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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 1448, Sat Aug 26 03:29:36 2006 UTC pkg/Matrix/src/Csparse.c revision 2684, Fri Aug 5 15:17:26 2011 UTC
# Line 1  Line 1
1                          /* Sparse matrices in compressed column-oriented form */                          /* Sparse matrices in compressed column-oriented form */
2
3    #include <stdint.h> // C99 for int64_t
4  #include "Csparse.h"  #include "Csparse.h"
5    #include "Tsparse.h"
6  #include "chm_common.h"  #include "chm_common.h"
7
8  SEXP Csparse_validate(SEXP x)  /** "Cheap" C version of  Csparse_validate() - *not* sorting : */
9    Rboolean isValid_Csparse(SEXP x)
10    {
11        /* NB: we do *NOT* check a potential 'x' slot here, at all */
12        SEXP pslot = GET_SLOT(x, Matrix_pSym),
13            islot = GET_SLOT(x, Matrix_iSym);
14        int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)), j,
15            nrow = dims[0],
16            ncol = dims[1],
17            *xp = INTEGER(pslot),
18            *xi = INTEGER(islot);
19
20        if (length(pslot) != dims[1] + 1)
21            return FALSE;
22        if (xp[0] != 0)
23            return FALSE;
24        if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
25            return FALSE;
26        for (j = 0; j < xp[ncol]; j++) {
27            if (xi[j] < 0 || xi[j] >= nrow)
28                return FALSE;
29        }
30        for (j = 0; j < ncol; j++) {
31            if (xp[j] > xp[j + 1])
32                return FALSE;
33        }
34        return TRUE;
35    }
36
37    SEXP Csparse_validate(SEXP x) {
38        return Csparse_validate_(x, FALSE);
39    }
40
41    SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
42        return Csparse_validate_(x, asLogical(maybe_modify));
43    }
44
45    SEXP Csparse_validate_(SEXP x, Rboolean maybe_modify)
46  {  {
47        /* NB: we do *NOT* check a potential 'x' slot here, at all */
48      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
49          islot = GET_SLOT(x, Matrix_iSym);          islot = GET_SLOT(x, Matrix_iSym);
50      int j, ncol = length(pslot) - 1,      Rboolean sorted, strictly;
51        int j, k,
52          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
53          nrow, *xp = INTEGER(pslot),          nrow = dims[0],
54            ncol = dims[1],
55            *xp = INTEGER(pslot),
56          *xi = INTEGER(islot);          *xi = INTEGER(islot);
57
58      nrow = dims[0];      if (length(pslot) != dims[1] + 1)
59      if (length(pslot) <= 0)          return mkString(_("slot p must have length = ncol(.) + 1"));
return mkString(_("slot p must have length > 0"));
60      if (xp[0] != 0)      if (xp[0] != 0)
61          return mkString(_("first element of slot p must be zero"));          return mkString(_("first element of slot p must be zero"));
62      if (length(islot) != xp[ncol])      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
63          return mkString(_("last element of slot p must match length of slots i and x"));          return
64                mkString(_("last element of slot p must match length of slots i and x"));
65        for (j = 0; j < xp[ncol]; j++) {
66            if (xi[j] < 0 || xi[j] >= nrow)
67                return mkString(_("all row indices must be between 0 and nrow-1"));
68        }
69        sorted = TRUE; strictly = TRUE;
70      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
71          if (xp[j] > xp[j+1])          if (xp[j] > xp[j+1])
72              return mkString(_("slot p must be non-decreasing"));              return mkString(_("slot p must be non-decreasing"));
73            if(sorted) /* only act if >= 2 entries in column j : */
74                for (k = xp[j] + 1; k < xp[j + 1]; k++) {
75                    if (xi[k] < xi[k - 1])
76                        sorted = FALSE;
77                    else if (xi[k] == xi[k - 1])
78                        strictly = FALSE;
79                }
80        }
81        if (!sorted) {
82            if(maybe_modify) {
83                CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
84                R_CheckStack();
85                as_cholmod_sparse(chx, x, FALSE, TRUE);/*-> cholmod_l_sort() ! */
86                /* as chx = AS_CHM_SP__(x)  but  ^^^^ sorting x in_place !!! */
87
88                /* Now re-check that row indices are *strictly* increasing
89                 * (and not just increasing) within each column : */
90                for (j = 0; j < ncol; j++) {
91                    for (k = xp[j] + 1; k < xp[j + 1]; k++)
92                        if (xi[k] == xi[k - 1])
93                            return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_l_sort)"));
94      }      }
95      for (j = 0; j < length(islot); j++) {          } else { /* no modifying sorting : */
96          if (xi[j] < 0 || xi[j] >= nrow)              return mkString(_("row indices are not sorted within columns"));
97              return mkString(_("all row indices must be between 0 and nrow-1"));          }
98        } else if(!strictly) {  /* sorted, but not strictly */
99            return mkString(_("slot i is not *strictly* increasing inside a column"));
100      }      }
101      return ScalarLogical(1);      return ScalarLogical(1);
102  }  }
103
104  SEXP Csparse_to_dense(SEXP x)  SEXP Rsparse_validate(SEXP x)
105  {  {
