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[matrix] Diff of /pkg/Matrix/src/Csparse.c
 [matrix] / pkg / Matrix / src / Csparse.c

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

pkg/src/Csparse.c revision 1710, Tue Dec 26 15:57:06 2006 UTC pkg/Matrix/src/Csparse.c revision 2586, Sun Jul 25 02:32:06 2010 UTC
# Line 1  Line 1
1                          /* Sparse matrices in compressed column-oriented form */                          /* Sparse matrices in compressed column-oriented form */
2  #include "Csparse.h"  #include "Csparse.h"
3    #include "Tsparse.h"
4  #include "chm_common.h"  #include "chm_common.h"
5
6  SEXP Csparse_validate(SEXP x)  /** "Cheap" C version of  Csparse_validate() - *not* sorting : */
7    Rboolean isValid_Csparse(SEXP x)
8  {  {
9      /* NB: we do *NOT* check a potential 'x' slot here, at all */      /* NB: we do *NOT* check a potential 'x' slot here, at all */
10      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
11          islot = GET_SLOT(x, Matrix_iSym);          islot = GET_SLOT(x, Matrix_iSym);
12      int j, k, sorted,      int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)), j,
13            nrow = dims[0],
14            ncol = dims[1],
15            *xp = INTEGER(pslot),
16            *xi = INTEGER(islot);
17
18        if (length(pslot) != dims[1] + 1)
19            return FALSE;
20        if (xp[0] != 0)
21            return FALSE;
22        if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
23            return FALSE;
24        for (j = 0; j < xp[ncol]; j++) {
25            if (xi[j] < 0 || xi[j] >= nrow)
26                return FALSE;
27        }
28        for (j = 0; j < ncol; j++) {
29            if (xp[j] > xp[j + 1])
30                return FALSE;
31        }
32        return TRUE;
33    }
34
35    SEXP Csparse_validate(SEXP x) {
36        return Csparse_validate_(x, FALSE);
37    }
38
39    SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
40        return Csparse_validate_(x, asLogical(maybe_modify));
41    }
42
43    SEXP Csparse_validate_(SEXP x, Rboolean maybe_modify)
44    {
45        /* NB: we do *NOT* check a potential 'x' slot here, at all */
46        SEXP pslot = GET_SLOT(x, Matrix_pSym),
47            islot = GET_SLOT(x, Matrix_iSym);
48        Rboolean sorted, strictly;
49        int j, k,
50          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
51          nrow = dims[0],          nrow = dims[0],
52          ncol = dims[1],          ncol = dims[1],
# Line 18  Line 57
57          return mkString(_("slot p must have length = ncol(.) + 1"));          return mkString(_("slot p must have length = ncol(.) + 1"));
58      if (xp[0] != 0)      if (xp[0] != 0)
59          return mkString(_("first element of slot p must be zero"));          return mkString(_("first element of slot p must be zero"));
60      if (length(islot) != xp[ncol])      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
61          return          return
62              mkString(_("last element of slot p must match length of slots i and x"));              mkString(_("last element of slot p must match length of slots i and x"));
63      for (j = 0; j < length(islot); j++) {      for (j = 0; j < xp[ncol]; j++) {
64          if (xi[j] < 0 || xi[j] >= nrow)          if (xi[j] < 0 || xi[j] >= nrow)
65              return mkString(_("all row indices must be between 0 and nrow-1"));              return mkString(_("all row indices must be between 0 and nrow-1"));
66      }      }
67      sorted = TRUE;      sorted = TRUE; strictly = TRUE;
68      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
69          if (xp[j] > xp[j+1])          if (xp[j] > xp[j+1])
70              return mkString(_("slot p must be non-decreasing"));              return mkString(_("slot p must be non-decreasing"));
71          for (k = xp[j] + 1; k < xp[j + 1]; k++)          if(sorted) /* only act if >= 2 entries in column j : */
72              if (xi[k] < xi[k - 1]) sorted = FALSE;              for (k = xp[j] + 1; k < xp[j + 1]; k++) {
73                    if (xi[k] < xi[k - 1])
74                        sorted = FALSE;
75                    else if (xi[k] == xi[k - 1])
76                        strictly = FALSE;
77                }
78      }      }
79      if (!sorted) {      if (!sorted) {
80          cholmod_sparse *chx = as_cholmod_sparse(x);          if(maybe_modify) {
81          cholmod_sort(chx, &c);              CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
82          Free(chx);              R_CheckStack();
83                as_cholmod_sparse(chx, x, FALSE, TRUE);/*-> cholmod_l_sort() ! */
84                /* as chx = AS_CHM_SP__(x)  but  ^^^^ sorting x in_place !!! */
85
86                /* Now re-check that row indices are *strictly* increasing
