#include "UFconfig/UFconfig.h"
#include "CHOLMOD/Include/cholmod.h"
#include "Mutils.h"

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Defines
#define	AS_CHM_DN(x) as_cholmod_dense ((CHM_DN)alloca(sizeof(cholmod_dense)), x )
#define	AS_CHM_FR(x) as_cholmod_factor ((CHM_FR)alloca(sizeof(cholmod_factor)), x )
#define	AS_CHM_SP(x) as_cholmod_sparse ((CHM_SP)alloca(sizeof(cholmod_sparse)), x, TRUE, FALSE)
#define	AS_CHM_SP__(x) as_cholmod_sparse ((CHM_SP)alloca(sizeof(cholmod_sparse)), x, FALSE, FALSE)
#define	AS_CHM_TR(x) as_cholmod_triplet((CHM_TR)alloca(sizeof(cholmod_triplet)),x, TRUE)
#define	AS_CHM_TR__(x) as_cholmod_triplet((CHM_TR)alloca(sizeof(cholmod_triplet)), x, FALSE)
#define	N_AS_CHM_DN(x, nr, nc) M_numeric_as_chm_dense((CHM_DN)alloca(sizeof(cholmod_dense)), x , nr, nc )
Typedefs
typedef cholmod_common *	CHM_CM
typedef cholmod_dense *	CHM_DN
typedef cholmod_factor *	CHM_FR
typedef cholmod_sparse *	CHM_SP
typedef cholmod_triplet *	CHM_TR
typedef const cholmod_dense *	const_CHM_DN
typedef const cholmod_factor *	const_CHM_FR
typedef const cholmod_sparse *	const_CHM_SP
typedef const cholmod_triplet *	const_CHM_TR
Functions
CHM_DN	as_cholmod_dense (CHM_DN ans, SEXP x)
	Populate ans with the pointers from x and modify its scalar elements accordingly.
CHM_FR	as_cholmod_factor (CHM_FR ans, SEXP x)
	Populate ans with the pointers from x and modify its scalar elements accordingly.
CHM_SP	as_cholmod_sparse (CHM_SP ans, SEXP x, Rboolean check_Udiag, Rboolean sort_in_place)
	Populate ans with the pointers from x and modify its scalar elements accordingly.
CHM_TR	as_cholmod_triplet (CHM_TR ans, SEXP x, Rboolean check_Udiag)
	Populate ans with the pointers from x and modify its scalar elements accordingly.
CHM_DN	as_cholmod_x_dense (CHM_DN ans, SEXP x)
Rboolean	check_sorted_chm (CHM_SP A)
SEXP	chm_dense_to_matrix (CHM_DN a, int dofree, SEXP dn)
	Copy the contents of a to a matrix object and, optionally, free a or free both a and its pointer to its contents.
SEXP	chm_dense_to_SEXP (CHM_DN a, int dofree, int Rkind, SEXP dn)
	Copy the contents of a to an appropriate denseMatrix object and, optionally, free a or free both a and its pointer to its contents.
void	chm_diagN2U (CHM_SP chx, int uploT, Rboolean do_realloc)
	Drop the (unit) diagonal entries from a cholmod_sparse matrix.
static R_INLINE Rboolean	chm_factor_ok (CHM_FR f)
SEXP	chm_factor_to_SEXP (CHM_FR f, int dofree)
	Copy the contents of f to an appropriate CHMfactor object and, optionally, free f or free both f and its pointer to its contents.
void	CHM_restore_common ()
SEXP	CHM_set_common_env (SEXP rho)
SEXP	chm_sparse_to_SEXP (CHM_SP a, int dofree, int uploT, int Rkind, const char *diag, SEXP dn)
	Copy the contents of a to an appropriate CsparseMatrix object and, optionally, free a or free both a and its the pointers to its contents.
void	CHM_store_common ()
SEXP	chm_triplet_to_SEXP (CHM_TR a, int dofree, int uploT, int Rkind, const char *diag, SEXP dn)
	Copy the contents of a to an appropriate TsparseMatrix object and, optionally, free a or free both a and its the pointers to its contents.
SEXP	CHMfactor_validate (SEXP obj)
SEXP	CHMsimpl_validate (SEXP obj)
SEXP	CHMsuper_validate (SEXP obj)
CHM_DN	numeric_as_chm_dense (CHM_DN ans, double *v, int nr, int nc)
void	R_cholmod_error (int status, const char file, int line, const char message)
int	R_cholmod_l_start (CHM_CM Common)
int	R_cholmod_start (CHM_CM Common)
	Initialize the CHOLMOD library and replace the print and error functions by R-specific versions.
Variables
cholmod_common	c
cholmod_common	cl

Define Documentation

#define AS_CHM_DN ( x ) as_cholmod_dense ((CHM_DN)alloca(sizeof(cholmod_dense)), x )

Definition at line 41 of file chm_common.h.

