The R Project SVN – R-packages – Diff – /branches/Matrix-APIchange/src/Csparse.c



		    strictly = FALSE;
	    }
    }
    if (!sorted) {
	CHM_SP chx = AS_CHM_SP(x);
	R_CheckStack();
 
	cholmod_sort(chx, &c);
	/* Now re-check that row indices are *strictly* increasing
	 * (and not just increasing) within each column : */
	for (j = 0; j < ncol; j++) {

    /* This loses the symmetry property, since cholmod_dense has none,
     * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
     * to numeric (CHOLMOD_REAL) ones : */
    CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
    int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
    R_CheckStack();
 
    return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
}
 
SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
{
    CHM_SP chxs = AS_CHM_SP(x);
    CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
    int tr = asLogical(tri);
    R_CheckStack();
 
    return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
			      tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
			      0, tr ? diag_P(x) : "",
			      GET_SLOT(x, Matrix_DimNamesSym));

{
    CHM_SP chxs = AS_CHM_SP(x);
    CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
    int tr = asLogical(tri);
    int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
    R_CheckStack();
 
    return chm_triplet_to_SEXP(chxt, 1,
			       tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
			       Rkind, tr ? diag_P(x) : "",
			       GET_SLOT(x, Matrix_DimNamesSym));

/* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
SEXP Csparse_symmetric_to_general(SEXP x)
{
    CHM_SP chx = AS_CHM_SP(x), chgx;
    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
    R_CheckStack();
 
    if (!(chx->stype))
	error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
    chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
    /* xtype: pattern, "real", complex or .. */

SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
{
    CHM_SP chx = AS_CHM_SP(x), chgx;
    int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;
    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
    R_CheckStack();
 
    chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
    /* xtype: pattern, "real", complex or .. */
    return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
			      GET_SLOT(x, Matrix_DimNamesSym));

    CHM_SP chx = AS_CHM_SP(x);
    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
    CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
    SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
    int tr = asLogical(tri);
    R_CheckStack();
 
    tmp = VECTOR_ELT(dn, 0);	/* swap the dimnames */
    SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
    SET_VECTOR_ELT(dn, 1, tmp);
    UNPROTECT(1);

SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
{
    CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b);
    CHM_SP chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);
    SEXP dn = allocVector(VECSXP, 2);
    R_CheckStack();
 
    SET_VECTOR_ELT(dn, 0,	/* establish dimnames */
		   duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
    SET_VECTOR_ELT(dn, 1,
		   duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));

SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
{
    int tr = asLogical(trans);
    CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b), chTr, chc;
    SEXP dn = allocVector(VECSXP, 2);
    R_CheckStack();
 
    chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
    chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
			 0, cha->xtype, 1, &c);
    cholmod_free_sparse(&chTr, &c);

    CHM_DN chb = AS_CHM_DN(b_M);
    CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
					chb->xtype, &c);
    SEXP dn = PROTECT(allocVector(VECSXP, 2));
    double one[] = {1,0}, zero[] = {0,0};
    R_CheckStack();
 
    cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
    SET_VECTOR_ELT(dn, 0,	/* establish dimnames */
		   duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
    SET_VECTOR_ELT(dn, 1,

    CHM_DN chb = AS_CHM_DN(b_M);
    CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
					chb->xtype, &c);
    SEXP dn = PROTECT(allocVector(VECSXP, 2));
    double one[] = {1,0}, zero[] = {0,0};
    R_CheckStack();
 
    cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
    SET_VECTOR_ELT(dn, 0,	/* establish dimnames */
		   duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
    SET_VECTOR_ELT(dn, 1,

	tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
    CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
    CHM_SP chcp, chxt,
	chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c) : AS_CHM_SP(x);
    SEXP dn = PROTECT(allocVector(VECSXP, 2));
    R_CheckStack();
 
    if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
    chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
    if(!chcp) error(_("Csparse_crossprod(): error return from cholmod_aat()"));
    cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);

{
    CHM_SP chx = AS_CHM_SP(x);
    CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
    double dtol = asReal(tol);
    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
    R_CheckStack();
 
    if(!cholmod_drop(dtol, ans, &c))
	error(_("cholmod_drop() failed"));
    return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
			      GET_SLOT(x, Matrix_DimNamesSym));