87                 * (and not just increasing) within each column : */
88                for (j = 0; j < ncol; j++) {
89                    for (k = xp[j] + 1; k < xp[j + 1]; k++)
90                        if (xi[k] == xi[k - 1])
91                            return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_l_sort)"));
92                }
93            } else { /* no modifying sorting : */
94                return mkString(_("row indices are not sorted within columns"));
95            }
96        } else if(!strictly) {  /* sorted, but not strictly */
97            return mkString(_("slot i is not *strictly* increasing inside a column"));
98      }      }
99      return ScalarLogical(1);      return ScalarLogical(1);
100  }  }
101
102    SEXP Rsparse_validate(SEXP x)
103    {
104        /* NB: we do *NOT* check a potential 'x' slot here, at all */
105        SEXP pslot = GET_SLOT(x, Matrix_pSym),
106            jslot = GET_SLOT(x, Matrix_jSym);
107        Rboolean sorted, strictly;
108        int i, k,
109            *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
110            nrow = dims[0],
111            ncol = dims[1],
112            *xp = INTEGER(pslot),
113            *xj = INTEGER(jslot);
114
115        if (length(pslot) != dims[0] + 1)
116            return mkString(_("slot p must have length = nrow(.) + 1"));
117        if (xp[0] != 0)
118            return mkString(_("first element of slot p must be zero"));
119        if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
120            return
121                mkString(_("last element of slot p must match length of slots j and x"));
122        for (i = 0; i < length(jslot); i++) {
123            if (xj[i] < 0 || xj[i] >= ncol)
124                return mkString(_("all column indices must be between 0 and ncol-1"));
125        }
126        sorted = TRUE; strictly = TRUE;
127        for (i = 0; i < nrow; i++) {
128            if (xp[i] > xp[i+1])
129                return mkString(_("slot p must be non-decreasing"));
130            if(sorted)
131                for (k = xp[i] + 1; k < xp[i + 1]; k++) {
132                    if (xj[k] < xj[k - 1])
133                        sorted = FALSE;
134                    else if (xj[k] == xj[k - 1])
135                        strictly = FALSE;
136                }
137        }
138        if (!sorted)
139            /* cannot easily use cholmod_l_sort(.) ... -> "error out" :*/
140            return mkString(_("slot j is not increasing inside a column"));
141        else if(!strictly) /* sorted, but not strictly */
142            return mkString(_("slot j is not *strictly* increasing inside a column"));
143
144        return ScalarLogical(1);
145    }
146
147
148    /* Called from ../R/Csparse.R : */
149    /* Can only return [dln]geMatrix (no symm/triang);
150     * FIXME: replace by non-CHOLMOD code ! */
151  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
152  {  {
153      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
154      cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);      /* This loses the symmetry property, since cholmod_dense has none,
155         * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
156         * to numeric (CHOLMOD_REAL) ones : */
157        CHM_DN chxd = cholmod_l_sparse_to_dense(chxs, &c);
158        int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
159        R_CheckStack();
160
161      Free(chxs);      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
return chm_dense_to_SEXP(chxd, 1, Real_kind(x),
GET_SLOT(x, Matrix_DimNamesSym));
162  }  }
163
164  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
165  {  {
166      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
167      cholmod_sparse      CHM_SP chxcp = cholmod_l_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
168          *chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      int tr = asLogical(tri);
169      int uploT = 0; char *diag = "";      R_CheckStack();
170
171      Free(chxs);      return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
172      if (asLogical(tri)) {       /* triangular sparse matrices */                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
173          uploT = (*uplo_P(x) == 'U') ? 1 : -1;                                0, tr ? diag_P(x) : "",
diag = CHAR(asChar(GET_SLOT(x, Matrix_diagSym)));
}
return chm_sparse_to_SEXP(chxcp, 1, uploT, 0, diag,
174                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
175  }  }
176
177  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
178  {  {
179      cholmod_sparse *chxs = as_cholmod_sparse(x);      return chm_dense_to_matrix(cholmod_l_sparse_to_dense(AS_CHM_SP__(x), &c),
180      cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));

Free(chxs);
