Diff of /pkg/Matrix/src/Csparse.c

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	revision 2586, Sun Jul 25 02:32:06 2010 UTC	revision 3143, Wed Sep 2 21:29:32 2015 UTC
#	Line 1	Line 1
1	/* Sparse matrices in compressed column-oriented form */	/** @file Csparse.c
2		* The "CsparseMatrix" class from R package Matrix:
3		*
4		* Sparse matrices in compressed column-oriented form
5		*/
6	#include "Csparse.h"	#include "Csparse.h"
7	#include "Tsparse.h"	#include "Tsparse.h"
8	#include "chm_common.h"	#include "chm_common.h"
#	Line 36	Line 40
40	return Csparse_validate_(x, FALSE);	return Csparse_validate_(x, FALSE);
41	}	}
42
	SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
	return Csparse_validate_(x, asLogical(maybe_modify));
	}
43
44	SEXP Csparse_validate_(SEXP x, Rboolean maybe_modify)	#define _t_Csparse_validate
45	{	#include "t_Csparse_validate.c"
	/* NB: we do *NOT* check a potential 'x' slot here, at all */
	SEXP pslot = GET_SLOT(x, Matrix_pSym),
	islot = GET_SLOT(x, Matrix_iSym);
	Rboolean sorted, strictly;
	int j, k,
	*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
	nrow = dims[0],
	ncol = dims[1],
	*xp = INTEGER(pslot),
	*xi = INTEGER(islot);
46
47	if (length(pslot) != dims[1] + 1)	#define _t_Csparse_sort
48	return mkString(_("slot p must have length = ncol(.) + 1"));	#include "t_Csparse_validate.c"
	if (xp[0] != 0)
	return mkString(_("first element of slot p must be zero"));
	if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
	return
	mkString(_("last element of slot p must match length of slots i and x"));
	for (j = 0; j < xp[ncol]; j++) {
	if (xi[j] < 0 || xi[j] >= nrow)
	return mkString(_("all row indices must be between 0 and nrow-1"));
	}
	sorted = TRUE; strictly = TRUE;
	for (j = 0; j < ncol; j++) {
	if (xp[j] > xp[j + 1])
	return mkString(_("slot p must be non-decreasing"));
	if(sorted) /* only act if >= 2 entries in column j : */
	for (k = xp[j] + 1; k < xp[j + 1]; k++) {
	if (xi[k] < xi[k - 1])
	sorted = FALSE;
	else if (xi[k] == xi[k - 1])
	strictly = FALSE;
	}
	}
	if (!sorted) {
	if(maybe_modify) {
	CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
	R_CheckStack();
	as_cholmod_sparse(chx, x, FALSE, TRUE);/*-> cholmod_l_sort() ! */
	/* as chx = AS_CHM_SP__(x)  but  ^^^^ sorting x in_place !!! */
49
50	/* Now re-check that row indices are *strictly* increasing	// R: .validateCsparse(x, sort.if.needed = FALSE) :
51	* (and not just increasing) within each column : */	SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
52	for (j = 0; j < ncol; j++) {	return Csparse_validate_(x, asLogical(maybe_modify));
	for (k = xp[j] + 1; k < xp[j + 1]; k++)
	if (xi[k] == xi[k - 1])
	return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_l_sort)"));
	}
	} else { /* no modifying sorting : */
	return mkString(_("row indices are not sorted within columns"));
	}
	} else if(!strictly) {  /* sorted, but not strictly */
	return mkString(_("slot i is not *strictly* increasing inside a column"));
53	}	}
54	return ScalarLogical(1);
55		// R: Matrix:::.sortCsparse(x) :
56		SEXP Csparse_sort (SEXP x) {
57		int ok = Csparse_sort_2(x, TRUE); // modifying x directly
58		if(!ok) warning(_("Csparse_sort(x): x is not a valid (apart from sorting) CsparseMatrix"));
59		return x;
60	}	}
61
62	SEXP Rsparse_validate(SEXP x)	SEXP Rsparse_validate(SEXP x)
#	Line 136	Line 96
96	}	}
97	}	}
98	if (!sorted)	if (!sorted)
99	/* cannot easily use cholmod_l_sort(.) ... -> "error out" :*/	/* cannot easily use cholmod_sort(.) ... -> "error out" :*/
100	return mkString(_("slot j is not increasing inside a column"));	return mkString(_("slot j is not increasing inside a column"));
101	else if(!strictly) /* sorted, but not strictly */	else if(!strictly) /* sorted, but not strictly */
102	return mkString(_("slot j is not *strictly* increasing inside a column"));	return mkString(_("slot j is not *strictly* increasing inside a column"));
#	Line 144	Line 104
104	return ScalarLogical(1);	return ScalarLogical(1);
105	}	}
106
107		/** @brief From a CsparseMatrix, produce a dense one.
108	/* Called from ../R/Csparse.R : */	*
109	/* Can only return [dln]geMatrix (no symm/triang);	* Directly deals with symmetric, triangular and general.
110	* FIXME: replace by non-CHOLMOD code ! */	* Called from ../R/Csparse.R's  C2dense()
111	SEXP Csparse_to_dense(SEXP x)	*
112		* @param x a CsparseMatrix: currently all 9 of  "[dln][gst]CMatrix"
113		* @param symm_or_tri integer (NA, < 0, > 0, = 0) specifying the knowledge of the caller about x:
114		*      NA  : unknown => will be determined
115		*      = 0 : "generalMatrix" (not symm or tri);
116		*      < 0 : "triangularMatrix"
117		*      > 0 : "symmetricMatrix"
118		*
119		* @return a "denseMatrix"
120		*/
121		SEXP Csparse_to_dense(SEXP x, SEXP symm_or_tri)
122	{	{
123	CHM_SP chxs = AS_CHM_SP__(x);	Rboolean is_sym, is_tri;
124	/* This loses the symmetry property, since cholmod_dense has none,	int is_sym_or_tri = asInteger(symm_or_tri),
125		ctype = 0; // <- default = "dgC"
126		static const char *valid[] = { MATRIX_VALID_Csparse, ""};
127		if(is_sym_or_tri == NA_INTEGER) { // find if  is(x, "symmetricMatrix") :
128		ctype = Matrix_check_class_etc(x, valid);
129		is_sym = (ctype % 3 == 1);
130		is_tri = (ctype % 3 == 2);
131		} else {
132		is_sym = is_sym_or_tri > 0;
133		is_tri = is_sym_or_tri < 0;
134		// => both are FALSE  iff  is_.. == 0
135		if(is_sym || is_tri)
136		ctype = Matrix_check_class_etc(x, valid);
137		}
138		CHM_SP chxs = AS_CHM_SP__(x);// -> chxs->stype = +- 1 <==> symmetric
139		R_CheckStack();
140		if(is_tri && *diag_P(x) == 'U') { // ==>  x := diagU2N(x), directly for chxs
141		CHM_SP eye = cholmod_speye(chxs->nrow, chxs->ncol, chxs->xtype, &c);
142		double one[] = {1, 0};
143		CHM_SP ans = cholmod_add(chxs, eye, one, one,