106      cholmod_sparse *chxs = as_cholmod_sparse(x);      /* NB: we do *NOT* check a potential 'x' slot here, at all */
107      cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);      SEXP pslot = GET_SLOT(x, Matrix_pSym),
108            jslot = GET_SLOT(x, Matrix_jSym);
109        Rboolean sorted, strictly;
110        int i, k,
111            *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
112            nrow = dims[0],
113            ncol = dims[1],
114            *xp = INTEGER(pslot),
115            *xj = INTEGER(jslot);
116
117        if (length(pslot) != dims[0] + 1)
118            return mkString(_("slot p must have length = nrow(.) + 1"));
119        if (xp[0] != 0)
120            return mkString(_("first element of slot p must be zero"));
121        if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
122            return
123                mkString(_("last element of slot p must match length of slots j and x"));
124        for (i = 0; i < length(jslot); i++) {
125            if (xj[i] < 0 || xj[i] >= ncol)
126                return mkString(_("all column indices must be between 0 and ncol-1"));
127        }
128        sorted = TRUE; strictly = TRUE;
129        for (i = 0; i < nrow; i++) {
130            if (xp[i] > xp[i+1])
131                return mkString(_("slot p must be non-decreasing"));
132            if(sorted)
133                for (k = xp[i] + 1; k < xp[i + 1]; k++) {
134                    if (xj[k] < xj[k - 1])
135                        sorted = FALSE;
136                    else if (xj[k] == xj[k - 1])
137                        strictly = FALSE;
138                }
139        }
140        if (!sorted)
141            /* cannot easily use cholmod_sort(.) ... -> "error out" :*/
142            return mkString(_("slot j is not increasing inside a column"));
143        else if(!strictly) /* sorted, but not strictly */
144            return mkString(_("slot j is not *strictly* increasing inside a column"));
145
146      Free(chxs);      return ScalarLogical(1);
return chm_dense_to_SEXP(chxd, 1);
147  }  }
148
149  SEXP Csparse_to_logical(SEXP x, SEXP tri)
150    /* Called from ../R/Csparse.R : */
151    /* Can only return [dln]geMatrix (no symm/triang);
152     * FIXME: replace by non-CHOLMOD code ! */
153    SEXP Csparse_to_dense(SEXP x)
154  {  {
155      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
156      cholmod_sparse      /* This loses the symmetry property, since cholmod_dense has none,
157          *chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
158      int uploT = 0; char *diag = "";       * to numeric (CHOLMOD_REAL) ones : */
159        CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
160        int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
161        R_CheckStack();
162
163        return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
164    }
165
166    // FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
167    SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
168    {
169        CHM_SP chxs = AS_CHM_SP__(x);
170        CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
171        int tr = asLogical(tri);
172        R_CheckStack();
173
174        return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
175                                  tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
176                                  0, tr ? diag_P(x) : "",
177                                  GET_SLOT(x, Matrix_DimNamesSym));
178    }
179
180      Free(chxs);  // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
181      if (asLogical(tri)) {       /* triangular sparse matrices */  SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
182          uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?  {
183              -1 : 1;      return nz2Csparse(x, asInteger(res_kind));
diag = CHAR(asChar(GET_SLOT(x, Matrix_diagSym)));
184      }      }
185      return chm_sparse_to_SEXP(chxcp, 1, uploT, diag,  // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
186                                  GET_SLOT(x, Matrix_DimNamesSym));  SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
187    {
188        const char *cl_x = class_P(x);
189        if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));
190        if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
191        int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
192        SEXP ans;
193        char *ncl = strdup(cl_x);
194        double *dx_x; int *ix_x;
195        ncl[0] = (r_kind == x_double ? 'd' :
196                  (r_kind == x_logical ? 'l' :
197                   /* else (for now):  r_kind == x_integer : */ 'i'));
198        PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
199        // create a correct 'x' slot:
200        switch(r_kind) {
201            int i;
202        case x_double: // 'd'
203            dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
204            for (i=0; i < nnz; i++) dx_x[i] = 1.;
205            break;
206        case x_logical: // 'l'
207            ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
208            for (i=0; i < nnz; i++) ix_x[i] = TRUE;
209            break;
210        case x_integer: // 'i'
211            ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
212            for (i=0; i < nnz; i++) ix_x[i] = 1;
213            break;
214
215        default:
216            error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