return chm_dense_to_matrix(chxd, 1,
GET_SLOT(x, Matrix_DimNamesSym));
181  }  }
182
183  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
184  {  {
185      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
186      cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_l_sparse_to_triplet(chxs, &c);
187      int uploT = 0;      int tr = asLogical(tri);
188      char *diag = "";      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
189      int Rkind = (chxs->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      R_CheckStack();
190
191      Free(chxs);      return chm_triplet_to_SEXP(chxt, 1,
192      if (asLogical(tri)) {       /* triangular sparse matrices */                                 tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
193          uploT = (*uplo_P(x) == 'U') ? 1 : -1;                                 Rkind, tr ? diag_P(x) : "",
diag = diag_P(x);
}
return chm_triplet_to_SEXP(chxt, 1, uploT, Rkind, diag,
194                                 GET_SLOT(x, Matrix_DimNamesSym));                                 GET_SLOT(x, Matrix_DimNamesSym));
195  }  }
196
197  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
198  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
199  {  {
200      cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
201      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
202        R_CheckStack();
203
204      if (!(chx->stype))      if (!(chx->stype))
205          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
206      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);
207      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
Free(chx);
208      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
209                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
210  }  }
211
212  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
213  {  {
214      cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
215      int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
216      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
217        R_CheckStack();
218
219      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ uploT, chx->xtype, &c);
220      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
Free(chx);
221      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
222                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
223  }  }
224
225  SEXP Csparse_transpose(SEXP x, SEXP tri)  SEXP Csparse_transpose(SEXP x, SEXP tri)
226  {  {
227      cholmod_sparse *chx = as_cholmod_sparse(x);      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
228      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;       *       since cholmod (& cs) lacks sparse 'int' matrices */
229      cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);      CHM_SP chx = AS_CHM_SP__(x);
230        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
231        CHM_SP chxt = cholmod_l_transpose(chx, chx->xtype, &c);
232      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
233      int uploT = 0; char *diag = "";      int tr = asLogical(tri);
234        R_CheckStack();
235
Free(chx);
236      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
237      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
238      SET_VECTOR_ELT(dn, 1, tmp);      SET_VECTOR_ELT(dn, 1, tmp);
239      UNPROTECT(1);      UNPROTECT(1);
240      if (asLogical(tri)) { /* triangular sparse matrices : SWAP 'uplo' */      return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
241          uploT = (*uplo_P(x) == 'U') ? -1 : 1;                                tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
242          diag = diag_P(x);                                Rkind, tr ? diag_P(x) : "", dn);
}
return chm_sparse_to_SEXP(chxt, 1, uploT, Rkind, diag, dn);
243  }  }
244
245  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
246  {  {
247      cholmod_sparse      CHM_SP
248          *cha = as_cholmod_sparse(a),          cha = AS_CHM_SP(a),
249          *chb = as_cholmod_sparse(b);          chb = AS_CHM_SP(b),
250      cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);          chc = cholmod_l_ssmult(cha, chb, /*out_stype:*/ 0,
251      SEXP dn = allocVector(VECSXP, 2);                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
252                                   /*out sorted:*/ 1, &c);
253        const char *cl_a = class_P(a), *cl_b = class_P(b);
254        char diag[] = {'\0', '\0'};
255        int uploT = 0;
256        SEXP dn = PROTECT(allocVector(VECSXP, 2));
257        R_CheckStack();
258
259      Free(cha); Free(chb);  #ifdef DEBUG_Matrix_verbose
260        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
261    #endif
262
263        /* Preserve triangularity and even unit-triangularity if appropriate.