 
SEXP Csparse_horzcat(SEXP x, SEXP y)
{
    CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);
    int Rkind = 0; /* only for "d" - FIXME */
    R_CheckStack();
 
    /* FIXME: currently drops dimnames */
    return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
			      1, 0, Rkind, "", R_NilValue);
}
 
SEXP Csparse_vertcat(SEXP x, SEXP y)
{
    CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);
    int Rkind = 0; /* only for "d" - FIXME */
    R_CheckStack();
 
    /* FIXME: currently drops dimnames */
    return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
			      1, 0, Rkind, "", R_NilValue);
}

SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
{
    CHM_SP chx = AS_CHM_SP(x);
    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
    CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
    R_CheckStack();
 
    return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
			      GET_SLOT(x, Matrix_DimNamesSym));
}
 

	double one[] = {1, 0};
	CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
	int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
 
	R_CheckStack();
	cholmod_free_sparse(&eye, &c);
	return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
				  GET_SLOT(x, Matrix_DimNamesSym));
    }
}

{
    CHM_SP chx = AS_CHM_SP(x);
    int rsize = (isNull(i)) ? -1 : LENGTH(i),
	csize = (isNull(j)) ? -1 : LENGTH(j);
    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
    R_CheckStack();
 
    if (rsize >= 0 && !isInteger(i))
	error(_("Index i must be NULL or integer"));
    if (csize >= 0 && !isInteger(j))
	error(_("Index j must be NULL or integer"));