217                  r_kind);
218        }
219
220        // now copy all other slots :
221        slot_dup(ans, x, Matrix_iSym);
222        slot_dup(ans, x, Matrix_pSym);
223        slot_dup(ans, x, Matrix_DimSym);
224        slot_dup(ans, x, Matrix_DimNamesSym);
225        if(ncl[1] != 'g') { // symmetric or triangular ...
226            slot_dup_if_has(ans, x, Matrix_uploSym);
227            slot_dup_if_has(ans, x, Matrix_diagSym);
228        }
229        UNPROTECT(1);
230        return ans;
231  }  }
232
233  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
234  {  {
235      cholmod_sparse *chxs = as_cholmod_sparse(x);      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),
236      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));
237  }  }
238
239  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
240  {  {
241      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
242      cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
243      int uploT = 0; char *diag = "";      int tr = asLogical(tri);
244        int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
245      Free(chxs);      R_CheckStack();
246      if (asLogical(tri)) {       /* triangular sparse matrices */
247          uploT = (*uplo_P(x) == 'U') ? -1 : 1;      return chm_triplet_to_SEXP(chxt, 1,
248          diag = diag_P(x);                                 tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
249      }                                 Rkind, tr ? diag_P(x) : "",
return chm_triplet_to_SEXP(chxt, 1, uploT, diag,
250                                 GET_SLOT(x, Matrix_DimNamesSym));                                 GET_SLOT(x, Matrix_DimNamesSym));
251  }  }
252
253  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
254  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
255  {  {
256      cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
257        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
258        R_CheckStack();
259
260      if (!(chx->stype))      if (!(chx->stype))
261          error(_("Nonsymmetric matrix in Csparse_symmeteric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
262      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
263      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
264      Free(chx);      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
265      return chm_sparse_to_SEXP(chgx, 1, 0, "",                                GET_SLOT(x, Matrix_DimNamesSym));
266    }
267
268    SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
269    {
270        CHM_SP chx = AS_CHM_SP__(x), chgx;
271        int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
272        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
273        R_CheckStack();
274
275        chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
276        /* xtype: pattern, "real", complex or .. */
277        return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
278                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
279  }  }
280
281  SEXP Csparse_transpose(SEXP x, SEXP tri)  SEXP Csparse_transpose(SEXP x, SEXP tri)
282  {  {
283      cholmod_sparse *chx = as_cholmod_sparse(x);      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
284      cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);       *       since cholmod (& cs) lacks sparse 'int' matrices */
285        CHM_SP chx = AS_CHM_SP__(x);
286        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
287        CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
288      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
289      int uploT = 0; char *diag = "";      int tr = asLogical(tri);
290        R_CheckStack();
291
Free(chx);
292      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
293      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
294      SET_VECTOR_ELT(dn, 1, tmp);      SET_VECTOR_ELT(dn, 1, tmp);
295      UNPROTECT(1);      UNPROTECT(1);
296      if (asLogical(tri)) {       /* triangular sparse matrices */      return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
297          uploT = (*uplo_P(x) == 'U') ? -1 : 1;                                tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
298          diag = diag_P(x);                                Rkind, tr ? diag_P(x) : "", dn);
}
return chm_sparse_to_SEXP(chxt, 1, uploT, diag, dn);
299  }  }
300
301  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
302  {  {
303      cholmod_sparse *cha = as_cholmod_sparse(a),      CHM_SP
304          *chb = as_cholmod_sparse(b);          cha = AS_CHM_SP(a),
305      cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);          chb = AS_CHM_SP(b),
306      SEXP dn = allocVector(VECSXP, 2);          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
307                                   /* values:= is_numeric (T/F) */ cha->xtype > 0,
308                                   /*out sorted:*/ 1, &c);
309        const char *cl_a = class_P(a), *cl_b = class_P(b);
310        char diag[] = {'\0', '\0'};
311        int uploT = 0;
312        SEXP dn = PROTECT(allocVector(VECSXP, 2));
313        R_CheckStack();
314
315      Free(cha); Free(chb);  #ifdef DEBUG_Matrix_verbose
316        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
317    #endif
318
319        /* Preserve triangularity and even unit-triangularity if appropriate.