264         * Note that in that case, the multiplication itself should happen
265         * faster.  But there's no support for that in CHOLMOD */
266
267        /* UGLY hack -- rather should have (fast!) C-level version of
268         *       is(a, "triangularMatrix") etc */
269        if (cl_a[1] == 't' && cl_b[1] == 't')
270            /* FIXME: fails for "Cholesky","BunchKaufmann"..*/
271            if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
272                uploT = (*uplo_P(a) == 'U') ? 1 : -1;
273                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
274                    /* "remove the diagonal entries": */
275                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
276                    diag[0]= 'U';
277                }
278                else diag[0]= 'N';
279            }
280      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
281                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
282      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
283                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
284      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      UNPROTECT(1);
285        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
286  }  }
287
288  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
289  {  {
290      int tr = asLogical(trans);      int tr = asLogical(trans);
291      cholmod_sparse      CHM_SP
292          *cha = as_cholmod_sparse(a),          cha = AS_CHM_SP(a),
293          *chb = as_cholmod_sparse(b);          chb = AS_CHM_SP(b),
294      cholmod_sparse *chTr, *chc;          chTr, chc;
295      SEXP dn = allocVector(VECSXP, 2);      const char *cl_a = class_P(a), *cl_b = class_P(b);
296        char diag[] = {'\0', '\0'};
297  /*     cholmod_sparse *chTr = cholmod_transpose(cha, 1, &c); */      int uploT = 0;
298  /*     cholmod_sparse *chc = cholmod_ssmult(chTr, chb, 0, cha->xtype, 1, &c); */      SEXP dn = PROTECT(allocVector(VECSXP, 2));
299        R_CheckStack();
if (tr)
chTr = cholmod_transpose(chb, chb->xtype, &c);
else
chTr = cholmod_transpose(cha, cha->xtype, &c);
chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
0, cha->xtype, 1, &c);

Free(cha); Free(chb); cholmod_free_sparse(&chTr, &c);
300
301        chTr = cholmod_l_transpose((tr) ? chb : cha, chb->xtype, &c);
302        chc = cholmod_l_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
303                             /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
304        cholmod_l_free_sparse(&chTr, &c);
305
306        /* Preserve triangularity and unit-triangularity if appropriate;
307         * see Csparse_Csparse_prod() for comments */
308        if (cl_a[1] == 't' && cl_b[1] == 't')
309            if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
310                uploT = (*uplo_P(b) == 'U') ? 1 : -1;
311                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
312                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
313                    diag[0]= 'U';
314                }
315                else diag[0]= 'N';
316            }
317      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
318                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
319      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
320                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
321      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      UNPROTECT(1);
322        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
323  }  }
324
325  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
326  {  {
327      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
328      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
329      cholmod_dense *chb = as_cholmod_dense(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
330      cholmod_dense *chc =      CHM_DN chc = cholmod_l_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
331          cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);                                          chb->xtype, &c);
332      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
333      double alpha[] = {1,0}, beta[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
334        R_CheckStack();
335
336      cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);      cholmod_l_sdmult(cha, 0, one, zero, chb, chc, &c);
Free(cha); Free(chb);
UNPROTECT(1);
337      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
338                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
339      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
340                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
341        UNPROTECT(2);
342      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
343  }  }
344
345  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
346  {  {
347      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
348      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
349      cholmod_dense *chb = as_cholmod_dense(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
350      cholmod_dense *chc =      CHM_DN chc = cholmod_l_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
351          cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);                                          chb->xtype, &c);
352      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
353      double alpha[] = {1,0}, beta[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
354        R_CheckStack();
355
356      cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);      cholmod_l_sdmult(cha, 1, one, zero, chb, chc, &c);
Free(cha); Free(chb);
UNPROTECT(1);
357      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
358                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
359      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
360                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
361        UNPROTECT(2);
362      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
363  }  }
364
365  /* Computes   x'x  or  x x'  -- see Csparse_Csparse_crossprod above for  x'y and x y' */  /* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
366       see Csparse_Csparse_crossprod above for  x'y and x y' */
367  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
368  {  {
369      int trip = asLogical(triplet),      int trip = asLogical(triplet),
370          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
371      cholmod_triplet  #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
372          *cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
373      cholmod_sparse *chcp, *chxt,  #else /* workaround needed:*/
374          *chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)      SEXP xx = PROTECT(Tsparse_diagU2N(x));
375          : as_cholmod_sparse(x);      CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
376    #endif
377        CHM_SP chcp, chxt,
378            chx = (trip ?