The R Project SVN R-packages

(root)/branches/Matrix-APIchange/src/Csparse.c @ 4560 – Rev 4530 → 4558

Rev 4530		Rev 4558
Line 38...		Line 38...
38	`strictly = FALSE;`	38	`strictly = FALSE;`
39	`}`	39	`}`
40	`}`	40	`}`
41	`if (!sorted) {`	41	`if (!sorted) {`
42	`CHM_SP chx = AS_CHM_SP(x);`	42	`CHM_SP chx = AS_CHM_SP(x);`
-		43	`R_CheckStack();`
43		44
44	`cholmod_sort(chx, &c);`	45	`cholmod_sort(chx, &c);`
45	`/* Now re-check that row indices are strictly increasing`	46	`/* Now re-check that row indices are strictly increasing`
46	`* (and not just increasing) within each column : */`	47	`* (and not just increasing) within each column : */`
47	`for (j = 0; j < ncol; j++) {`	48	`for (j = 0; j < ncol; j++) {`
Line 65...		Line 66...
65	`/* This loses the symmetry property, since cholmod_dense has none,`	66	`/* This loses the symmetry property, since cholmod_dense has none,`
66	`* BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices`	67	`* BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices`
67	`* to numeric (CHOLMOD_REAL) ones : */`	68	`* to numeric (CHOLMOD_REAL) ones : */`
68	`CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);`	69	`CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);`
69	`int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);`	70	`int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);`
-		71	`R_CheckStack();`
70		72
71	`return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));`	73	`return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));`
72	`}`	74	`}`
73		75
74	`SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)`	76	`SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)`
75	`{`	77	`{`
76	`CHM_SP chxs = AS_CHM_SP(x);`	78	`CHM_SP chxs = AS_CHM_SP(x);`
77	`CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);`	79	`CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);`
78	`int tr = asLogical(tri);`	80	`int tr = asLogical(tri);`
-		81	`R_CheckStack();`
79		82
80	`return chm_sparse_to_SEXP(chxcp, 1/do_free/,`	83	`return chm_sparse_to_SEXP(chxcp, 1/do_free/,`
81	`tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,`	84	`tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,`
82	`0, tr ? diag_P(x) : "",`	85	`0, tr ? diag_P(x) : "",`
83	`GET_SLOT(x, Matrix_DimNamesSym));`	86	`GET_SLOT(x, Matrix_DimNamesSym));`
Line 93...		Line 96...
93	`{`	96	`{`
94	`CHM_SP chxs = AS_CHM_SP(x);`	97	`CHM_SP chxs = AS_CHM_SP(x);`
95	`CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);`	98	`CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);`
96	`int tr = asLogical(tri);`	99	`int tr = asLogical(tri);`
97	`int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`	100	`int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`
-		101	`R_CheckStack();`
98		102
99	`return chm_triplet_to_SEXP(chxt, 1,`	103	`return chm_triplet_to_SEXP(chxt, 1,`
100	`tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,`	104	`tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,`
101	`Rkind, tr ? diag_P(x) : "",`	105	`Rkind, tr ? diag_P(x) : "",`
102	`GET_SLOT(x, Matrix_DimNamesSym));`	106	`GET_SLOT(x, Matrix_DimNamesSym));`
Line 105...		Line 109...
105	`/* this used to be called sCMatrix_to_gCMatrix(..) [in ./dsCMatrix.c ]: */`	109	`/* this used to be called sCMatrix_to_gCMatrix(..) [in ./dsCMatrix.c ]: */`
106	`SEXP Csparse_symmetric_to_general(SEXP x)`	110	`SEXP Csparse_symmetric_to_general(SEXP x)`
107	`{`	111	`{`
108	`CHM_SP chx = AS_CHM_SP(x), chgx;`	112	`CHM_SP chx = AS_CHM_SP(x), chgx;`
109	`int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`	113	`int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`
-		114	`R_CheckStack();`
110		115
111	`if (!(chx->stype))`	116	`if (!(chx->stype))`
112	`error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));`	117	`error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));`
113	`chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);`	118	`chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);`
114	`/* xtype: pattern, "real", complex or .. */`	119	`/* xtype: pattern, "real", complex or .. */`
Line 119...		Line 124...
119	`SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)`	124	`SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)`
120	`{`	125	`{`
121	`CHM_SP chx = AS_CHM_SP(x), chgx;`	126	`CHM_SP chx = AS_CHM_SP(x), chgx;`
122	`int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;`	127	`int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;`
123	`int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`	128	`int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`
-		129	`R_CheckStack();`
124		130
125	`chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);`	131	`chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);`
126	`/* xtype: pattern, "real", complex or .. */`	132	`/* xtype: pattern, "real", complex or .. */`
127	`return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",`	133	`return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",`
128	`GET_SLOT(x, Matrix_DimNamesSym));`	134	`GET_SLOT(x, Matrix_DimNamesSym));`
Line 135...		Line 141...
135	`CHM_SP chx = AS_CHM_SP(x);`	141	`CHM_SP chx = AS_CHM_SP(x);`