320         * Note that in that case, the multiplication itself should happen
321         * faster.  But there's no support for that in CHOLMOD */
322
323        /* UGLY hack -- rather should have (fast!) C-level version of
324         *       is(a, "triangularMatrix") etc */
325        if (cl_a[1] == 't' && cl_b[1] == 't')
326            /* FIXME: fails for "Cholesky","BunchKaufmann"..*/
327            if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
328                uploT = (*uplo_P(a) == 'U') ? 1 : -1;
329                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
330                    /* "remove the diagonal entries": */
331                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
332                    diag[0]= 'U';
333                }
334                else diag[0]= 'N';
335            }
336      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
337                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
338      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
339                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
340      return chm_sparse_to_SEXP(chc, 1, 0, "", dn);      UNPROTECT(1);
341        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
342    }
343
344    SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
345    {
346        int tr = asLogical(trans);
347        CHM_SP
348            cha = AS_CHM_SP(a),
349            chb = AS_CHM_SP(b),
350            chTr, chc;
351        const char *cl_a = class_P(a), *cl_b = class_P(b);
352        char diag[] = {'\0', '\0'};
353        int uploT = 0;
354        SEXP dn = PROTECT(allocVector(VECSXP, 2));
355        R_CheckStack();
356
357        chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
358        chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
359                             /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
360        cholmod_free_sparse(&chTr, &c);
361
362        /* Preserve triangularity and unit-triangularity if appropriate;
363         * see Csparse_Csparse_prod() for comments */
364        if (cl_a[1] == 't' && cl_b[1] == 't')
365            if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
366                uploT = (*uplo_P(b) == 'U') ? 1 : -1;
367                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
368                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
369                    diag[0]= 'U';
370                }
371                else diag[0]= 'N';
372            }
373        SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
374                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
375        SET_VECTOR_ELT(dn, 1,
376                       duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
377        UNPROTECT(1);
378        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
379  }  }
380
381  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
382  {  {
383      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
384      cholmod_dense *chb = as_cholmod_dense(b);      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
385      cholmod_dense *chc =      CHM_DN chb = AS_CHM_DN(b_M);
386          cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
387      double alpha[] = {1,0}, beta[] = {0,0};                                          chb->xtype, &c);
388        SEXP dn = PROTECT(allocVector(VECSXP, 2));
389      cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);      double one[] = {1,0}, zero[] = {0,0};
390      Free(cha); Free(chb);      int nprot = 2;
391      return chm_dense_to_SEXP(chc, 1);      R_CheckStack();
392        /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
393        if(cha->xtype == CHOLMOD_PATTERN) {
394            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
395            /*        " --> slightly inefficient coercion")); */
396
397            // This *fails* to produce a CHOLMOD_REAL ..