379                   cholmod_l_triplet_to_sparse(cht, cht->nnz, &c) :
380                   AS_CHM_SP(x));
381      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
382        R_CheckStack();
383
384      if (!tr)      if (!tr) chxt = cholmod_l_transpose(chx, chx->xtype, &c);
385          chxt = cholmod_transpose(chx, chx->xtype, &c);      chcp = cholmod_l_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
386      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      if(!chcp) {
387      if(!chcp)          UNPROTECT(1);
388          error(_("Csparse_crossprod(): error return from cholmod_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_l_aat()"));
cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
chcp->stype = 1;
if (trip) {
cholmod_free_sparse(&chx, &c);
Free(cht);
} else {
Free(chx);
389      }      }
390      if (!tr) cholmod_free_sparse(&chxt, &c);      cholmod_l_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
391                                  /* create dimnames */      chcp->stype = 1;
392      SET_VECTOR_ELT(dn, 0,      if (trip) cholmod_l_free_sparse(&chx, &c);
393        if (!tr) cholmod_l_free_sparse(&chxt, &c);
394        SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
395                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
396                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
397      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
398    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
399      UNPROTECT(1);      UNPROTECT(1);
400    #else
401        UNPROTECT(2);
402    #endif
403      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
404  }  }
405
406  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
407  {  {
408      cholmod_sparse *chx = as_cholmod_sparse(x),      const char *cl = class_P(x);
409          *ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
410        int tr = (cl[1] == 't');
411        CHM_SP chx = AS_CHM_SP__(x);
412        CHM_SP ans = cholmod_l_copy(chx, chx->stype, chx->xtype, &c);
413      double dtol = asReal(tol);      double dtol = asReal(tol);
414      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
415        R_CheckStack();
416
417      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_l_drop(dtol, ans, &c))
418          error(_("cholmod_drop() failed"));          error(_("cholmod_l_drop() failed"));
419      Free(chx);      return chm_sparse_to_SEXP(ans, 1,
420      /* FIXME: currently drops dimnames */                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
421      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);                                Rkind, tr ? diag_P(x) : "",
422                                  GET_SLOT(x, Matrix_DimNamesSym));
423  }  }
424

425  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
426  {  {
427      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
428          *chy = as_cholmod_sparse(y), *ans;      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
429      int Rkind = 0; /* only for "d" - FIXME */          Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
430            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
431      ans = cholmod_horzcat(chx, chy, 1, &c);      R_CheckStack();
432      Free(chx); Free(chy);
433      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
434      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_l_horzcat(chx, chy, 1, &c),
435                                  1, 0, Rkind, "", R_NilValue);
436  }  }
437
438  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
439  {  {
440      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
441          *chy = as_cholmod_sparse(y), *ans;      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
442      int Rkind = 0; /* only for "d" - FIXME */          Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
443            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
444      ans = cholmod_vertcat(chx, chy, 1, &c);      R_CheckStack();
445      Free(chx); Free(chy);
446      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
447      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_l_vertcat(chx, chy, 1, &c),
448                                  1, 0, Rkind, "", R_NilValue);
449  }  }
450
451  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
452  {  {
453      cholmod_sparse *chx = as_cholmod_sparse(x), *ans;      CHM_SP chx = AS_CHM_SP__(x);
454      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
455        CHM_SP ans = cholmod_l_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
456        R_CheckStack();
457
458      ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
459      Free(chx);                                GET_SLOT(x, Matrix_DimNamesSym));
return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
460  }  }
461
462  SEXP Csparse_diagU2N(SEXP x)  SEXP Csparse_diagU2N(SEXP x)
463  {  {
