

Definition at line 1017 of file cholmod-common.c.

References _.

Referenced by R_init_Matrix().

◆ cholmod_factor_update()

cholmod_factor * cholmod_factor_update	(	cholmod_factor *	L,
		cholmod_sparse *	A,
		double	beta
	)

Update a Cholesky factorization.

Updates in-place the Cholesky factorization of a symmetric matrix X+alpha*I with the Cholesky factorization of (1) A+beta*I, where A is a symmetric matrix sharing the nonzero pattern of X, or (2) A*A'+beta*I, where A is a general matrix sharing the nonzero pattern of Y, assuming that X = Y*Y'.

Parameters

L	a pointer to a cholmod_factor struct, to be modified in-place.
A	a pointer to a cholmod_sparse struct.
beta	a multiplier, typically positive, to guarantee strict diagonal dominance.

Returns: L.

Definition at line 1064 of file cholmod-common.c.

References _, and c.

Referenced by R_init_Matrix().

◆ cholmod_sparse_as_sexp()

SEXP cholmod_sparse_as_sexp	(	cholmod_sparse *	A,
		int	doFree,
		int	ttype,
		int	doLogic,
		const char *	diagString,
		SEXP	dimnames
	)

Coerce from (cholmod_sparse *) to CsparseMatrix.

Allocates an S4 object inheriting from virtual class CsparseMatrix and copies into the slots from members of a pointed-to cholmod_sparse struct. The specific class of the result is determined by struct members xtype and stype and by arguments ttype and doLogic.

Parameters

A	a pointer to a cholmod_sparse struct.
doFree	a flag indicating if and how to free A before returning. (0) don't free, (>0) free with cholmod_free_sparse, (<0) free with R_Free.
ttype	a flag indicating if the result should be a .tCMatrix. (0) not .tCMatrix, (>0) .tCMatrix with uplo="U", (<0) .tCMatrix with uplo="L". If ttype=0, then the result is a .gCMatrix or .sCMatrix depending on stype. (0) .gCMatrix, (>0) .sCMatrix with uplo="U", (<0) .sCMatrix with uplo="L".
doLogic	a flag indicating if the result should be a l.CMatrix if xtype=CHOLMOD_REAL.
diagString	a null-terminated string or NULL. The diag slot of a .tCMatrix result is "N" if and only if diagString is NULL or diagString[0] is 'N'.
dimnames	an R object specifying the Dimnames slot of the result, unused if not a list of length 2.

Returns: A CsparseMatrix.

Definition at line 732 of file cholmod-common.c.

References _, c, FREE_THEN, GET_SLOT, Matrix_diagSym, Matrix_DimNamesSym, Matrix_DimSym, Matrix_iSym, Matrix_pSym, Matrix_uploSym, Matrix_xSym, newObject(), and SET_SLOT.

Referenced by R_init_Matrix().

◆ cholmod_triplet_as_sexp()

SEXP cholmod_triplet_as_sexp	(	cholmod_triplet *	A,
		int	doFree,
		int	ttype,
		int	doLogic,
		const char *	diagString,
		SEXP	dimnames
	)

Coerce from (cholmod_triplet *) to TsparseMatrix.

Allocates an S4 object inheriting from virtual class TsparseMatrix and copies into the slots from members of a pointed-to cholmod_triplet struct. The specific class of the result is determined by struct members xtype and stype and by arguments ttype and doLogic.

Parameters

A	a pointer to a cholmod_triplet struct.
doFree	a flag indicating if and how to free A before returning. (0) don't free, (>0) free with cholmod_free_triplet, (<0) free with R_Free.
ttype	a flag indicating if the result should be a .tTMatrix. (0) not .tTMatrix, (>0) .tTMatrix with uplo="U", (<0) .tTMatrix with uplo="L". If ttype=0, then the result is a .gTMatrix or .sTMatrix depending on stype. (0) .gTMatrix, (>0) .sTMatrix with uplo="U", (<0) .sTMatrix with uplo="L".
doLogic	a flag indicating if the result should be an l.TMatrix if xtype=CHOLMOD_REAL.
diagString	a null-terminated string or NULL. The diag slot of a .tTMatrix result is "N" if and only if diagString is NULL or diagString[0] is 'N'.
dimnames	an R object specifying the Dimnames slot of the result, unused if not a list of length 2.

Returns: A TsparseMatrix.

Definition at line 848 of file cholmod-common.c.

References _, FREE_THEN, GET_SLOT, Matrix_diagSym, Matrix_DimNamesSym, Matrix_DimSym, Matrix_iSym, Matrix_jSym, Matrix_uploSym, Matrix_xSym, newObject(), and SET_SLOT.

Referenced by R_init_Matrix().

◆ numeric_as_cholmod_dense()

cholmod_dense * numeric_as_cholmod_dense	(	cholmod_dense *	A,
		double *	data,
		int	nrow,
		int	ncol
	)

Coerce from (double *) to (cholmod_dense *) with given dimensions.

An analogue of base::matrix(data, nrow, ncol), where typeof(data)=="double" and length(data)==nrow*ncol.