144		/* values: */ ((ctype / 3) != 2), // TRUE iff not "nMatrix"
145		TRUE, &c);
146		cholmod_free_sparse(&eye, &c);
147		chxs = cholmod_copy_sparse(ans, &c);
148		cholmod_free_sparse(&ans, &c);
149		}
150		/* The following loses the symmetry property, since cholmod_dense has none,
151	* BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices	* BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
152	* to numeric (CHOLMOD_REAL) ones : */	* to numeric (CHOLMOD_REAL) ones {and we "revert" via chm_dense_to_SEXP()}: */
153	CHM_DN chxd = cholmod_l_sparse_to_dense(chxs, &c);	CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
154	int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);	int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
	R_CheckStack();
155
156	return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));	SEXP ans = chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym),
157		/* transp: */ FALSE);
158		// -> a [dln]geMatrix
159		if(is_sym) { // ==> want  [dln]syMatrix
160		const char cl1 = class_P(ans)[0];
161		PROTECT(ans);
162		SEXP aa = PROTECT(NEW_OBJECT(MAKE_CLASS((cl1 == 'd') ? "dsyMatrix" :
163		((cl1 == 'l') ? "lsyMatrix" : "nsyMatrix"))));
164		// No need to duplicate() as slots of ans are freshly allocated and ans will not be used
165		SET_SLOT(aa, Matrix_xSym,       GET_SLOT(ans, Matrix_xSym));
166		SET_SLOT(aa, Matrix_DimSym,     GET_SLOT(ans, Matrix_DimSym));
167		SET_SLOT(aa, Matrix_DimNamesSym,GET_SLOT(ans, Matrix_DimNamesSym));
168		SET_SLOT(aa, Matrix_uploSym, mkString((chxs->stype > 0) ? "U" : "L"));
169		UNPROTECT(2);
170		return aa;
171		}
172		else if(is_tri) { // ==> want  [dln]trMatrix
173		const char cl1 = class_P(ans)[0];
174		PROTECT(ans);
175		SEXP aa = PROTECT(NEW_OBJECT(MAKE_CLASS((cl1 == 'd') ? "dtrMatrix" :
176		((cl1 == 'l') ? "ltrMatrix" : "ntrMatrix"))));
177		// No need to duplicate() as slots of ans are freshly allocated and ans will not be used
178		SET_SLOT(aa, Matrix_xSym,       GET_SLOT(ans, Matrix_xSym));
179		SET_SLOT(aa, Matrix_DimSym,     GET_SLOT(ans, Matrix_DimSym));
180		SET_SLOT(aa, Matrix_DimNamesSym,GET_SLOT(ans, Matrix_DimNamesSym));
181		slot_dup(aa, x, Matrix_uploSym);
182		/* already by NEW_OBJECT(..) above:
183		SET_SLOT(aa, Matrix_diagSym, mkString("N")); */
184		UNPROTECT(2);
185		return aa;
186		}
187		else
188		return ans;
189	}	}
190
191	SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)	// FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
192		SEXP Csparse2nz(SEXP x, Rboolean tri)
193	{	{
194	CHM_SP chxs = AS_CHM_SP__(x);	CHM_SP chxs = AS_CHM_SP__(x);
195	CHM_SP chxcp = cholmod_l_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);	CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
	int tr = asLogical(tri);
196	R_CheckStack();	R_CheckStack();
197
198	return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,	return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
199	tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,	tri ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
200	0, tr ? diag_P(x) : "",	/* Rkind: pattern */ 0,
201		/* diag = */ tri ? diag_P(x) : "",
202	GET_SLOT(x, Matrix_DimNamesSym));	GET_SLOT(x, Matrix_DimNamesSym));
203	}	}
204		SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
205		{
206		int tr_ = asLogical(tri);
207		if(tr_ == NA_LOGICAL) {
208		warning(_("Csparse_to_nz_pattern(x, tri = NA): 'tri' is taken as TRUE"));
209		tr_ = TRUE;
210		}
211		return Csparse2nz(x, (Rboolean) tr_);
212		}
213
214	SEXP Csparse_to_matrix(SEXP x)	// n.CMatrix --> [dli].CMatrix  (not going through CHM!)
215		SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
216	{	{
217	return chm_dense_to_matrix(cholmod_l_sparse_to_dense(AS_CHM_SP__(x), &c),	return nz2Csparse(x, asInteger(res_kind));
218	1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));	}
219
220		// n.CMatrix --> [dli].CMatrix  (not going through CHM!)
221		// NOTE: use chm_MOD_xtype(() to change type of  'cholmod_sparse' matrix
222		SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
223		{
224		const char *cl_x = class_P(x);
225		// quick check - if ok, fast
226		if(cl_x[0] != 'n' || cl_x[2] != 'C') {
227		// e.g. class = "A", from  setClass("A", contains = "ngCMatrix")
228		static const char *valid[] = { MATRIX_VALID_nCsparse, ""};
229		int ctype = Matrix_check_class_etc(x, valid);
230		if(ctype < 0)
231		error(_("not a 'n.CMatrix'"));
232		else // fine : get a valid  cl_x  class_P()-like string :
233		cl_x = valid[ctype];
234		}
235		int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
236		SEXP ans;
237		char *ncl = alloca(strlen(cl_x) + 1); /* not much memory required */
238		strcpy(ncl, cl_x);
239		double *dx_x; int *ix_x;
240		ncl[0] = (r_kind == x_double ? 'd' :
241		(r_kind == x_logical ? 'l' :
242		/* else (for now):  r_kind == x_integer : */ 'i'));
243		PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
244		// create a correct 'x' slot:
245		switch(r_kind) {
246		int i;
247		case x_double: // 'd'
248		dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
249		for (i=0; i < nnz; i++) dx_x[i] = 1.;
250		break;
251		case x_logical: // 'l'
252		ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
253		for (i=0; i < nnz; i++) ix_x[i] = TRUE;
254		break;
255		case x_integer: // 'i'
256		ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
257		for (i=0; i < nnz; i++) ix_x[i] = 1;
258		break;
259
260		default:
261		error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
262		r_kind);
263		}
264
265		// now copy all other slots :
266		slot_dup(ans, x, Matrix_iSym);
267		slot_dup(ans, x, Matrix_pSym);
268		slot_dup(ans, x, Matrix_DimSym);
269		slot_dup(ans, x, Matrix_DimNamesSym);
270		if(ncl[1] != 'g') { // symmetric or triangular ...