464      if (*diag_P(x) != 'U') {/* "trivially fast" when there's no 'diag' slot at all */      const char *cl = class_P(x);
465        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
466        if (cl[1] != 't' || *diag_P(x) != 'U') {
467            /* "trivially fast" when not triangular (<==> no 'diag' slot),
468               or not *unit* triangular */
469          return (x);          return (x);
470      }      }
471      else {      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
472          cholmod_sparse *chx = as_cholmod_sparse(x);          CHM_SP chx = AS_CHM_SP__(x);
473          cholmod_sparse *eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_l_speye(chx->nrow, chx->ncol, chx->xtype, &c);
474          double one[] = {1, 0};          double one[] = {1, 0};
475          cholmod_sparse *ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_l_add(chx, eye, one, one, TRUE, TRUE, &c);
476          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
477          int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
478
479          Free(chx); cholmod_free_sparse(&eye, &c);          R_CheckStack();
480            cholmod_l_free_sparse(&eye, &c);
481          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
482                                    duplicate(GET_SLOT(x, Matrix_DimNamesSym)));                                    GET_SLOT(x, Matrix_DimNamesSym));
483        }
484    }
485
486    SEXP Csparse_diagN2U(SEXP x)
487    {
488        const char *cl = class_P(x);
489        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
490        if (cl[1] != 't' || *diag_P(x) != 'N') {
491            /* "trivially fast" when not triangular (<==> no 'diag' slot),
492               or already *unit* triangular */
493            return (x);
494        }
495        else { /* triangular with diag='N'): now drop the diagonal */
496            /* duplicate, since chx will be modified: */
497            CHM_SP chx = AS_CHM_SP__(duplicate(x));
498            int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
499                Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
500            R_CheckStack();
501
502            chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
503
504            return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
505                                      uploT, Rkind, "U",
506                                      GET_SLOT(x, Matrix_DimNamesSym));
507      }      }
508  }  }
509
510    /**
511     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
512     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
513     * @param x CsparseMatrix
514     * @param i row     indices (0-origin), or NULL (R's)
515     * @param j columns indices (0-origin), or NULL
516     *
517     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
518     */
519  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
520  {  {
521      cholmod_sparse *chx = as_cholmod_sparse(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
522      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
523          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
524      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
525        R_CheckStack();
526
527      if (rsize >= 0 && !isInteger(i))      if (rsize >= 0 && !isInteger(i))
528          error(_("Index i must be NULL or integer"));          error(_("Index i must be NULL or integer"));
529      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
530          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
531      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,
532                                                  INTEGER(j), csize,      if (chx->stype) /* symmetricMatrix */
533            /* for now, cholmod_submatrix() only accepts "generalMatrix" */
534            chx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);
535
536        return chm_sparse_to_SEXP(cholmod_l_submatrix(chx,
537                                    (rsize < 0) ? NULL : INTEGER(i), rsize,
538                                    (csize < 0) ? NULL : INTEGER(j), csize,
539                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
540                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "",
541                                  /* FIXME: drops dimnames */ R_NilValue);
542    }
543
544    SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
545    {
546        FILE *f = fopen(CHAR(asChar(fname)), "w");
547
548        if (!f)
549            error(_("failure to open file \"%s\" for writing"),
550                  CHAR(asChar(fname)));
551        if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),
552                                  (CHM_SP)NULL, (char*) NULL, &c))
553            error(_("cholmod_l_write_sparse returned error code"));
554        fclose(f);
555        return R_NilValue;
556    }
557
558
559    /**
560     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
561     * cholmod_sparse factor (LDL = TRUE).