398            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
399            // --> use our Matrix-classes
400            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
401            cha = AS_CHM_SP(da);
402        }
403        cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
404        SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
405                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
406        SET_VECTOR_ELT(dn, 1,
407                       duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
408        UNPROTECT(nprot);
409        return chm_dense_to_SEXP(chc, 1, 0, dn);
410  }  }
411
412  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
413  {  {
414      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
415      cholmod_dense *chb = as_cholmod_dense(b);      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
416      cholmod_dense *chc =      CHM_DN chb = AS_CHM_DN(b_M);
417          cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
418      double alpha[] = {1,0}, beta[] = {0,0};                                          chb->xtype, &c);
419        SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
420      cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);      double one[] = {1,0}, zero[] = {0,0};
421      Free(cha); Free(chb);      R_CheckStack();
422      return chm_dense_to_SEXP(chc, 1);      // -- see Csparse_dense_prod() above :
423        if(cha->xtype == CHOLMOD_PATTERN) {
424            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
425            cha = AS_CHM_SP(da);
426        }
427        cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
428        SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
429                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
430        SET_VECTOR_ELT(dn, 1,
431                       duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
432        UNPROTECT(nprot);
433        return chm_dense_to_SEXP(chc, 1, 0, dn);
434  }  }
435
436    /* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
437       see Csparse_Csparse_crossprod above for  x'y and x y' */
438  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
439  {  {
440      int trip = asLogical(triplet),      int trip = asLogical(triplet),
441          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
442      cholmod_triplet  #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
443          *cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
444      cholmod_sparse *chcp, *chxt,  #else /* workaround needed:*/
445          *chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)      SEXP xx = PROTECT(Tsparse_diagU2N(x));
446          : as_cholmod_sparse(x);      CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
447    #endif
448        CHM_SP chcp, chxt,
449            chx = (trip ?
450                   cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
451                   AS_CHM_SP(x));
452      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
453        R_CheckStack();
454
455      if (!tr)      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
chxt = cholmod_transpose(chx, chx->xtype, &c);
456      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
457      if(!chcp)      if(!chcp) {
458          error("Csparse_crossprod(): error return from cholmod_aat()");          UNPROTECT(1);
459            error(_("Csparse_crossprod(): error return from cholmod_aat()"));
460        }
461      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
462      chcp->stype = 1;      chcp->stype = 1;
463      if (trip) {      if (trip) cholmod_free_sparse(&chx, &c);
cholmod_free_sparse(&chx, &c);
Free(cht);
} else {
Free(chx);
}
464      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
465                                  /* create dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
SET_VECTOR_ELT(dn, 0,
466                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
467                                          (tr) ? 1 : 0)));                                          (tr) ? 0 : 1)));
468      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
469    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
470      UNPROTECT(1);      UNPROTECT(1);
471      return chm_sparse_to_SEXP(chcp, 1, 0, "", dn);  #else
472        UNPROTECT(2);
473    #endif
474        return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
475    }
476
477    /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
478    *  at least all "explicit" zeros */
479    SEXP Csparse_drop(SEXP x, SEXP tol)
480    {
481        const char *cl = class_P(x);
482        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
483        int tr = (cl[1] == 't');
484        CHM_SP chx = AS_CHM_SP__(x);
485        CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
486        double dtol = asReal(tol);
487        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
488        R_CheckStack();
489
490        if(!cholmod_drop(dtol, ans, &c))
491            error(_("cholmod_drop() failed"));
492        return chm_sparse_to_SEXP(ans, 1,
493                                  tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
494                                  Rkind, tr ? diag_P(x) : "",
495                                  GET_SLOT(x, Matrix_DimNamesSym));
496  }  }
497
498  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
499  {  {
500      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
501          *chy = as_cholmod_sparse(y), *ans;      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
502            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
503      ans = cholmod_horzcat(chx, chy, 1, &c);          Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
504      Free(chx); Free(chy);      R_CheckStack();
505      /* FIXME: currently drops dimnames */
506      return chm_sparse_to_SEXP(ans, 1, 0, "", R_NilValue);      /* TODO: currently drops dimnames - and we fix at R level */
507        return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
508                                  1, 0, Rkind, "", R_NilValue);
509  }  }
510
511  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
512  {  {
513      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
514          *chy = as_cholmod_sparse(y), *ans;      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