271		slot_dup_if_has(ans, x, Matrix_uploSym);
272		slot_dup_if_has(ans, x, Matrix_diagSym);
273		}
274		UNPROTECT(1);
275		return ans;
276		}
277
278		SEXP Csparse_to_matrix(SEXP x, SEXP chk, SEXP symm)
279		{
280		int is_sym = asLogical(symm);
281		if(is_sym == NA_LOGICAL) { // find if  is(x, "symmetricMatrix") :
282		static const char *valid[] = { MATRIX_VALID_Csparse, ""};
283		int ctype = Matrix_check_class_etc(x, valid);
284		is_sym = (ctype % 3 == 1);
285		}
286		return chm_dense_to_matrix(
287		cholmod_sparse_to_dense(AS_CHM_SP2(x, asLogical(chk)), &c),
288		1 /*do_free*/,
289		(is_sym
290		? symmetric_DimNames(GET_SLOT(x, Matrix_DimNamesSym))
291		:                    GET_SLOT(x, Matrix_DimNamesSym)));
292		}
293
294		SEXP Csparse_to_vector(SEXP x)
295		{
296		return chm_dense_to_vector(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c), 1);
297	}	}
298
299	SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)	SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
300	{	{
301	CHM_SP chxs = AS_CHM_SP__(x);	CHM_SP chxs = AS_CHM_SP__(x);
302	CHM_TR chxt = cholmod_l_sparse_to_triplet(chxs, &c);	CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
303	int tr = asLogical(tri);	int tr = asLogical(tri);
304	int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;	int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
305	R_CheckStack();	R_CheckStack();
#	Line 194	Line 310
310	GET_SLOT(x, Matrix_DimNamesSym));	GET_SLOT(x, Matrix_DimNamesSym));
311	}	}
312
313	/* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */	SEXP Csparse_to_tCsparse(SEXP x, SEXP uplo, SEXP diag)
314		{
315		CHM_SP chxs = AS_CHM_SP__(x);
316		int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
317		R_CheckStack();
318		return chm_sparse_to_SEXP(chxs, /* dofree = */ 0,
319		/* uploT = */ (*CHAR(asChar(uplo)) == 'U')? 1: -1,
320		Rkind, /* diag = */ CHAR(STRING_ELT(diag, 0)),
321		GET_SLOT(x, Matrix_DimNamesSym));
322		}
323
324		SEXP Csparse_to_tTsparse(SEXP x, SEXP uplo, SEXP diag)
325		{
326		CHM_SP chxs = AS_CHM_SP__(x);
327		CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
328		int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
329		R_CheckStack();
330		return chm_triplet_to_SEXP(chxt, 1,
331		/* uploT = */ (*CHAR(asChar(uplo)) == 'U')? 1: -1,
332		Rkind, /* diag = */ CHAR(STRING_ELT(diag, 0)),
333		GET_SLOT(x, Matrix_DimNamesSym));
334		}
335
336
337	SEXP Csparse_symmetric_to_general(SEXP x)	SEXP Csparse_symmetric_to_general(SEXP x)
338	{	{
339	CHM_SP chx = AS_CHM_SP__(x), chgx;	CHM_SP chx = AS_CHM_SP__(x), chgx;
#	Line 203	Line 342
342
343	if (!(chx->stype))	if (!(chx->stype))
344	error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));	error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
345	chgx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);	chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
346	/* xtype: pattern, "real", complex or .. */	/* xtype: pattern, "real", complex or .. */
347	return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",	return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
348	GET_SLOT(x, Matrix_DimNamesSym));	symmetric_DimNames(GET_SLOT(x, Matrix_DimNamesSym)));
349	}	}
350
351	SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)	SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo, SEXP sym_dmns)
352	{	{
353		int *adims = INTEGER(GET_SLOT(x, Matrix_DimSym)), n = adims[0];
354		if(n != adims[1]) {
355		error(_("Csparse_general_to_symmetric(): matrix is not square!"));
356		return R_NilValue; /* -Wall */
357		}
358	CHM_SP chx = AS_CHM_SP__(x), chgx;	CHM_SP chx = AS_CHM_SP__(x), chgx;
359	int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;	int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;
360	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
361	R_CheckStack();	R_CheckStack();
362		chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
363
364	chgx = cholmod_l_copy(chx, /* stype: */ uploT, chx->xtype, &c);	SEXP dns = GET_SLOT(x, Matrix_DimNamesSym);
365		if(asLogical(sym_dmns))
366		dns = symmetric_DimNames(dns);
367		else if((!isNull(VECTOR_ELT(dns, 0)) &&
368		!isNull(VECTOR_ELT(dns, 1))) ||
369		!isNull(getAttrib(dns, R_NamesSymbol))) {
370		/* symmetrize them if both are not NULL
371		* or names(dimnames(.)) is asymmetric : */
372		dns = PROTECT(duplicate(dns));
373		if(!equal_string_vectors(VECTOR_ELT(dns, 0),
374		VECTOR_ELT(dns, 1))) {
375		if(uploT == 1)
376		SET_VECTOR_ELT(dns, 0, VECTOR_ELT(dns,1));
377		else
378		SET_VECTOR_ELT(dns, 1, VECTOR_ELT(dns,0));
379		}
380		SEXP nms_dns = getAttrib(dns, R_NamesSymbol);
381		if(!isNull(nms_dns) &&  // names(dimnames(.)) :
382		!R_compute_identical(STRING_ELT(nms_dns, 0),
383		STRING_ELT(nms_dns, 1), 16)) {
384		if(uploT == 1)
385		SET_STRING_ELT(nms_dns, 0, STRING_ELT(nms_dns,1));
386		else
387		SET_STRING_ELT(nms_dns, 1, STRING_ELT(nms_dns,0));
388		setAttrib(dns, R_NamesSymbol, nms_dns);
389		}
390		UNPROTECT(1);
391		}
392	/* xtype: pattern, "real", complex or .. */	/* xtype: pattern, "real", complex or .. */
393	return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",	return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "", dns);
	GET_SLOT(x, Matrix_DimNamesSym));
394	}	}
395
396	SEXP Csparse_transpose(SEXP x, SEXP tri)	SEXP Csparse_transpose(SEXP x, SEXP tri)
#	Line 228	Line 399
399	*       since cholmod (& cs) lacks sparse 'int' matrices */	*       since cholmod (& cs) lacks sparse 'int' matrices */
400	CHM_SP chx = AS_CHM_SP__(x);	CHM_SP chx = AS_CHM_SP__(x);
401	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
402	CHM_SP chxt = cholmod_l_transpose(chx, chx->xtype, &c);	CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
403	SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;	SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
404	int tr = asLogical(tri);	int tr = asLogical(tri);
405	R_CheckStack();	R_CheckStack();
#	Line 236	Line 407
407	tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */	tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
408	SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));	SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
409	SET_VECTOR_ELT(dn, 1, tmp);	SET_VECTOR_ELT(dn, 1, tmp);
410		if(!isNull(tmp = getAttrib(dn, R_NamesSymbol))) { // swap names(dimnames(.)):
411		SEXP nms_dns = PROTECT(allocVector(VECSXP, 2));
412		SET_VECTOR_ELT(nms_dns, 1, STRING_ELT(tmp, 0));
413		SET_VECTOR_ELT(nms_dns, 0, STRING_ELT(tmp, 1));
414		setAttrib(dn, R_NamesSymbol, nms_dns);
415		UNPROTECT(1);
416		}
417	UNPROTECT(1);	UNPROTECT(1);
418	return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */	return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
419	tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,	tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
420	Rkind, tr ? diag_P(x) : "", dn);	Rkind, tr ? diag_P(x) : "", dn);
421	}	}
422
423	SEXP Csparse_Csparse_prod(SEXP a, SEXP b)	/** @brief  A %*% B  - for matrices of class CsparseMatrix (R package "Matrix")
424		*
425		* @param a
426		* @param b
427		* @param bool_arith
428		*
429		* @return
430		*
431		* NOTA BENE:  cholmod_ssmult(A,B, ...) ->  ./CHOLMOD/MatrixOps/cholmod_ssmult.c
432		* ---------  computes a patter*n* matrix __always_ when
433		* *one* of A or B is pattern*n*, because of this (line 73-74):
434		---------------------------------------------------------------------------
435		values = values &&
436		(A->xtype != CHOLMOD_PATTERN) && (B->xtype != CHOLMOD_PATTERN) ;
437		---------------------------------------------------------------------------
438		* ==> Often need to copy the patter*n* to a *l*ogical matrix first !!!