562     *
563     * @param n  dimension of the matrix.
564     * @param x_p  'p' (column pointer) slot contents
565     * @param x_x  'x' (non-zero entries) slot contents
566     * @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
567     * @param resultKind a (SEXP) string indicating which kind of result is desired.
568     *
569     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
570     */
571    SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)
572    /*                                ^^^^^^ FIXME[Generalize] to int / ... */
573    {
574        const char* res_ch = CHAR(STRING_ELT(resultKind,0));
575        enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log
576        } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
577                      ((!strcmp(res_ch, "sumLog")) ? sum_log :
578                       ((!strcmp(res_ch, "prod")) ? prod :
579                        ((!strcmp(res_ch, "diag")) ? diag :
580                         ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
581                          -1)))));
582        int i, n_x, i_from = 0;
583        SEXP ans = PROTECT(allocVector(REALSXP,
584    /*                                 ^^^^  FIXME[Generalize] */
585                                       (res_kind == diag ||
586                                        res_kind == diag_backpermuted) ? n : 1));
587        double *v = REAL(ans);
588    /*  ^^^^^^      ^^^^  FIXME[Generalize] */
589
590    #define for_DIAG(v_ASSIGN)                                              \
591        for(i = 0; i < n; i++, i_from += n_x) {                             \
592            /* looking at i-th column */                                    \
593            n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
594            v_ASSIGN;                                                       \
595        }
596
597        /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
598         *            for uplo = "U" (makes sense with a "dtCMatrix" !),
599         *            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],
600         *            where nx = (x_p[i+1] - x_p[i])
601         */
602
603        switch(res_kind) {
604        case trace:
605            v[0] = 0.;
606            for_DIAG(v[0] += x_x[i_from]);
607            break;
608
609        case sum_log:
610            v[0] = 0.;
611            for_DIAG(v[0] += log(x_x[i_from]));
612            break;
613
614        case prod:
615            v[0] = 1.;
616            for_DIAG(v[0] *= x_x[i_from]);
617            break;
618
619        case diag:
620            for_DIAG(v[i] = x_x[i_from]);
621            break;
622
623        case diag_backpermuted:
624            for_DIAG(v[i] = x_x[i_from]);
625
626            warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));
627            /* now back_permute : */
628            for(i = 0; i < n; i++) {
629                double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
630                /*^^^^ FIXME[Generalize] */
631            }
632            break;
633
634        default: /* -1 from above */
635            error(_("diag_tC(): invalid 'resultKind'"));
636            /* Wall: */ ans = R_NilValue; v = REAL(ans);
637        }
638
639        UNPROTECT(1);
640        return ans;
641    }
642
643    /**
644     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
645     * cholmod_sparse factor (LDL = TRUE).
646     *
647     * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
648     * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
649     * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
650     *                   only used for "diagBack"
651     * @param resultKind a (SEXP) string indicating which kind of result is desired.
652     *
653     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
654     */
655    SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)
656    {
657        int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
658            *x_p  = INTEGER(pslot),
659            *perm = INTEGER(perm_slot);
660        double *x_x = REAL(xslot);
661    /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
662
663        return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
664    }
665
666    /**
667     * Create a Csparse matrix object from indices and/or pointers.
668     *
669     * @param cls name of actual class of object to create
670     * @param i optional integer vector of length nnz of row indices
671     * @param j optional integer vector of length nnz of column indices
672     * @param p optional integer vector of length np of row or column pointers
673     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
674     * @param x optional vector of values
675     * @param nnz length of vectors i, j and/or x, whichever is to be used
676     * @param dims optional integer vector of length 2 to be used as
677     *     dimensions.  If dims == (int*)NULL then the maximum row and column
678     *     index are used as the dimensions.