Referenced by CHMfactor_solve(), Csparse_dense_crossprod(), Csparse_dense_prod(), dense_to_Csparse(), dgCMatrix_cholsol(), and dsCMatrix_matrix_solve().

#define AS_CHM_FR ( x ) as_cholmod_factor ((CHM_FR)alloca(sizeof(cholmod_factor)), x )

Definition at line 42 of file chm_common.h.

Referenced by CHMfactor_ldetL2(), CHMfactor_ldetL2up(), CHMfactor_solve(), CHMfactor_spsolve(), CHMfactor_to_sparse(), CHMfactor_update(), destructive_CHM_update(), and internal_chm_factor().

#define AS_CHM_SP ( x ) as_cholmod_sparse ((CHM_SP)alloca(sizeof(cholmod_sparse)), x, TRUE, FALSE)

Definition at line 43 of file chm_common.h.

Referenced by Csparse_crossprod(), Csparse_Csparse_crossprod(), Csparse_Csparse_prod(), Csparse_dense_crossprod(), Csparse_dense_prod(), Csparse_MatrixMarket(), Csparse_submatrix(), dgCMatrix_cholsol(), and dsCMatrix_Csparse_solve().

#define AS_CHM_SP__ ( x ) as_cholmod_sparse ((CHM_SP)alloca(sizeof(cholmod_sparse)), x, FALSE, FALSE)

#define AS_CHM_TR ( x ) as_cholmod_triplet((CHM_TR)alloca(sizeof(cholmod_triplet)),x, TRUE)

Definition at line 44 of file chm_common.h.

Referenced by Csparse_crossprod().

#define AS_CHM_TR__ ( x ) as_cholmod_triplet((CHM_TR)alloca(sizeof(cholmod_triplet)), x, FALSE)

Definition at line 47 of file chm_common.h.

Referenced by Csparse_crossprod(), Tsparse_to_Csparse(), and Tsparse_to_tCsparse().

#define N_AS_CHM_DN	(	x,
		nr,
		nc
	)	M_numeric_as_chm_dense((CHM_DN)alloca(sizeof(cholmod_dense)), x , nr, nc )

Definition at line 50 of file chm_common.h.

Typedef Documentation

typedef cholmod_common* CHM_CM

Definition at line 18 of file chm_common.h.

typedef cholmod_dense* CHM_DN

Definition at line 19 of file chm_common.h.

typedef cholmod_factor* CHM_FR

Definition at line 21 of file chm_common.h.

typedef cholmod_sparse* CHM_SP

Definition at line 23 of file chm_common.h.

typedef cholmod_triplet* CHM_TR

Definition at line 25 of file chm_common.h.

typedef const cholmod_dense* const_CHM_DN

Definition at line 20 of file chm_common.h.

typedef const cholmod_factor* const_CHM_FR

Definition at line 22 of file chm_common.h.

typedef const cholmod_sparse* const_CHM_SP

Definition at line 24 of file chm_common.h.

typedef const cholmod_triplet* const_CHM_TR

Definition at line 26 of file chm_common.h.

Function Documentation

CHM_DN as_cholmod_dense	(	CHM_DN	ans,
		SEXP	x
	)

Populate ans with the pointers from x and modify its scalar elements accordingly.

Note that later changes to the contents of ans will change the contents of the SEXP.

In most cases this function is called through the macro AS_CHM_DN. It is unusual to call it directly.

Parameters:

ans	a CHM_DN pointer.
x	pointer to an object that inherits from (denseMatrix ^ generalMatrix)

Returns:: ans containing pointers to the slots of x.

Definition at line 593 of file chm_common.c.

References _AS_cholmod_dense_1, _AS_cholmod_dense_2, Matrix_xSym, and RallocedREAL().

Referenced by R_init_Matrix().

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CHM_FR as_cholmod_factor	(	CHM_FR	ans,
		SEXP	x
	)

Populate ans with the pointers from x and modify its scalar elements accordingly.

Note that later changes to the contents of ans will change the contents of the SEXP.

In most cases this function is called through the macro AS_CHM_FR. It is unusual to call it directly.

Parameters:

ans	an CHM_FR object
x	pointer to an object that inherits from CHMfactor

Returns:: ans containing pointers to the slots of x.

Definition at line 865 of file chm_common.c.