439		*/
440		SEXP Csparse_Csparse_prod(SEXP a, SEXP b, SEXP bool_arith)
441	{	{
442	CHM_SP	CHM_SP
443	cha = AS_CHM_SP(a),	cha = AS_CHM_SP(a),
444	chb = AS_CHM_SP(b),	chb = AS_CHM_SP(b), chc;
	chc = cholmod_l_ssmult(cha, chb, /*out_stype:*/ 0,
	/* values:= is_numeric (T/F) */ cha->xtype > 0,
	/*out sorted:*/ 1, &c);
	const char *cl_a = class_P(a), *cl_b = class_P(b);
	char diag[] = {'\0', '\0'};
	int uploT = 0;
	SEXP dn = PROTECT(allocVector(VECSXP, 2));
445	R_CheckStack();	R_CheckStack();
446		static const char *valid_tri[] = { MATRIX_VALID_tri_Csparse, "" };
447		char diag[] = {'\0', '\0'};
448		int uploT = 0, nprot = 1,
449		do_bool = asLogical(bool_arith); // TRUE / NA / FALSE
450		Rboolean
451		a_is_n = (cha->xtype == CHOLMOD_PATTERN),
452		b_is_n = (chb->xtype == CHOLMOD_PATTERN),
453		force_num = (do_bool == FALSE),
454		maybe_bool= (do_bool == NA_LOGICAL);
455
456	#ifdef DEBUG_Matrix_verbose	#ifdef DEBUG_Matrix_verbose
457	Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);	Rprintf("DBG Csparse_C*_prod(%s, %s)\n", class_P(a), class_P(b));
458	#endif	#endif
459
460		if(a_is_n && (force_num || (maybe_bool && !b_is_n))) {
461		/* coerce 'a' to  double;
462		* have no CHOLMOD function (pattern -> logical) --> use "our" code */
463		SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
464		cha = AS_CHM_SP(da);
465		R_CheckStack();
466		a_is_n = FALSE;
467		}
468		else if(b_is_n && (force_num || (maybe_bool && !a_is_n))) {
469		// coerce 'b' to  double
470		SEXP db = PROTECT(nz2Csparse(b, x_double)); nprot++;
471		chb = AS_CHM_SP(db);
472		R_CheckStack();
473		b_is_n = FALSE;
474		}
475		chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
476		/* values : */ do_bool != TRUE,
477		/* sorted = TRUE: */ 1, &c);
478
479	/* Preserve triangularity and even unit-triangularity if appropriate.	/* Preserve triangularity and even unit-triangularity if appropriate.
480	* Note that in that case, the multiplication itself should happen	* Note that in that case, the multiplication itself should happen
481	* faster.  But there's no support for that in CHOLMOD */	* faster.  But there's no support for that in CHOLMOD */
482
483	/* UGLY hack -- rather should have (fast!) C-level version of	if(Matrix_check_class_etc(a, valid_tri) >= 0 &&
484	*       is(a, "triangularMatrix") etc */	Matrix_check_class_etc(b, valid_tri) >= 0)
	if (cl_a[1] == 't' && cl_b[1] == 't')
	/* FIXME: fails for "Cholesky","BunchKaufmann"..*/
485	if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */	if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
486	uploT = (*uplo_P(a) == 'U') ? 1 : -1;	uploT = (*uplo_P(a) == 'U') ? 1 : -1;
487	if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */	if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
#	Line 277	Line 491
491	}	}
492	else diag[0]= 'N';	else diag[0]= 'N';
493	}	}
494
495		SEXP dn = PROTECT(allocVector(VECSXP, 2));
496	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
497	duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));	duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
498	SET_VECTOR_ELT(dn, 1,	SET_VECTOR_ELT(dn, 1,
499	duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));	duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
500	UNPROTECT(1);	UNPROTECT(nprot);
501	return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);	return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
502	}	}
503
504	SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)	/** @brief [t]crossprod (<Csparse>, <Csparse>)
505		*
506		* @param a a "CsparseMatrix" object
507		* @param b a "CsparseMatrix" object
508		* @param trans trans = FALSE:  crossprod(a,b)
509		*              trans = TRUE : tcrossprod(a,b)
510		* @param bool_arith logical (TRUE / NA / FALSE): Should boolean arithmetic be used.
511		*
512		* @return a CsparseMatrix, the (t)cross product of a and b.
513		*/
514		SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans, SEXP bool_arith)
515	{	{
516	int tr = asLogical(trans);	int tr = asLogical(trans), nprot = 1,
517		do_bool = asLogical(bool_arith); // TRUE / NA / FALSE
518	CHM_SP	CHM_SP
519	cha = AS_CHM_SP(a),	cha = AS_CHM_SP(a),
520	chb = AS_CHM_SP(b),	chb = AS_CHM_SP(b),
521	chTr, chc;	chTr, chc;
522	const char *cl_a = class_P(a), *cl_b = class_P(b);	R_CheckStack();
523		static const char *valid_tri[] = { MATRIX_VALID_tri_Csparse, "" };
524	char diag[] = {'\0', '\0'};	char diag[] = {'\0', '\0'};
525	int uploT = 0;	int uploT = 0;
526	SEXP dn = PROTECT(allocVector(VECSXP, 2));	Rboolean
527		a_is_n = (cha->xtype == CHOLMOD_PATTERN),
528		b_is_n = (chb->xtype == CHOLMOD_PATTERN),
529		force_num = (do_bool == FALSE),
530		maybe_bool= (do_bool == NA_LOGICAL);
531
532		if(a_is_n && (force_num || (maybe_bool && !b_is_n))) {
533		// coerce 'a' to  double
534		SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
535		cha = AS_CHM_SP(da);
536	R_CheckStack();	R_CheckStack();
537		// a_is_n = FALSE;
538	chTr = cholmod_l_transpose((tr) ? chb : cha, chb->xtype, &c);	}
539	chc = cholmod_l_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,	else if(b_is_n && (force_num || (maybe_bool && !a_is_n))) {
540	/*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);	// coerce 'b' to  double
541	cholmod_l_free_sparse(&chTr, &c);	SEXP db = PROTECT(nz2Csparse(b, x_double)); nprot++;
542		chb = AS_CHM_SP(db);
543		R_CheckStack();
544		// b_is_n = FALSE;
545		}
546		else if(do_bool == TRUE) { // Want boolean arithmetic: sufficient if *one* is pattern:
547		if(!a_is_n && !b_is_n) {
548		// coerce 'a' to pattern
549		SEXP da = PROTECT(Csparse2nz(a, /* tri = */
550		Matrix_check_class_etc(a, valid_tri) >= 0)); nprot++;
551		cha = AS_CHM_SP(da);
552		R_CheckStack();
553		// a_is_n = TRUE;
554		}
555		}
556		chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
557		chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
558		/*out_stype:*/ 0, /* values : */ do_bool != TRUE,
559		/* sorted = TRUE: */ 1, &c);
560		cholmod_free_sparse(&chTr, &c);
561
562	/* Preserve triangularity and unit-triangularity if appropriate;	/* Preserve triangularity and unit-triangularity if appropriate;
563	* see Csparse_Csparse_prod() for comments */	* see Csparse_Csparse_prod() for comments */
564	if (cl_a[1] == 't' && cl_b[1] == 't')	if(Matrix_check_class_etc(a, valid_tri) >= 0 &&
565		Matrix_check_class_etc(b, valid_tri) >= 0)
566	if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */	if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
567	uploT = (*uplo_P(b) == 'U') ? 1 : -1;	uploT = (*uplo_P(b) == 'U') ? 1 : -1;
568	if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */	if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
#	Line 314	Line 571
571	}	}
572	else diag[0]= 'N';	else diag[0]= 'N';
573	}	}
574
575		SEXP dn = PROTECT(allocVector(VECSXP, 2));
576	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
577	duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));	duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym),
578		(tr) ? 0 : 1)));
579	SET_VECTOR_ELT(dn, 1,	SET_VECTOR_ELT(dn, 1,
580	duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));	duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym),
581	UNPROTECT(1);	(tr) ? 0 : 1)));
582		UNPROTECT(nprot);
583	return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);	return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
584	}	}
585
586	SEXP Csparse_dense_prod(SEXP a, SEXP b)	/**
587		* All (dense * sparse)  Matrix products and cross products
588		*
589		*   f( f(<Csparse>)  %*%  f(<dense>) )   where  f ()  is either t () [tranpose] or the identity.
590		*
591		* @param a CsparseMatrix  (n x m)
592		* @param b numeric vector, matrix, or denseMatrix (m x k) or (k x m)  if `transp` is '2' or 'B'
593		* @param transp character.