679     * @param dimnames optional list of length 2 to be used as dimnames
680     * @param index1 indicator of 1-based indices
681     *
682     * @return an SEXP of class cls inheriting from CsparseMatrix.
683     */
684    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
685                        void* x, int nnz, int* dims, SEXP dimnames,
686                        int index1)
687    {
688        SEXP ans;
689        int *ij = (int*)NULL, *tri, *trj,
690            mi, mj, mp, nrow = -1, ncol = -1;
691        int xtype = -1;             /* -Wall */
692        CHM_TR T;
693        CHM_SP A;
694
695        if (np < 0 || nnz < 0)
696            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
697                  np, nnz);
698        if (1 != ((mi = (i == (int*)NULL)) +
699                  (mj = (j == (int*)NULL)) +
700                  (mp = (p == (int*)NULL))))
701            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
702        if (mp) {
703            if (np) error(_("np = %d, must be zero when p is NULL"), np);
704        } else {
705            if (np) {               /* Expand p to form i or j */
706                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
707                for (int ii = 0; ii < np; ii++)
708                    if (p[ii] > p[ii + 1])
709                        error(_("p must be non-decreasing"));
710                if (p[np] != nnz)
711                    error("p[np] = %d != nnz = %d", p[np], nnz);
712                ij = Calloc(nnz, int);
713                if (mi) {
714                    i = ij;
715                    nrow = np;
716                } else {
717                    j = ij;
718                    ncol = np;
719                }
720                                    /* Expand p to 0-based indices */
721                for (int ii = 0; ii < np; ii++)
722                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
723            } else {
724                if (nnz)
725                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
726                          nnz);
727            }
728        }
729                                    /* calculate nrow and ncol */
730        if (nrow < 0) {
731            for (int ii = 0; ii < nnz; ii++) {
732                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
733                if (i1 < 1) error(_("invalid row index at position %d"), ii);
734                if (i1 > nrow) nrow = i1;
735            }
736        }
737        if (ncol < 0) {
738            for (int jj = 0; jj < nnz; jj++) {
739                int j1 = j[jj] + (index1 ? 0 : 1);
740                if (j1 < 1) error(_("invalid column index at position %d"), jj);
741                if (j1 > ncol) ncol = j1;
742            }
743        }
744        if (dims != (int*)NULL) {
745            if (dims[0] > nrow) nrow = dims[0];
746            if (dims[1] > ncol) ncol = dims[1];
747        }
748                                    /* check the class name */
749        if (strlen(cls) != 8)
750            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
751        if (!strcmp(cls + 2, "CMatrix"))
752            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
753        switch(cls[0]) {
754        case 'd':
755        case 'l':
756               xtype = CHOLMOD_REAL;
757               break;
758        case 'n':
759               xtype = CHOLMOD_PATTERN;
760               break;
761        default:
762               error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
763        }
764        if (cls[1] != 'g')
765            error(_("Only 'g'eneral sparse matrix types allowed"));
766                                    /* allocate and populate the triplet */
767        T = cholmod_l_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
768                                        xtype, &c);
769        T->x = x;
770        tri = (int*)T->i;
771        trj = (int*)T->j;
772        for (int ii = 0; ii < nnz; ii++) {
773            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
774            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
775        }
776                                    /* create the cholmod_sparse structure */
777        A = cholmod_l_triplet_to_sparse(T, nnz, &c);
778        cholmod_l_free_triplet(&T, &c);
779                                    /* copy the information to the SEXP */
780        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
781    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
782                                    /* allocate and copy common slots */
783        nnz = cholmod_l_nnz(A, &c);
784        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
785        dims[0] = A->nrow; dims[1] = A->ncol;
786        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
787        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
788        switch(cls[1]) {
789        case 'd':
790            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
791            break;
792        case 'l':
793            error(_("code not yet written for cls = \"lgCMatrix\""));
794        }
795        cholmod_l_free_sparse(&A, &c);
796        UNPROTECT(1);
797        return ans;
798  }  }

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