Parameters

A	a pointer to a cholmod_dense struct, to be modified in-place.
data	a pointer to an nrowncolsizeof(double) block of memory.
nrow	the desired number of rows.
ncol	the desired number of columns.

Returns: A.

Definition at line 554 of file cholmod-common.c.

Referenced by R_init_Matrix().

◆ R_cholmod_common_envget()

void R_cholmod_common_envget ( void )

Definition at line 1217 of file cholmod-common.c.

References c, cholmod_common_env, GET_MEMBER_FROM_FRAME, and m0_ordSym.

Referenced by dpCMatrix_trf_(), and R_cholmod_error_handler().

◆ R_cholmod_common_envini()

SEXP R_cholmod_common_envini ( SEXP rho )

Definition at line 1154 of file cholmod-common.c.

References cholmod_common_env, dboundSym, ERROR_INVALID_TYPE, final_asisSym, final_llSym, final_monotonicSym, final_packSym, final_resymbolSym, final_superSym, grow0Sym, grow1Sym, grow2Sym, m0_ordSym, maxrankSym, nmethodsSym, postorderSym, prefer_upperSym, prefer_zomplexSym, quick_return_if_not_posdefSym, R_cholmod_common_envset(), supernodal_switchSym, and supernodalSym.

◆ R_cholmod_common_envset()

void R_cholmod_common_envset ( void )

Definition at line 1181 of file cholmod-common.c.

References c, cholmod_common_env, m0_ordSym, and SET_FRAME_FROM_MEMBER.

Referenced by dpCMatrix_trf_(), and R_cholmod_common_envini().

◆ R_cholmod_error_handler()

static void R_cholmod_error_handler	(	int	status,
		const char *	file,
		int	line,
		const char *	message
	)

static

Definition at line 1092 of file cholmod-common.c.

References _, and R_cholmod_common_envget().

Referenced by R_cholmod_start().

◆ R_cholmod_finish()

int R_cholmod_finish ( cholmod_common * Common )

Definition at line 1122 of file cholmod-common.c.

References _.

Referenced by R_unload_Matrix().

◆ R_cholmod_start()

int R_cholmod_start ( cholmod_common * Common )

Definition at line 1104 of file cholmod-common.c.

References _, and R_cholmod_error_handler().

Referenced by R_init_Matrix().

◆ sexp_as_cholmod_dense()

cholmod_dense * sexp_as_cholmod_dense	(	cholmod_dense *	A,
		SEXP	from
	)

Coerce from [nlidz]geMatrix or vector to (cholmod_dense *)

Sets the members of a pointed-to cholmod_dense struct, using "data" obtained from slots of a [nlidz]geMatrix. The result should not be freed using cholmod_free_dense, as the resulting members point to memory controlled by R, not by CHOLMOD.

Parameters

A	a pointer to a cholmod_dense struct, to be modified in-place.
from	an S4 object inheriting from class [nlidz]geMatrix or a traditional vector of type "logical", "integer", "double", or "complex" (to be handled as a 1-column matrix if not a matrix).

Returns: A.

Definition at line 470 of file cholmod-common.c.

References ERROR_INVALID_TYPE, GET_SLOT, Matrix_DimSym, Matrix_xSym, and valid.

Referenced by R_init_Matrix().

◆ sexp_as_cholmod_factor()

cholmod_factor * sexp_as_cholmod_factor	(	cholmod_factor *	L,
		SEXP	from
	)

Coerce from CHMfactor to (cholmod_factor *)

Sets the members of a pointed-to cholmod_factor struct, using "data" obtained from slots of a CHMfactor. The result should not be freed using cholmod_free_factor, as the resulting members point to memory controlled by R, not by CHOLMOD.

Parameters

L	a pointer to a cholmod_factor struct, to be modified in-place.
from	an S4 object inheriting from virtual class CHMfactor.

Returns: L.

Definition at line 80 of file cholmod-common.c.

References _, c, ERROR_INVALID_CLASS, ERROR_INVALID_TYPE, GET_SLOT, Matrix_DimSym, Matrix_iSym, Matrix_permSym, Matrix_pSym, Matrix_xSym, and valid.

Referenced by R_init_Matrix().

◆ sexp_as_cholmod_sparse()

cholmod_sparse * sexp_as_cholmod_sparse	(	cholmod_sparse *	A,
		SEXP	from,
		Rboolean	checkUnit,
		Rboolean	sortInPlace
	)

Coerce from CsparseMatrix to (cholmod_sparse *)

Sets the members of a pointed-to cholmod_sparse struct, using "data" obtained from slots of a CsparseMatrix. The result should not be freed using cholmod_free_sparse, as the resulting members point to memory controlled by R, not by CHOLMOD.

Parameters

A	a pointer to a cholmod_sparse struct, to be modified in-place.
from	an S4 object inheriting from virtual class CsparseMatrix.
checkUnit	a boolean indicating if the unit diagonal of formally unit triangular CsparseMatrix should be allocated.
sortInPlace	a boolean indicating if unsorted CsparseMatrix should be sorted in place to avoid an allocation.

Returns: A.

Definition at line 188 of file cholmod-common.c.