515            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
516      ans = cholmod_vertcat(chx, chy, 1, &c);          Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
517      Free(chx); Free(chy);      R_CheckStack();
518      /* FIXME: currently drops dimnames */
519      return chm_sparse_to_SEXP(ans, 1, 0, "", R_NilValue);      /* TODO: currently drops dimnames - and we fix at R level */
520        return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
521                                  1, 0, Rkind, "", R_NilValue);
522  }  }
523
524  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
525  {  {
526      cholmod_sparse *chx = as_cholmod_sparse(x), *ans;      CHM_SP chx = AS_CHM_SP__(x);
527        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
528        CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
529        R_CheckStack();
530
531      ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
532      Free(chx);                                GET_SLOT(x, Matrix_DimNamesSym));
return chm_sparse_to_SEXP(ans, 1, 0, "", R_NilValue);
533  }  }
534
535  SEXP Csparse_diagU2N(SEXP x)  SEXP Csparse_diagU2N(SEXP x)
536  {  {
537      cholmod_sparse *chx = as_cholmod_sparse(x);      const char *cl = class_P(x);
538      cholmod_sparse *eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
539        if (cl[1] != 't' || *diag_P(x) != 'U') {
540            /* "trivially fast" when not triangular (<==> no 'diag' slot),
541               or not *unit* triangular */
542            return (x);
543        }
544        else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
545            CHM_SP chx = AS_CHM_SP__(x);
546            CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
547      double one[] = {1, 0};      double one[] = {1, 0};
548      cholmod_sparse *ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
549      int uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
550          -1 : 1;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
551
552      Free(chx); cholmod_free_sparse(&eye, &c);          R_CheckStack();
553      return chm_sparse_to_SEXP(ans, 1, uploT, "N",          cholmod_free_sparse(&eye, &c);
554                                duplicate(GET_SLOT(x, Matrix_DimNamesSym)));          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
555                                      GET_SLOT(x, Matrix_DimNamesSym));
556        }
557    }
558
559    SEXP Csparse_diagN2U(SEXP x)
560    {
561        const char *cl = class_P(x);
562        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
563        if (cl[1] != 't' || *diag_P(x) != 'N') {
564            /* "trivially fast" when not triangular (<==> no 'diag' slot),
565               or already *unit* triangular */
566            return (x);
567        }
568        else { /* triangular with diag='N'): now drop the diagonal */
569            /* duplicate, since chx will be modified: */
570            CHM_SP chx = AS_CHM_SP__(duplicate(x));
571            int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
572                Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
573            R_CheckStack();
574
575            chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
576
577            return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
578                                      uploT, Rkind, "U",
579                                      GET_SLOT(x, Matrix_DimNamesSym));
580        }
581  }  }
582
583    /**
584     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
585     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
586     * @param x CsparseMatrix
587     * @param i row     indices (0-origin), or NULL (R's)
588     * @param j columns indices (0-origin), or NULL
589     *
590     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
591     */
592  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
593  {  {
594      cholmod_sparse *chx = as_cholmod_sparse(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
595      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
596          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
597        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
598        R_CheckStack();
599
600      if (rsize >= 0 && !isInteger(i))      if (rsize >= 0 && !isInteger(i))
601          error(_("Index i must be NULL or integer"));          error(_("Index i must be NULL or integer"));
602      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
603          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
604      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,
605                                                  INTEGER(j), csize,      if (chx->stype) /* symmetricMatrix */
606            /* for now, cholmod_submatrix() only accepts "generalMatrix" */
607            chx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
608
609        return chm_sparse_to_SEXP(cholmod_submatrix(chx,
610                                    (rsize < 0) ? NULL : INTEGER(i), rsize,
611                                    (csize < 0) ? NULL : INTEGER(j), csize,
612                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
613                                1, 0, "", R_NilValue);                                1, 0, Rkind, "",
614                                  /* FIXME: drops dimnames */ R_NilValue);
615    }
616
617    #define _d_Csp_
618    #include "t_Csparse_subassign.c"
619
620    #define _l_Csp_
621    #include "t_Csparse_subassign.c"
622
623    #define _i_Csp_
624    #include "t_Csparse_subassign.c"
625
626    #define _n_Csp_
627    #include "t_Csparse_subassign.c"
628
629    #define _z_Csp_
630    #include "t_Csparse_subassign.c"
631
632
633
634    SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
635    {
636        FILE *f = fopen(CHAR(asChar(fname)), "w");
637
638        if (!f)
639            error(_("failure to open file \"%s\" for writing"),
640                  CHAR(asChar(fname)));
641        if (!cholmod_write_sparse(f, AS_CHM_SP(x),
642                                  (CHM_SP)NULL, (char*) NULL, &c))
643            error(_("cholmod_write_sparse returned error code"));
644        fclose(f);
645        return R_NilValue;
646    }
647
648
649    /**
650     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
651     * cholmod_sparse factor (LDL = TRUE).