136	`int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`	142	`int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`
137	`CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);`	143	`CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);`
138	`SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;`	144	`SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;`
139	`int tr = asLogical(tri);`	145	`int tr = asLogical(tri);`
-		146	`R_CheckStack();`
140		147
141	`tmp = VECTOR_ELT(dn, 0); /* swap the dimnames */`	148	`tmp = VECTOR_ELT(dn, 0); /* swap the dimnames */`
142	`SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));`	149	`SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));`
143	`SET_VECTOR_ELT(dn, 1, tmp);`	150	`SET_VECTOR_ELT(dn, 1, tmp);`
144	`UNPROTECT(1);`	151	`UNPROTECT(1);`
Line 150...		Line 157...
150	`SEXP Csparse_Csparse_prod(SEXP a, SEXP b)`	157	`SEXP Csparse_Csparse_prod(SEXP a, SEXP b)`
151	`{`	158	`{`
152	`CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b);`	159	`CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b);`
153	`CHM_SP chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);`	160	`CHM_SP chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);`
154	`SEXP dn = allocVector(VECSXP, 2);`	161	`SEXP dn = allocVector(VECSXP, 2);`
-		162	`R_CheckStack();`
155		163
156	`SET_VECTOR_ELT(dn, 0, /* establish dimnames */`	164	`SET_VECTOR_ELT(dn, 0, /* establish dimnames */`
157	`duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));`	165	`duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));`
158	`SET_VECTOR_ELT(dn, 1,`	166	`SET_VECTOR_ELT(dn, 1,`
159	`duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));`	167	`duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));`
Line 163...		Line 171...
163	`SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)`	171	`SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)`
164	`{`	172	`{`
165	`int tr = asLogical(trans);`	173	`int tr = asLogical(trans);`
166	`CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b), chTr, chc;`	174	`CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b), chTr, chc;`
167	`SEXP dn = allocVector(VECSXP, 2);`	175	`SEXP dn = allocVector(VECSXP, 2);`
-		176	`R_CheckStack();`
168		177
169	`chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);`	178	`chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);`
170	`chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,`	179	`chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,`
171	`0, cha->xtype, 1, &c);`	180	`0, cha->xtype, 1, &c);`
172	`cholmod_free_sparse(&chTr, &c);`	181	`cholmod_free_sparse(&chTr, &c);`
Line 185...		Line 194...
185	`CHM_DN chb = AS_CHM_DN(b_M);`	194	`CHM_DN chb = AS_CHM_DN(b_M);`
186	`CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,`	195	`CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,`
187	`chb->xtype, &c);`	196	`chb->xtype, &c);`
188	`SEXP dn = PROTECT(allocVector(VECSXP, 2));`	197	`SEXP dn = PROTECT(allocVector(VECSXP, 2));`
189	`double one[] = {1,0}, zero[] = {0,0};`	198	`double one[] = {1,0}, zero[] = {0,0};`
-		199	`R_CheckStack();`
190		200
191	`cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);`	201	`cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);`
192	`SET_VECTOR_ELT(dn, 0, /* establish dimnames */`	202	`SET_VECTOR_ELT(dn, 0, /* establish dimnames */`
193	`duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));`	203	`duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));`
194	`SET_VECTOR_ELT(dn, 1,`	204	`SET_VECTOR_ELT(dn, 1,`
Line 204...		Line 214...
204	`CHM_DN chb = AS_CHM_DN(b_M);`	214	`CHM_DN chb = AS_CHM_DN(b_M);`
205	`CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,`	215	`CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,`
206	`chb->xtype, &c);`	216	`chb->xtype, &c);`
207	`SEXP dn = PROTECT(allocVector(VECSXP, 2));`	217	`SEXP dn = PROTECT(allocVector(VECSXP, 2));`
208	`double one[] = {1,0}, zero[] = {0,0};`	218	`double one[] = {1,0}, zero[] = {0,0};`
-		219	`R_CheckStack();`
209		220
210	`cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);`	221	`cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);`
211	`SET_VECTOR_ELT(dn, 0, /* establish dimnames */`	222	`SET_VECTOR_ELT(dn, 0, /* establish dimnames */`
212	`duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));`	223	`duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));`
213	`SET_VECTOR_ELT(dn, 1,`	224	`SET_VECTOR_ELT(dn, 1,`
Line 223...		Line 234...
223	`tr = asLogical(trans); /* gets reversed because _aat is tcrossprod */`	234	`tr = asLogical(trans); /* gets reversed because _aat is tcrossprod */`
224	`CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;`	235	`CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;`
225	`CHM_SP chcp, chxt,`	236	`CHM_SP chcp, chxt,`
226	`chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c) : AS_CHM_SP(x);`	237	`chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c) : AS_CHM_SP(x);`
227	`SEXP dn = PROTECT(allocVector(VECSXP, 2));`	238	`SEXP dn = PROTECT(allocVector(VECSXP, 2));`
-		239	`R_CheckStack();`
228		240