References _, c, Matrix_check_class_etc(), Matrix_iSym, Matrix_permSym, Matrix_pSym, MATRIX_VALID_CHMfactor, and Matrix_xSym.

Referenced by R_init_Matrix().

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CHM_SP as_cholmod_sparse	(	CHM_SP	ans,
		SEXP	x,
		Rboolean	check_Udiag,
		Rboolean	sort_in_place
	)

Populate ans with the pointers from x and modify its scalar elements accordingly.

Note that later changes to the contents of ans will change the contents of the SEXP.

In most cases this function is called through the macros AS_CHM_SP() or AS_CHM_SP__(). It is unusual to call it directly.

Parameters:

ans	a CHM_SP pointer
x	pointer to an object that inherits from CsparseMatrix
check_Udiag	boolean - should a check for (and consequent expansion of) a unit diagonal be performed.
sort_in_place	boolean - if the i and x slots are to be sorted should they be sorted in place? If the i and x slots are pointers to an input SEXP they should not be modified.

Returns:: ans containing pointers to the slots of x, *unless* check_Udiag and x is unitriangular.

Definition at line 217 of file chm_common.c.

References _, c, check_sorted_chm(), chm2Ralloc(), diag_P, isValid_Csparse(), Matrix_check_class_etc(), Matrix_DimSym, Matrix_iSym, Matrix_pSym, stype(), xpt(), and xtype().

Referenced by Csparse_validate_(), and R_init_Matrix().

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CHM_TR as_cholmod_triplet	(	CHM_TR	ans,
		SEXP	x,
		Rboolean	check_Udiag
	)

Populate ans with the pointers from x and modify its scalar elements accordingly.

Note that later changes to the contents of ans will change the contents of the SEXP.

In most cases this function is called through the macros AS_CHM_TR() or AS_CHM_TR__(). It is unusual to call it directly.

Parameters:

ans	a CHM_TR pointer
x	pointer to an object that inherits from TsparseMatrix
check_Udiag	boolean - should a check for (and consequent expansion of) a unit diagonal be performed.

Returns:: ans containing pointers to the slots of x, *unless* check_Udiag and x is unitriangular.

Definition at line 410 of file chm_common.c.

References _, c, chTr2Ralloc(), diag_P, Matrix_check_class_etc(), Matrix_DimSym, Matrix_iSym, Matrix_jSym, MATRIX_VALID_Tsparse, stype(), xpt(), and xtype().

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CHM_DN as_cholmod_x_dense	(	CHM_DN	ans,
		SEXP	x
	)

Definition at line 652 of file chm_common.c.

References _AS_cholmod_dense_1, _AS_cholmod_dense_2, Matrix_xSym, and RallocedREAL().

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Rboolean check_sorted_chm ( CHM_SP A )

Definition at line 141 of file chm_common.c.

Referenced by as_cholmod_sparse().

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SEXP chm_dense_to_matrix	(	CHM_DN	a,
		int	dofree,
		SEXP	dn
	)

Copy the contents of a to a matrix object and, optionally, free a or free both a and its pointer to its contents.

Parameters:

a	cholmod_dense structure to be converted
dofree	0 - don't free a; > 0 cholmod_free a; < 0 Free a
dn	either R_NilValue or an SEXP suitable for the Dimnames slot.

Returns:: SEXP containing a copy of a as a matrix object

Definition at line 809 of file chm_common.c.

References _, and c.

Referenced by Csparse_to_matrix().

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SEXP chm_dense_to_SEXP	(	CHM_DN	a,
		int	dofree,
		int	Rkind,
		SEXP	dn
	)

Copy the contents of a to an appropriate denseMatrix object and, optionally, free a or free both a and its pointer to its contents.

Parameters:

a	matrix to be converted
dofree	0 - don't free a; > 0 cholmod_free a; < 0 Free a
Rkind	type of R matrix to be generated (special to this function)
dn	-- dimnames [list(.,.) or NULL]

Returns:: SEXP containing a copy of a

Definition at line 736 of file chm_common.c.

References _, ALLOC_SLOT(), c, cl, Matrix_DimNamesSym, Matrix_DimSym, and Matrix_xSym.

Referenced by CHMfactor_solve(), Csparse_dense_crossprod(), Csparse_dense_prod(), Csparse_to_dense(), and dsCMatrix_matrix_solve().

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void chm_diagN2U	(	CHM_SP	chx,
		int	uploT,
		Rboolean	do_realloc
	)

Drop the (unit) diagonal entries from a cholmod_sparse matrix.

Parameters:

chx	cholmod_sparse matrix. Note that the matrix "slots" are modified _in place_
uploT	integer code (= +/- 1) indicating if chx is upper (+1) or lower (-1) triangular
do_realloc	Rboolean indicating, if a cholmod_sprealloc() should finalize the procedure; not needed, e.g. when the result is converted to a SEXP immediately afterwards.