594		*        = " " : nothing transposed {apart from a}
595		*        = "2" : "transpose 2nd arg": use  t(b) instead of b (= 2nd argument)
596		*        = "c" : "transpose c":       Return  t(c) instead of c
597		*        = "B" : "transpose both":    use t(b) and return t(c) instead of c
598		* NB: For "2", "c", "B", need to transpose a *dense* matrix, B or C --> chm_transpose_dense()
599		*
600		* @return a dense matrix, the matrix product c = g(a,b) :
601		*
602		*                                                Condition (R)   Condition (C)
603		*   R notation            Math notation          cross  transp   t.a t.b t.ans
604		*   ~~~~~~~~~~~~~~~~~     ~~~~~~~~~~~~~~~~~~     ~~~~~~~~~~~~~   ~~~~~~~~~~~~~
605		*   c <-   a %*%   b      C :=      A B            .       " "    .   .   .
606		*   c <-   a %*% t(b)     C :=      A B'           .       "2"    .   |   .
607		*   c <- t(a %*%   b)     C := (A B)'  = B'A'      .       "c"    .   .   |
608		*   c <- t(a %*% t(b))    C := (A B')' = B A'      .       "B"    .   |   |
609		*
610		*   c <-   t(a) %*%   b   C :=      A'B           TRUE     " "    |   .   .
611		*   c <-   t(a) %*% t(b)  C :=      A'B'          TRUE     "2"    |   |   .
612		*   c <- t(t(a) %*%   b)  C := (A'B)'  = B'A      TRUE     "c"    |   .   |
613		*   c <- t(t(a) %*% t(b)) C := (A'B')' = B A      TRUE     "B"    |   |   |
614		*/
615		SEXP Csp_dense_products(SEXP a, SEXP b,
616		Rboolean transp_a, Rboolean transp_b, Rboolean transp_ans)
617	{	{
618	CHM_SP cha = AS_CHM_SP(a);	CHM_SP cha = AS_CHM_SP(a);
619	SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));	int a_nc = transp_a ? cha->nrow : cha->ncol,
620	CHM_DN chb = AS_CHM_DN(b_M);	a_nr = transp_a ? cha->ncol : cha->nrow;
621	CHM_DN chc = cholmod_l_allocate_dense(cha->nrow, chb->ncol, cha->nrow,	Rboolean
622	chb->xtype, &c);	maybe_transp_b = (a_nc == 1),
623	SEXP dn = PROTECT(allocVector(VECSXP, 2));	b_is_vector = FALSE;
624	double one[] = {1,0}, zero[] = {0,0};	/* NOTE: trans_b {<--> "use t(b) instead of b" }
625		----  "interferes" with the  case automatic treatment of *vector* b.
626		In that case,  t(b) or b is used "whatever make more sense",
627		according to the general R philosophy of treating vectors in matrix products.
628		*/
629
630		/* repeating a "cheap part" of  mMatrix_as_dgeMatrix2(b, .)  to see if
631		* we have a vector that we might 'transpose_if_vector' : */
632		static const char *valid[] = {"_NOT_A_CLASS_", MATRIX_VALID_ddense, ""};
633		/* int ctype = Matrix_check_class_etc(b, valid);
634		* if (ctype > 0)   /.* a ddenseMatrix object */
635		if (Matrix_check_class_etc(b, valid) < 0) {
636		// not a ddenseM*:  is.matrix() or vector:
637		b_is_vector = !isMatrix(b);
638		}
639
640		if(b_is_vector) {
641		/* determine *if* we want/need to transpose at all:
642		* if (length(b) == ncol(A)) have match: use dim = c(n, 1) (<=> do *not* transp);
643		*  otherwise, try to transpose: ok  if (ncol(A) == 1) [see also above]:  */
644		maybe_transp_b = (LENGTH(b) != a_nc);
645		// Here, we transpose already in mMatrix_as_dge*()  ==> don't do it later:
646		transp_b = FALSE;
647		}
648		SEXP b_M = PROTECT(mMatrix_as_dgeMatrix2(b, maybe_transp_b));
649
650		CHM_DN chb = AS_CHM_DN(b_M), b_t;
651	R_CheckStack();	R_CheckStack();
652		int ncol_b;
653		if(transp_b) { // transpose b:
654		b_t = cholmod_allocate_dense(chb->ncol, chb->nrow, chb->ncol, chb->xtype, &c);
655		chm_transpose_dense(b_t, chb);
656		ncol_b = b_t->ncol;
657		} else
658		ncol_b = chb->ncol;
659		// Result C {with dim() before it may be transposed}:
660		CHM_DN chc = cholmod_allocate_dense(a_nr, ncol_b, a_nr, chb->xtype, &c);
661		double one[] = {1,0}, zero[] = {0,0};
662		int nprot = 2;
663
664	cholmod_l_sdmult(cha, 0, one, zero, chb, chc, &c);	/* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
665	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */	if(cha->xtype == CHOLMOD_PATTERN) {
666	duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));	/* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
667	SET_VECTOR_ELT(dn, 1,	/*        " --> slightly inefficient coercion")); */
668	duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
669	UNPROTECT(2);	// This *fails* to produce a CHOLMOD_REAL ..
670	return chm_dense_to_SEXP(chc, 1, 0, dn);	// CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
671		// --> use our Matrix-classes
672		SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
673		cha = AS_CHM_SP(da);
674		}
675
676		/* cholmod_sdmult(A, transp, alpha, beta, X,  Y,  &c): depending on transp == 0 / != 0:
677		*  Y := alpha*(A*X) + beta*Y or alpha*(A'*X) + beta*Y;  here, alpha = 1, beta = 0:
678		*  Y := A*X  or  A'*X
679		*                       NB: always  <sparse> %*% <dense> !
680		*/
681		cholmod_sdmult(cha, transp_a, one, zero, (transp_b ? b_t : chb), /* -> */ chc, &c);
682
683		SEXP dn = PROTECT(allocVector(VECSXP, 2));  /* establish dimnames */
684		SET_VECTOR_ELT(dn, transp_ans ? 1 : 0,
685		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), transp_a ? 1 : 0)));
686		SET_VECTOR_ELT(dn, transp_ans ? 0 : 1,
687		duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym),
688		transp_b ? 0 : 1)));
689		if(transp_b) cholmod_free_dense(&b_t, &c);
690		UNPROTECT(nprot);
691		return chm_dense_to_SEXP(chc, 1, 0, dn, transp_ans);
692	}	}
693
694	SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
695		SEXP Csparse_dense_prod(SEXP a, SEXP b, SEXP transp)
696	{	{
697	CHM_SP cha = AS_CHM_SP(a);	return
698	SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));	Csp_dense_products(a, b,
699	CHM_DN chb = AS_CHM_DN(b_M);	/* transp_a = */ FALSE,
700	CHM_DN chc = cholmod_l_allocate_dense(cha->ncol, chb->ncol, cha->ncol,	/* transp_b   = */ (*CHAR(asChar(transp)) == '2' || *CHAR(asChar(transp)) == 'B'),
701	chb->xtype, &c);	/* transp_ans = */ (*CHAR(asChar(transp)) == 'c' || *CHAR(asChar(transp)) == 'B'));
702	SEXP dn = PROTECT(allocVector(VECSXP, 2));	}
	double one[] = {1,0}, zero[] = {0,0};
	R_CheckStack();
703
704	cholmod_l_sdmult(cha, 1, one, zero, chb, chc, &c);	SEXP Csparse_dense_crossprod(SEXP a, SEXP b, SEXP transp)
705	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */	{
706	duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));	return
707	SET_VECTOR_ELT(dn, 1,	Csp_dense_products(a, b,
708	duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));	/* transp_a = */ TRUE,
709	UNPROTECT(2);	/* transp_b   = */ (*CHAR(asChar(transp)) == '2' || *CHAR(asChar(transp)) == 'B'),
710	return chm_dense_to_SEXP(chc, 1, 0, dn);	/* transp_ans = */ (*CHAR(asChar(transp)) == 'c' || *CHAR(asChar(transp)) == 'B'));
711	}	}
712
713	/* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
714	see Csparse_Csparse_crossprod above for  x'y and x y' */	/** @brief Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
715	SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)	see Csparse_Csparse_crossprod above for  x'y and x y'
716		*/
717		SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet, SEXP bool_arith)
718	{	{
719	int trip = asLogical(triplet),	int tripl = asLogical(triplet),
720	tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */	tr   = asLogical(trans), /* gets reversed because _aat is tcrossprod */
721		do_bool = asLogical(bool_arith); // TRUE / NA / FALSE
722	#ifdef AS_CHM_DIAGU2N_FIXED_FINALLY	#ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
723	CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;	CHM_TR cht = tripl ? AS_CHM_TR(x) : (CHM_TR) NULL;  int nprot = 1;
724	#else /* workaround needed:*/	#else /* workaround needed:*/
725	SEXP xx = PROTECT(Tsparse_diagU2N(x));	SEXP xx = PROTECT(Tsparse_diagU2N(x));
726	CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;	CHM_TR cht = tripl ? AS_CHM_TR__(xx) : (CHM_TR) NULL; int nprot = 2;
727	#endif	#endif
728	CHM_SP chcp, chxt,	CHM_SP chcp, chxt, chxc,
729	chx = (trip ?	chx = (tripl ?