652     *
653     * @param n  dimension of the matrix.
654     * @param x_p  'p' (column pointer) slot contents
655     * @param x_x  'x' (non-zero entries) slot contents
656     * @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
657     * @param resultKind a (SEXP) string indicating which kind of result is desired.
658     *
659     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
660     */
661    SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)
662    /*                                ^^^^^^ FIXME[Generalize] to int / ... */
663    {
664        const char* res_ch = CHAR(STRING_ELT(resultKind,0));
665        enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log
666        } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
667                      ((!strcmp(res_ch, "sumLog")) ? sum_log :
668                       ((!strcmp(res_ch, "prod")) ? prod :
669                        ((!strcmp(res_ch, "diag")) ? diag :
670                         ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
671                          -1)))));
672        int i, n_x, i_from = 0;
673        SEXP ans = PROTECT(allocVector(REALSXP,
674    /*                                 ^^^^  FIXME[Generalize] */
675                                       (res_kind == diag ||
676                                        res_kind == diag_backpermuted) ? n : 1));
677        double *v = REAL(ans);
678    /*  ^^^^^^      ^^^^  FIXME[Generalize] */
679
680    #define for_DIAG(v_ASSIGN)                                              \
681        for(i = 0; i < n; i++, i_from += n_x) {                             \
682            /* looking at i-th column */                                    \
683            n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
684            v_ASSIGN;                                                       \
685        }
686
687        /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
688         *            for uplo = "U" (makes sense with a "dtCMatrix" !),
689         *            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],
690         *            where nx = (x_p[i+1] - x_p[i])
691         */
692
693        switch(res_kind) {
694        case trace:
695            v[0] = 0.;
696            for_DIAG(v[0] += x_x[i_from]);
697            break;
698
699        case sum_log:
700            v[0] = 0.;
701            for_DIAG(v[0] += log(x_x[i_from]));
702            break;
703
704        case prod:
705            v[0] = 1.;
706            for_DIAG(v[0] *= x_x[i_from]);
707            break;
708
709        case diag:
710            for_DIAG(v[i] = x_x[i_from]);
711            break;
712
713        case diag_backpermuted:
714            for_DIAG(v[i] = x_x[i_from]);
715
716            warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));
717            /* now back_permute : */
718            for(i = 0; i < n; i++) {
719                double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
720                /*^^^^ FIXME[Generalize] */
721            }
722            break;
723
724        default: /* -1 from above */
725            error(_("diag_tC(): invalid 'resultKind'"));
726            /* Wall: */ ans = R_NilValue; v = REAL(ans);
727        }
728
729        UNPROTECT(1);
730        return ans;
731    }
732
733    /**
734     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
735     * cholmod_sparse factor (LDL = TRUE).
736     *
737     * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
738     * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
739     * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
740     *                   only used for "diagBack"
741     * @param resultKind a (SEXP) string indicating which kind of result is desired.
742     *
743     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
744     */
745    SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)
746    {
747        int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
748            *x_p  = INTEGER(pslot),
749            *perm = INTEGER(perm_slot);
750        double *x_x = REAL(xslot);
751    /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
752
753        return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
754    }
755
756    /**
757     * Create a Csparse matrix object from indices and/or pointers.
758     *
759     * @param cls name of actual class of object to create
760     * @param i optional integer vector of length nnz of row indices
761     * @param j optional integer vector of length nnz of column indices
762     * @param p optional integer vector of length np of row or column pointers
763     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
764     * @param x optional vector of values
765     * @param nnz length of vectors i, j and/or x, whichever is to be used
766     * @param dims optional integer vector of length 2 to be used as
767     *     dimensions.  If dims == (int*)NULL then the maximum row and column
768     *     index are used as the dimensions.