Definition at line 1019 of file chm_common.c.

References _, _i, _p, _x, and c.

Referenced by Csparse_Csparse_crossprod(), Csparse_Csparse_prod(), and Csparse_diagN2U().

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static R_INLINE Rboolean chm_factor_ok ( CHM_FR f ) [static]

Definition at line 52 of file chm_common.h.

Referenced by chm_factor_to_SEXP(), dsCMatrix_Csparse_solve(), and dsCMatrix_matrix_solve().

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SEXP chm_factor_to_SEXP	(	CHM_FR	f,
		int	dofree
	)

Copy the contents of f to an appropriate CHMfactor object and, optionally, free f or free both f and its pointer to its contents.

Parameters:

f	cholmod_factor object to be converted
dofree	0 - don't free a; > 0 cholmod_free a; < 0 Free a

Returns:: SEXP containing a copy of a

Definition at line 940 of file chm_common.c.

References _, ALLOC_SLOT(), c, chm_factor_ok(), Matrix_iSym, Matrix_pSym, Matrix_xSym, and xtype().

Referenced by CHMfactor_update(), destructive_CHM_update(), dgCMatrix_cholsol(), dsCMatrix_Cholesky(), internal_chm_factor(), and R_init_Matrix().

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void CHM_restore_common ( )

Definition at line 41 of file chm_common.c.

References c, chm_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, and supernodalSym.

Referenced by internal_chm_factor(), and R_cholmod_error().

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SEXP CHM_set_common_env ( SEXP rho )

Definition at line 65 of file chm_common.c.

References _, chm_common_env, CHM_store_common(), 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, and supernodalSym.

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SEXP chm_sparse_to_SEXP	(	CHM_SP	a,
		int	dofree,
		int	uploT,
		int	Rkind,
		const char *	diag,
		SEXP	dn
	)

Copy the contents of a to an appropriate CsparseMatrix object and, optionally, free a or free both a and its the pointers to its contents.

Parameters:

a	(cholmod_sparse) matrix to be converted
dofree	0 - don't free a; > 0 cholmod_free a; < 0 Free a
uploT	0 - not triangular; > 0 upper triangular; < 0 lower
Rkind	- vector type to store for a->xtype == CHOLMOD_REAL, 0 - REAL; 1 - LOGICAL
diag	character string suitable for the diag slot of a triangular matrix (not accessed if uploT == 0).
dn	either R_NilValue or an SEXP suitable for the Dimnames slot.

Returns:: SEXP containing a copy of a

Definition at line 311 of file chm_common.c.

References _, ALLOC_SLOT(), c, cl, Matrix_diagSym, Matrix_DimNamesSym, Matrix_DimSym, Matrix_iSym, Matrix_pSym, Matrix_uploSym, and Matrix_xSym.

Referenced by CHMfactor_spsolve(), CHMfactor_to_sparse(), Csparse_band(), Csparse_crossprod(), Csparse_Csparse_crossprod(), Csparse_Csparse_prod(), Csparse_diagN2U(), Csparse_diagU2N(), Csparse_drop(), Csparse_general_to_symmetric(), Csparse_horzcat(), Csparse_submatrix(), Csparse_symmetric_to_general(), Csparse_to_nz_pattern(), Csparse_transpose(), Csparse_vertcat(), dense_to_Csparse(), dsCMatrix_chol(), dsCMatrix_Csparse_solve(), R_init_Matrix(), Tsparse_to_Csparse(), and Tsparse_to_tCsparse().

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void CHM_store_common ( )

Definition at line 16 of file chm_common.c.

References c, chm_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, and supernodalSym.

Referenced by CHM_set_common_env(), and internal_chm_factor().

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SEXP chm_triplet_to_SEXP	(	CHM_TR	a,
		int	dofree,
		int	uploT,
		int	Rkind,
		const char *	diag,
		SEXP	dn
	)

Copy the contents of a to an appropriate TsparseMatrix object and, optionally, free a or free both a and its the pointers to its contents.

Parameters:

a	matrix to be converted
dofree	0 - don't free a; > 0 cholmod_free a; < 0 Free a
uploT	0 - not triangular; > 0 upper triangular; < 0 lower
Rkind	- vector type to store for a->xtype == CHOLMOD_REAL, 0 - REAL; 1 - LOGICAL
diag	character string suitable for the diag slot of a triangular matrix (not accessed if uploT == 0).
dn	either R_NilValue or an SEXP suitable for the Dimnames slot.