229	`if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);`	241	`if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);`
230	`chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);`	242	`chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);`
231	`if(!chcp) error(_("Csparse_crossprod(): error return from cholmod_aat()"));`	243	`if(!chcp) error(_("Csparse_crossprod(): error return from cholmod_aat()"));`
232	`cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);`	244	`cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);`
Line 245...		Line 257...
245	`{`	257	`{`
246	`CHM_SP chx = AS_CHM_SP(x);`	258	`CHM_SP chx = AS_CHM_SP(x);`
247	`CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);`	259	`CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);`
248	`double dtol = asReal(tol);`	260	`double dtol = asReal(tol);`
249	`int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`	261	`int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`
-		262	`R_CheckStack();`
250		263
251	`if(!cholmod_drop(dtol, ans, &c))`	264	`if(!cholmod_drop(dtol, ans, &c))`
252	`error(_("cholmod_drop() failed"));`	265	`error(_("cholmod_drop() failed"));`
253	`return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",`	266	`return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",`
254	`GET_SLOT(x, Matrix_DimNamesSym));`	267	`GET_SLOT(x, Matrix_DimNamesSym));`
Line 256...		Line 269...
256		269
257	`SEXP Csparse_horzcat(SEXP x, SEXP y)`	270	`SEXP Csparse_horzcat(SEXP x, SEXP y)`
258	`{`	271	`{`
259	`CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);`	272	`CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);`
260	`int Rkind = 0; /* only for "d" - FIXME */`	273	`int Rkind = 0; /* only for "d" - FIXME */`
-		274	`R_CheckStack();`
261		275
262	`/* FIXME: currently drops dimnames */`	276	`/* FIXME: currently drops dimnames */`
263	`return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),`	277	`return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),`
264	`1, 0, Rkind, "", R_NilValue);`	278	`1, 0, Rkind, "", R_NilValue);`
265	`}`	279	`}`
266		280
267	`SEXP Csparse_vertcat(SEXP x, SEXP y)`	281	`SEXP Csparse_vertcat(SEXP x, SEXP y)`
268	`{`	282	`{`
269	`CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);`	283	`CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);`
270	`int Rkind = 0; /* only for "d" - FIXME */`	284	`int Rkind = 0; /* only for "d" - FIXME */`
-		285	`R_CheckStack();`
271		286
272	`/* FIXME: currently drops dimnames */`	287	`/* FIXME: currently drops dimnames */`
273	`return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),`	288	`return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),`
274	`1, 0, Rkind, "", R_NilValue);`	289	`1, 0, Rkind, "", R_NilValue);`
275	`}`	290	`}`
Line 277...		Line 292...
277	`SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)`	292	`SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)`
278	`{`	293	`{`
279	`CHM_SP chx = AS_CHM_SP(x);`	294	`CHM_SP chx = AS_CHM_SP(x);`
280	`int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`	295	`int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`
281	`CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);`	296	`CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);`
-		297	`R_CheckStack();`
282		298
283	`return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",`	299	`return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",`
284	`GET_SLOT(x, Matrix_DimNamesSym));`	300	`GET_SLOT(x, Matrix_DimNamesSym));`
285	`}`	301	`}`
286		302
Line 295...		Line 311...
295	`double one[] = {1, 0};`	311	`double one[] = {1, 0};`
296	`CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);`	312	`CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);`
297	`int uploT = (*uplo_P(x) == 'U') ? 1 : -1;`	313	`int uploT = (*uplo_P(x) == 'U') ? 1 : -1;`
298	`int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`	314	`int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`
299		315
-		316	`R_CheckStack();`
300	`cholmod_free_sparse(&eye, &c);`	317	`cholmod_free_sparse(&eye, &c);`
301	`return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",`	318	`return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",`
302	`GET_SLOT(x, Matrix_DimNamesSym));`	319	`GET_SLOT(x, Matrix_DimNamesSym));`
303	`}`	320	`}`
304	`}`	321	`}`
Line 307...		Line 324...
307	`{`	324	`{`
308	`CHM_SP chx = AS_CHM_SP(x);`	325	`CHM_SP chx = AS_CHM_SP(x);`
309	`int rsize = (isNull(i)) ? -1 : LENGTH(i),`	326	`int rsize = (isNull(i)) ? -1 : LENGTH(i),`
310	`csize = (isNull(j)) ? -1 : LENGTH(j);`	327	`csize = (isNull(j)) ? -1 : LENGTH(j);`
311	`int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`	328	`int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;`
-		329	`R_CheckStack();`
312		330
313	`if (rsize >= 0 && !isInteger(i))`	331	`if (rsize >= 0 && !isInteger(i))`
314	`error(_("Index i must be NULL or integer"));`	332	`error(_("Index i must be NULL or integer"));`
315	`if (csize >= 0 && !isInteger(j))`	333	`if (csize >= 0 && !isInteger(j))`
316	`error(_("Index j must be NULL or integer"));`	334	`error(_("Index j must be NULL or integer"));`