730	cholmod_l_triplet_to_sparse(cht, cht->nnz, &c) :	cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
731	AS_CHM_SP(x));	AS_CHM_SP(x));
732	SEXP dn = PROTECT(allocVector(VECSXP, 2));	SEXP dn = PROTECT(allocVector(VECSXP, 2));
733	R_CheckStack();	R_CheckStack();
734		Rboolean
735		x_is_n = (chx->xtype == CHOLMOD_PATTERN),
736		x_is_sym = chx->stype != 0,
737		force_num = (do_bool == FALSE);
738
739		if(x_is_n && force_num) {
740		// coerce 'x' to  double
741		SEXP dx = PROTECT(nz2Csparse(x, x_double)); nprot++;
742		chx = AS_CHM_SP(dx);
743		R_CheckStack();
744		}
745		else if(do_bool == TRUE && !x_is_n) { // Want boolean arithmetic; need patter[n]
746		// coerce 'x' to pattern
747		static const char *valid_tri[] = { MATRIX_VALID_tri_Csparse, "" };
748		SEXP dx = PROTECT(Csparse2nz(x, /* tri = */
749		Matrix_check_class_etc(x, valid_tri) >= 0)); nprot++;
750		chx = AS_CHM_SP(dx);
751		R_CheckStack();
752		}
753
754		if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
755
756	if (!tr) chxt = cholmod_l_transpose(chx, chx->xtype, &c);	if (x_is_sym) // cholmod_aat() does not like symmetric
757	chcp = cholmod_l_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);	chxc = cholmod_copy(tr ? chx : chxt, /* stype: */ 0,
758		chx->xtype, &c);
759		// CHOLMOD/Core/cholmod_aat.c :
760		chcp = cholmod_aat(x_is_sym ? chxc : (tr ? chx : chxt),
761		(int *) NULL, 0, /* mode: */ chx->xtype, &c);
762	if(!chcp) {	if(!chcp) {
763	UNPROTECT(1);	UNPROTECT(1);
764	error(_("Csparse_crossprod(): error return from cholmod_l_aat()"));	error(_("Csparse_crossprod(): error return from cholmod_aat()"));
765	}	}
766	cholmod_l_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);	cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
767	chcp->stype = 1;	chcp->stype = 1; // symmetric
768	if (trip) cholmod_l_free_sparse(&chx, &c);	if (tripl) cholmod_free_sparse(&chx, &c);
769	if (!tr) cholmod_l_free_sparse(&chxt, &c);	if (!tr) cholmod_free_sparse(&chxt, &c);
770	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
771	duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),	duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
772	(tr) ? 0 : 1)));	(tr) ? 0 : 1)));
773	SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));	SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
774	#ifdef AS_CHM_DIAGU2N_FIXED_FINALLY	UNPROTECT(nprot);
775	UNPROTECT(1);	// FIXME: uploT for symmetric ?
	#else
	UNPROTECT(2);
	#endif
776	return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);	return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
777	}	}
778
779		/** @brief Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
780		*  at least all "explicit" zeros. */
781	SEXP Csparse_drop(SEXP x, SEXP tol)	SEXP Csparse_drop(SEXP x, SEXP tol)
782	{	{
783	const char *cl = class_P(x);	const char *cl = class_P(x);
784	/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */	/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
785	int tr = (cl[1] == 't');	int tr = (cl[1] == 't'); // FIXME - rather  Matrix_check_class_etc(..)
786	CHM_SP chx = AS_CHM_SP__(x);	CHM_SP chx = AS_CHM_SP__(x);
787	CHM_SP ans = cholmod_l_copy(chx, chx->stype, chx->xtype, &c);	CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
788	double dtol = asReal(tol);	double dtol = asReal(tol);
789	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
790	R_CheckStack();	R_CheckStack();
791
792	if(!cholmod_l_drop(dtol, ans, &c))	if(!cholmod_drop(dtol, ans, &c))
793	error(_("cholmod_l_drop() failed"));	error(_("cholmod_drop() failed"));
794	return chm_sparse_to_SEXP(ans, 1,	return chm_sparse_to_SEXP(ans, 1,
795	tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,	tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
796	Rkind, tr ? diag_P(x) : "",	Rkind, tr ? diag_P(x) : "",
797	GET_SLOT(x, Matrix_DimNamesSym));	GET_SLOT(x, Matrix_DimNamesSym));
798	}	}
799
800		/** @brief Horizontal Concatenation -  cbind( <Csparse>,  <Csparse>)
801		*/
802	SEXP Csparse_horzcat(SEXP x, SEXP y)	SEXP Csparse_horzcat(SEXP x, SEXP y)
803	{	{
804	CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);	#define CSPARSE_CAT(_KIND_)                                             \
805	int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,	CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);                  \
806	Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,	R_CheckStack();                                                     \
807	Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;	int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : -3,     \
808	R_CheckStack();	Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : -3, Rkind; \
809		if(Rk_x == -3 || Rk_y == -3) { /* at least one of them is patter"n" */ \
810		if(Rk_x == -3 && Rk_y == -3) { /* fine */                       \
811		} else { /* only one is a patter"n"                             \
812		* "Bug" in cholmod_horzcat()/vertcat(): returns patter"n" matrix if one of them is */ \
813		Rboolean ok;                                                \
814		if(Rk_x == -3) {                                            \
815		ok = chm_MOD_xtype(CHOLMOD_REAL, chx, &c); Rk_x = 0;    \
816		} else if(Rk_y == -3) {                                     \
817		ok = chm_MOD_xtype(CHOLMOD_REAL, chy, &c); Rk_y = 0;    \
818		} else                                                      \
819		error(_("Impossible Rk_x/Rk_y in Csparse_%s(), please report"), _KIND_); \
820		if(!ok)                                                     \
821		error(_("chm_MOD_xtype() was not successful in Csparse_%s(), please report"), \
822		_KIND_);                                          \
823		}                                                               \
824		}                                                                   \
825		Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0
826
827		CSPARSE_CAT("horzcat");
828		// TODO: currently drops dimnames - and we fix at R level;
829
830	/* TODO: currently drops dimnames - and we fix at R level */	return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
	return chm_sparse_to_SEXP(cholmod_l_horzcat(chx, chy, 1, &c),
831	1, 0, Rkind, "", R_NilValue);	1, 0, Rkind, "", R_NilValue);
832	}	}
833
834		/** @brief Vertical Concatenation -  rbind( <Csparse>,  <Csparse>)
835		*/
836	SEXP Csparse_vertcat(SEXP x, SEXP y)	SEXP Csparse_vertcat(SEXP x, SEXP y)
837	{	{
838	CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);	CSPARSE_CAT("vertcat");
839	int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,	// TODO: currently drops dimnames - and we fix at R level;
	Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
	Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
	R_CheckStack();
840
841	/* TODO: currently drops dimnames - and we fix at R level */	return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
	return chm_sparse_to_SEXP(cholmod_l_vertcat(chx, chy, 1, &c),
842	1, 0, Rkind, "", R_NilValue);	1, 0, Rkind, "", R_NilValue);
843	}	}
844
#	Line 452	Line 846
846	{	{
847	CHM_SP chx = AS_CHM_SP__(x);	CHM_SP chx = AS_CHM_SP__(x);
848	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