769     * @param dimnames optional list of length 2 to be used as dimnames
770     * @param index1 indicator of 1-based indices
771     *
772     * @return an SEXP of class cls inheriting from CsparseMatrix.
773     */
774    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
775                        void* x, int nnz, int* dims, SEXP dimnames,
776                        int index1)
777    {
778        SEXP ans;
779        int *ij = (int*)NULL, *tri, *trj,
780            mi, mj, mp, nrow = -1, ncol = -1;
781        int xtype = -1;             /* -Wall */
782        CHM_TR T;
783        CHM_SP A;
784
785        if (np < 0 || nnz < 0)
786            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
787                  np, nnz);
788        if (1 != ((mi = (i == (int*)NULL)) +
789                  (mj = (j == (int*)NULL)) +
790                  (mp = (p == (int*)NULL))))
791            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
792        if (mp) {
793            if (np) error(_("np = %d, must be zero when p is NULL"), np);
794        } else {
795            if (np) {               /* Expand p to form i or j */
796                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
797                for (int ii = 0; ii < np; ii++)
798                    if (p[ii] > p[ii + 1])
799                        error(_("p must be non-decreasing"));
800                if (p[np] != nnz)
801                    error("p[np] = %d != nnz = %d", p[np], nnz);
802                ij = Calloc(nnz, int);
803                if (mi) {
804                    i = ij;
805                    nrow = np;
806                } else {
807                    j = ij;
808                    ncol = np;
809                }
810                /* Expand p to 0-based indices */
811                for (int ii = 0; ii < np; ii++)
812                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
813            } else {
814                if (nnz)
815                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
816                          nnz);
817            }
818        }
819        /* calculate nrow and ncol */
820        if (nrow < 0) {
821            for (int ii = 0; ii < nnz; ii++) {
822                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
823                if (i1 < 1) error(_("invalid row index at position %d"), ii);
824                if (i1 > nrow) nrow = i1;
825            }
826        }
827        if (ncol < 0) {
828            for (int jj = 0; jj < nnz; jj++) {
829                int j1 = j[jj] + (index1 ? 0 : 1);
830                if (j1 < 1) error(_("invalid column index at position %d"), jj);
831                if (j1 > ncol) ncol = j1;
832            }
833        }
834        if (dims != (int*)NULL) {
835            if (dims[0] > nrow) nrow = dims[0];
836            if (dims[1] > ncol) ncol = dims[1];
837        }
838        /* check the class name */
839        if (strlen(cls) != 8)
840            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
841        if (!strcmp(cls + 2, "CMatrix"))
842            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
843        switch(cls[0]) {
844        case 'd':
845        case 'l':
846            xtype = CHOLMOD_REAL;
847        break;
848        case 'n':
849            xtype = CHOLMOD_PATTERN;
850            break;
851        default:
852            error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
853        }
854        if (cls[1] != 'g')
855            error(_("Only 'g'eneral sparse matrix types allowed"));
856        /* allocate and populate the triplet */
857        T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
858                                     xtype, &c);
859        T->x = x;
860        tri = (int*)T->i;
861        trj = (int*)T->j;
862        for (int ii = 0; ii < nnz; ii++) {
863            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
864            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
865        }
866        /* create the cholmod_sparse structure */
867        A = cholmod_triplet_to_sparse(T, nnz, &c);
868        cholmod_free_triplet(&T, &c);
869        /* copy the information to the SEXP */
870        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
871    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
872        /* allocate and copy common slots */
873        nnz = cholmod_nnz(A, &c);
874        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
875        dims[0] = A->nrow; dims[1] = A->ncol;
876        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
877        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
878        switch(cls[1]) {
879        case 'd':
880            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
881            break;
882        case 'l':
883            error(_("code not yet written for cls = \"lgCMatrix\""));
884        }
885    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
886        cholmod_free_sparse(&A, &c);
887        UNPROTECT(1);
888        return ans;
889  }  }

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