References _, c, checkpi(), ERROR_INVALID_CLASS, GET_SLOT, Matrix_diagSym, Matrix_DimSym, Matrix_iSym, Matrix_pSym, Matrix_uploSym, Matrix_xSym, and valid.

Referenced by R_init_Matrix().

◆ sexp_as_cholmod_triplet()

cholmod_triplet * sexp_as_cholmod_triplet	(	cholmod_triplet *	A,
		SEXP	from,
		Rboolean	checkUnit
	)

Coerce from TsparseMatrix to (cholmod_triplet *)

Sets the members of a pointed-to cholmod_triplet struct, using "data" obtained from slots of a TsparseMatrix. The result should not be freed using cholmod_free_sparse, as the resulting members point to memory controlled by R, not by CHOLMOD.

Parameters

A	a pointer to a cholmod_triplet struct, to be modified in-place.
from	an S4 object inheriting from virtual class TsparseMatrix.
checkUnit	a boolean indicating if the unit diagonal of formally unit triangular TsparseMatrix should be allocated.

Returns: A.

Definition at line 340 of file cholmod-common.c.

References ERROR_INVALID_CLASS, GET_SLOT, Matrix_diagSym, Matrix_DimSym, Matrix_iSym, Matrix_pSym, Matrix_uploSym, Matrix_xSym, Matrix_zone, and valid.

Referenced by R_init_Matrix().

Variable Documentation

◆ cholmod_common_env

SEXP cholmod_common_env

Definition at line 1130 of file cholmod-common.c.

Referenced by R_cholmod_common_envget(), R_cholmod_common_envini(), and R_cholmod_common_envset().

◆ dboundSym

SEXP dboundSym

static

Definition at line 1134 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ final_asisSym

SEXP final_asisSym

static

Definition at line 1141 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ final_llSym

SEXP final_llSym

static

Definition at line 1143 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ final_monotonicSym

SEXP final_monotonicSym

static

Definition at line 1145 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ final_packSym

SEXP final_packSym

static

Definition at line 1144 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ final_resymbolSym

SEXP final_resymbolSym

static

Definition at line 1146 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ final_superSym

SEXP final_superSym

static

Definition at line 1142 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ grow0Sym

SEXP grow0Sym

static

Definition at line 1135 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ grow1Sym

SEXP grow1Sym

static

Definition at line 1136 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ grow2Sym

SEXP grow2Sym

static

Definition at line 1137 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ m0_ordSym

SEXP m0_ordSym

static

Definition at line 1152 of file cholmod-common.c.

Referenced by R_cholmod_common_envget(), R_cholmod_common_envini(), and R_cholmod_common_envset().

◆ maxrankSym

SEXP maxrankSym

static

Definition at line 1138 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ nmethodsSym

SEXP nmethodsSym

static

Definition at line 1150 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ postorderSym

SEXP postorderSym

static

Definition at line 1151 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ prefer_upperSym

SEXP prefer_upperSym

static

Definition at line 1148 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ prefer_zomplexSym

SEXP prefer_zomplexSym

static

Definition at line 1147 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ quick_return_if_not_posdefSym

SEXP quick_return_if_not_posdefSym

static

Definition at line 1149 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ supernodal_switchSym

SEXP supernodal_switchSym

static

Definition at line 1139 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

◆ supernodalSym

SEXP supernodalSym

static

Definition at line 1140 of file cholmod-common.c.

Referenced by R_cholmod_common_envini().

Macros

Functions

Variables

Macro Definition Documentation

◆ FREE_THEN [1/4]

◆ FREE_THEN [2/4]

◆ FREE_THEN [3/4]

◆ FREE_THEN [4/4]

◆ GET_MEMBER_FROM_FRAME

◆ MKMS

◆ SET_FRAME_FROM_MEMBER

Function Documentation

◆ checkpi()

◆ cholmod_dense_as_sexp()

◆ cholmod_factor_as_sexp()

◆ cholmod_factor_ldetA()

◆ cholmod_factor_update()

◆ cholmod_sparse_as_sexp()

◆ cholmod_triplet_as_sexp()

◆ numeric_as_cholmod_dense()

◆ R_cholmod_common_envget()

◆ R_cholmod_common_envini()

◆ R_cholmod_common_envset()

◆ R_cholmod_error_handler()

◆ R_cholmod_finish()

◆ R_cholmod_start()

◆ sexp_as_cholmod_dense()

◆ sexp_as_cholmod_factor()

◆ sexp_as_cholmod_sparse()

◆ sexp_as_cholmod_triplet()

Variable Documentation

◆ cholmod_common_env

◆ dboundSym

◆ final_asisSym

◆ final_llSym

◆ final_monotonicSym

◆ final_packSym

◆ final_resymbolSym

◆ final_superSym

◆ grow0Sym

◆ grow1Sym

◆ grow2Sym

◆ m0_ordSym

◆ maxrankSym

◆ nmethodsSym

◆ postorderSym

◆ prefer_upperSym

◆ prefer_zomplexSym

◆ quick_return_if_not_posdefSym

◆ supernodal_switchSym

◆ supernodalSym