849	CHM_SP ans = cholmod_l_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);	CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
850	R_CheckStack();	R_CheckStack();
851
852	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
#	Line 470	Line 864
864	}	}
865	else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */	else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
866	CHM_SP chx = AS_CHM_SP__(x);	CHM_SP chx = AS_CHM_SP__(x);
867	CHM_SP eye = cholmod_l_speye(chx->nrow, chx->ncol, chx->xtype, &c);	CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
868	double one[] = {1, 0};	double one[] = {1, 0};
869	CHM_SP ans = cholmod_l_add(chx, eye, one, one, TRUE, TRUE, &c);	CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
870	int uploT = (*uplo_P(x) == 'U') ? 1 : -1;	int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
871	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
872
873	R_CheckStack();	R_CheckStack();
874	cholmod_l_free_sparse(&eye, &c);	cholmod_free_sparse(&eye, &c);
875	return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",	return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
876	GET_SLOT(x, Matrix_DimNamesSym));	GET_SLOT(x, Matrix_DimNamesSym));
877	}	}
#	Line 494	Line 888
888	}	}
889	else { /* triangular with diag='N'): now drop the diagonal */	else { /* triangular with diag='N'): now drop the diagonal */
890	/* duplicate, since chx will be modified: */	/* duplicate, since chx will be modified: */
891	CHM_SP chx = AS_CHM_SP__(duplicate(x));	SEXP xx = PROTECT(duplicate(x));
892		CHM_SP chx = AS_CHM_SP__(xx);
893	int uploT = (*uplo_P(x) == 'U') ? 1 : -1,	int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
894	Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;	Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
895	R_CheckStack();	R_CheckStack();
896
897	chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);	chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
898
899	return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,	SEXP ans = chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
900	uploT, Rkind, "U",	uploT, Rkind, "U",
901	GET_SLOT(x, Matrix_DimNamesSym));	GET_SLOT(x, Matrix_DimNamesSym));
902		UNPROTECT(1);// only now !
903		return ans;
904	}	}
905	}	}
906
907	/**	/**
908	* "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j	* Indexing aka subsetting : Compute  x[i,j], also for vectors i and j
909	* Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c	* Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
910	* @param x CsparseMatrix	* @param x CsparseMatrix
911	* @param i row     indices (0-origin), or NULL (R's)	* @param i row     indices (0-origin), or NULL (R, not C)
912	* @param j columns indices (0-origin), or NULL	* @param j columns indices (0-origin), or NULL
913	*	*
914	* @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames	* @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
#	Line 529	Line 926
926	if (csize >= 0 && !isInteger(j))	if (csize >= 0 && !isInteger(j))
927	error(_("Index j must be NULL or integer"));	error(_("Index j must be NULL or integer"));
928
929	if (chx->stype) /* symmetricMatrix */	#define CHM_SUB(_M_, _i_, _j_)                                  \
930		cholmod_submatrix(_M_,                                      \
931		(rsize < 0) ? NULL : INTEGER(_i_), rsize, \
932		(csize < 0) ? NULL : INTEGER(_j_), csize, \
933		TRUE, TRUE, &c)
934		CHM_SP ans;
935		if (!chx->stype) {/* non-symmetric Matrix */
936		ans = CHM_SUB(chx, i, j);
937		}
938		else {
939	/* for now, cholmod_submatrix() only accepts "generalMatrix" */	/* for now, cholmod_submatrix() only accepts "generalMatrix" */
940	chx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);	CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
941		ans = CHM_SUB(tmp, i, j);
942		cholmod_free_sparse(&tmp, &c);
943		}
944
945	return chm_sparse_to_SEXP(cholmod_l_submatrix(chx,	// "FIXME": currently dropping dimnames, and adding them afterwards in R :
946	(rsize < 0) ? NULL : INTEGER(i), rsize,	/* // dimnames: */
947	(csize < 0) ? NULL : INTEGER(j), csize,	/* SEXP x_dns = GET_SLOT(x, Matrix_DimNamesSym), */
948	TRUE, TRUE, &c),	/*  dn = PROTECT(allocVector(VECSXP, 2)); */
949	1, 0, Rkind, "",	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", /* dimnames: */ R_NilValue);
	/* FIXME: drops dimnames */ R_NilValue);
950	}	}
951
952		#define _d_Csp_
953		#include "t_Csparse_subassign.c"
954
955		#define _l_Csp_
956		#include "t_Csparse_subassign.c"
957
958		#define _i_Csp_
959		#include "t_Csparse_subassign.c"
960
961		#define _n_Csp_
962		#include "t_Csparse_subassign.c"
963
964		#define _z_Csp_
965		#include "t_Csparse_subassign.c"
966
967
968
969	SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)	SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
970	{	{
971	FILE *f = fopen(CHAR(asChar(fname)), "w");	FILE *f = fopen(CHAR(asChar(fname)), "w");
#	Line 548	Line 973
973	if (!f)	if (!f)
974	error(_("failure to open file \"%s\" for writing"),	error(_("failure to open file \"%s\" for writing"),
975	CHAR(asChar(fname)));	CHAR(asChar(fname)));
976	if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),	if (!cholmod_write_sparse(f, AS_CHM_SP(x),
977	(CHM_SP)NULL, (char*) NULL, &c))	(CHM_SP)NULL, (char*) NULL, &c))
978	error(_("cholmod_l_write_sparse returned error code"));	error(_("cholmod_write_sparse returned error code"));
979	fclose(f);	fclose(f);
980	return R_NilValue;	return R_NilValue;
981	}	}
#	Line 568	Line 993
993	*	*
994	* @return  a SEXP, either a (double) number or a length n-vector of diagonal entries	* @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
995	*/	*/
996	SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)	SEXP diag_tC_ptr(int n, int *x_p, double *x_x, Rboolean is_U, int *perm,
997	/*                                ^^^^^^ FIXME[Generalize] to int / ... */	/*                                ^^^^^^ FIXME[Generalize] to int / ... */
998		SEXP resultKind)
999	{	{
1000	const char* res_ch = CHAR(STRING_ELT(resultKind,0));	const char* res_ch = CHAR(STRING_ELT(resultKind,0));
1001	enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log	enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log, min, max, range
1002	} res_kind = ((!strcmp(res_ch, "trace")) ? trace :	} res_kind = ((!strcmp(res_ch, "trace")) ? trace :
1003	((!strcmp(res_ch, "sumLog")) ? sum_log :	((!strcmp(res_ch, "sumLog")) ? sum_log :
1004	((!strcmp(res_ch, "prod")) ? prod :	((!strcmp(res_ch, "prod")) ? prod :
1005		((!strcmp(res_ch, "min")) ? min :
1006		((!strcmp(res_ch, "max")) ? max :
1007		((!strcmp(res_ch, "range")) ? range :
1008	((!strcmp(res_ch, "diag")) ? diag :	((!strcmp(res_ch, "diag")) ? diag :
1009	((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :	((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
1010	-1)))));	-1))))))));
1011	int i, n_x, i_from = 0;	int i, n_x, i_from;
1012	SEXP ans = PROTECT(allocVector(REALSXP,	SEXP ans = PROTECT(allocVector(REALSXP,
1013	/*                                 ^^^^  FIXME[Generalize] */	/*                                 ^^^^  FIXME[Generalize] */
1014	(res_kind == diag ||	(res_kind == diag ||
1015	res_kind == diag_backpermuted) ? n : 1));	res_kind == diag_backpermuted) ? n :
1016		(res_kind == range ? 2 : 1)));
1017	double *v = REAL(ans);	double *v = REAL(ans);
1018	/*  ^^^^^^      ^^^^  FIXME[Generalize] */	/*  ^^^^^^      ^^^^  FIXME[Generalize] */
1019
1020		i_from = (is_U ? -1 : 0);
1021
1022	#define for_DIAG(v_ASSIGN)                                              \	#define for_DIAG(v_ASSIGN)                                              \
1023	for(i = 0; i < n; i++, i_from += n_x) {                             \	for(i = 0; i < n; i++) {                                    \
1024	/* looking at i-th column */                                    \	/* looking at i-th column */                                    \
1025	n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \	n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
1026		if( is_U) i_from += n_x;                                \
1027	v_ASSIGN;                                                       \	v_ASSIGN;                                                       \
1028		if(!is_U) i_from += n_x;                                \
1029	}	}
1030
1031	/* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix	/* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
1032	*            for uplo = "U" (makes sense with a "dtCMatrix" !),	*            for uplo = "U" (makes sense with a "dtCMatrix" !),
1033	*            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],	*            should use  x_x[i_from + (n_x - 1)] instead of x_x[i_from],
1034	*            where nx = (x_p[i+1] - x_p[i])	*            where n_x = (x_p[i+1] - x_p[i])
1035	*/	*/
1036
1037	switch(res_kind) {	switch(res_kind) {
1038	case trace:	case trace: // = sum
1039	v[0] = 0.;	v[0] = 0.;
1040	for_DIAG(v[0] += x_x[i_from]);	for_DIAG(v[0] += x_x[i_from]);
1041	break;	break;
#	Line 616	Line 1050
1050	for_DIAG(v[0] *= x_x[i_from]);	for_DIAG(v[0] *= x_x[i_from]);
1051	break;	break;
1052
1053		case min:
1054		v[0] = R_PosInf;
1055		for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from]);
1056		break;
1057
1058		case max:
1059		v[0] = R_NegInf;
1060		for_DIAG(if(v[0] < x_x[i_from]) v[0] = x_x[i_from]);
1061		break;
1062
1063		case range:
1064		v[0] = R_PosInf;
1065		v[1] = R_NegInf;
1066		for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from];
1067		if(v[1] < x_x[i_from]) v[1] = x_x[i_from]);
1068		break;
1069
1070	case diag:	case diag:
1071	for_DIAG(v[i] = x_x[i_from]);	for_DIAG(v[i] = x_x[i_from]);
1072	break;	break;
#	Line 623	Line 1074
1074	case diag_backpermuted:	case diag_backpermuted:
1075	for_DIAG(v[i] = x_x[i_from]);	for_DIAG(v[i] = x_x[i_from]);
1076
1077	warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));	warning(_("%s = '%s' (back-permuted) is experimental"),
1078		"resultKind", "diagBack");
1079	/* now back_permute : */	/* now back_permute : */
1080	for(i = 0; i < n; i++) {	for(i = 0; i < n; i++) {
1081	double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;	double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
#	Line 644	Line 1096
1096	* Extract the diagonal entries from *triangular* Csparse matrix  __or__ a	* Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
1097	* cholmod_sparse factor (LDL = TRUE).	* cholmod_sparse factor (LDL = TRUE).
1098	*	*
1099		* @param obj -- now a cholmod_sparse factor or a dtCMatrix
1100	* @param pslot  'p' (column pointer)   slot of Csparse matrix/factor	* @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
1101	* @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor	* @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
1102	* @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;	* @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
#	Line 652	Line 1105
1105	*	*
1106	* @return  a SEXP, either a (double) number or a length n-vector of diagonal entries	* @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
1107	*/	*/
1108	SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)	SEXP diag_tC(SEXP obj, SEXP resultKind)
1109	{	{
1110
1111		SEXP
1112		pslot = GET_SLOT(obj, Matrix_pSym),
1113		xslot = GET_SLOT(obj, Matrix_xSym);
1114		Rboolean is_U = (R_has_slot(obj, Matrix_uploSym) &&
1115		*CHAR(asChar(GET_SLOT(obj, Matrix_uploSym))) == 'U');
1116	int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */	int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
1117	*x_p  = INTEGER(pslot),	*x_p  = INTEGER(pslot), pp = -1, *perm;
	*perm = INTEGER(perm_slot);
1118	double *x_x = REAL(xslot);	double *x_x = REAL(xslot);
1119	/*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/	/*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
1120
1121	return diag_tC_ptr(n, x_p, x_x, perm, resultKind);	if(R_has_slot(obj, Matrix_permSym))
1122		perm = INTEGER(GET_SLOT(obj, Matrix_permSym));
1123		else perm = &pp;
1124
1125		return diag_tC_ptr(n, x_p, x_x, is_U, perm, resultKind);
1126	}	}
1127
1128
1129	/**	/**
1130	* Create a Csparse matrix object from indices and/or pointers.	* Create a Csparse matrix object from indices and/or pointers.
1131	*	*
#	Line 764	Line 1227
1227	if (cls[1] != 'g')	if (cls[1] != 'g')
1228	error(_("Only 'g'eneral sparse matrix types allowed"));	error(_("Only 'g'eneral sparse matrix types allowed"));
1229	/* allocate and populate the triplet */	/* allocate and populate the triplet */
1230	T = cholmod_l_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,	T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
1231	xtype, &c);	xtype, &c);
1232	T->x = x;	T->x = x;
1233	tri = (int*)T->i;	tri = (int*)T->i;
#	Line 774	Line 1237
1237	trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);	trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
1238	}	}
1239	/* create the cholmod_sparse structure */	/* create the cholmod_sparse structure */
1240	A = cholmod_l_triplet_to_sparse(T, nnz, &c);	A = cholmod_triplet_to_sparse(T, nnz, &c);
1241	cholmod_l_free_triplet(&T, &c);	cholmod_free_triplet(&T, &c);
1242	/* copy the information to the SEXP */	/* copy the information to the SEXP */
1243	ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));	ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
1244	/* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */	// FIXME: This has been copied from chm_sparse_to_SEXP in  chm_common.c
1245	/* allocate and copy common slots */	/* allocate and copy common slots */
1246	nnz = cholmod_l_nnz(A, &c);	nnz = cholmod_nnz(A, &c);
1247	dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));	dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
1248	dims[0] = A->nrow; dims[1] = A->ncol;	dims[0] = A->nrow; dims[1] = A->ncol;
1249	Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);	Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
#	Line 792	Line 1255
1255	case 'l':	case 'l':
1256	error(_("code not yet written for cls = \"lgCMatrix\""));	error(_("code not yet written for cls = \"lgCMatrix\""));
1257	}	}
1258	cholmod_l_free_sparse(&A, &c);	/* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
1259		cholmod_free_sparse(&A, &c);
1260	UNPROTECT(1);	UNPROTECT(1);
1261	return ans;	return ans;
1262	}	}

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Legend: Removed from v.2586   changed lines   Added in v.3143

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