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

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pkg/src/Csparse.c revision 2279, Fri Oct 3 09:15:54 2008 UTC pkg/Matrix/src/Csparse.c revision 2628, Sat Dec 11 16:56:51 2010 UTC
# Line 32  Line 32 
32      return TRUE;      return TRUE;
33  }  }
34    
35  SEXP Csparse_validate(SEXP x)  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 */      /* NB: we do *NOT* check a potential 'x' slot here, at all */
46      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
# Line 69  Line 77 
77              }              }
78      }      }
79      if (!sorted) {      if (!sorted) {
80            if(maybe_modify) {
81          CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));          CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
82          R_CheckStack();          R_CheckStack();
83          as_cholmod_sparse(chx, x, FALSE, TRUE); /* includes cholmod_sort() ! */              as_cholmod_sparse(chx, x, FALSE, TRUE);/*-> cholmod_l_sort() ! */
84          /* as chx = AS_CHM_SP__(x)  but  ^^^^  sorting x in_place (no copying)*/              /* as chx = AS_CHM_SP__(x)  but  ^^^^ sorting x in_place !!! */
85    
86          /* Now re-check that row indices are *strictly* increasing          /* Now re-check that row indices are *strictly* increasing
87           * (and not just increasing) within each column : */           * (and not just increasing) within each column : */
88          for (j = 0; j < ncol; j++) {          for (j = 0; j < ncol; j++) {
89              for (k = xp[j] + 1; k < xp[j + 1]; k++)              for (k = xp[j] + 1; k < xp[j + 1]; k++)
90                  if (xi[k] == xi[k - 1])                  if (xi[k] == xi[k - 1])
91                      return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_sort)"));                          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 */      } else if(!strictly) {  /* sorted, but not strictly */
97          return mkString(_("slot i is not *strictly* increasing inside a column"));          return mkString(_("slot i is not *strictly* increasing inside a column"));
98      }      }
# Line 125  Line 136 
136              }              }
137      }      }
138      if (!sorted)      if (!sorted)
139          /* cannot easily use cholmod_sort(.) ... -> "error out" :*/          /* cannot easily use cholmod_l_sort(.) ... -> "error out" :*/
140          return mkString(_("slot j is not increasing inside a column"));          return mkString(_("slot j is not increasing inside a column"));
141      else if(!strictly) /* sorted, but not strictly */      else if(!strictly) /* sorted, but not strictly */
142          return mkString(_("slot j is not *strictly* increasing inside a column"));          return mkString(_("slot j is not *strictly* increasing inside a column"));
# Line 143  Line 154 
154      /* This loses the symmetry property, since cholmod_dense has none,      /* This loses the symmetry property, since cholmod_dense has none,
155       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
156       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones : */
157      CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);      CHM_DN chxd = cholmod_l_sparse_to_dense(chxs, &c);
158      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
159      R_CheckStack();      R_CheckStack();
160    
161      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
162  }  }
163    
164    // FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
165  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
166  {  {
167      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
168      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_l_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
169      int tr = asLogical(tri);      int tr = asLogical(tri);
170      R_CheckStack();      R_CheckStack();
171    
# Line 163  Line 175 
175                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
176  }  }
177    
178    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
179    SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
180    {
181        return nz2Csparse(x, asInteger(res_kind));
182    }
183    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
184    SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
185    {
186        const char *cl_x = class_P(x);
187        if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));
188        if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
189        int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
190        SEXP ans;
191        char *ncl = strdup(cl_x);
192        double *dx_x; int *ix_x;
193        ncl[0] = (r_kind == x_double ? 'd' :
194                  (r_kind == x_logical ? 'l' :
195                   /* else (for now):  r_kind == x_integer : */ 'i'));
196        PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
197        // create a correct 'x' slot:
198        switch(r_kind) {
199            int i;
200        case x_double: // 'd'
201            dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
202            for (i=0; i < nnz; i++) dx_x[i] = 1.;
203            break;
204        case x_logical: // 'l'
205            ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
206            for (i=0; i < nnz; i++) ix_x[i] = TRUE;
207            break;
208        case x_integer: // 'i'
209            ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
210            for (i=0; i < nnz; i++) ix_x[i] = 1;
211            break;
212    
213        default:
214            error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
215                  r_kind);
216        }
217    
218        // now copy all other slots :
219        slot_dup(ans, x, Matrix_iSym);
220        slot_dup(ans, x, Matrix_pSym);
221        slot_dup(ans, x, Matrix_DimSym);
222        slot_dup(ans, x, Matrix_DimNamesSym);
223        if(ncl[1] != 'g') { // symmetric or triangular ...
224            slot_dup_if_has(ans, x, Matrix_uploSym);
225            slot_dup_if_has(ans, x, Matrix_diagSym);
226        }
227        UNPROTECT(1);
228        return ans;
229    }
230    
231  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
232  {  {
233      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),      return chm_dense_to_matrix(cholmod_l_sparse_to_dense(AS_CHM_SP__(x), &c),
234                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
235  }  }
236    
237  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
238  {  {
239      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
240      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_l_sparse_to_triplet(chxs, &c);
241      int tr = asLogical(tri);      int tr = asLogical(tri);
242      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
243      R_CheckStack();      R_CheckStack();
# Line 192  Line 257 
257    
258      if (!(chx->stype))      if (!(chx->stype))
259          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
260      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);
261      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
262      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
263                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 205  Line 270 
270      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
271      R_CheckStack();      R_CheckStack();
272    
273      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ uploT, chx->xtype, &c);
274      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
275      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
276                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 217  Line 282 
282       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
283      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
284      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
285      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_l_transpose(chx, chx->xtype, &c);
286      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
287      int tr = asLogical(tri);      int tr = asLogical(tri);
288      R_CheckStack();      R_CheckStack();
# Line 236  Line 301 
301      CHM_SP      CHM_SP
302          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
303          chb = AS_CHM_SP(b),          chb = AS_CHM_SP(b),
304          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_l_ssmult(cha, chb, /*out_stype:*/ 0,
305                               cha->xtype, /*out sorted:*/ 1, &c);                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
306                                   /*out sorted:*/ 1, &c);
307      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
308      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
309      int uploT = 0;      int uploT = 0;
310      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
311      R_CheckStack();      R_CheckStack();
312    
313    #ifdef DEBUG_Matrix_verbose
314        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
315    #endif
316    
317      /* Preserve triangularity and even unit-triangularity if appropriate.      /* Preserve triangularity and even unit-triangularity if appropriate.
318       * Note that in that case, the multiplication itself should happen       * Note that in that case, the multiplication itself should happen
319       * faster.  But there's no support for that in CHOLMOD */       * faster.  But there's no support for that in CHOLMOD */
# Line 265  Line 335 
335                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
336      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
337                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
338        UNPROTECT(1);
339      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
340  }  }
341    
# Line 278  Line 349 
349      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
350      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
351      int uploT = 0;      int uploT = 0;
352      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
353      R_CheckStack();      R_CheckStack();
354    
355      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_l_transpose((tr) ? chb : cha, chb->xtype, &c);
356      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_l_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
357                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
358      cholmod_free_sparse(&chTr, &c);      cholmod_l_free_sparse(&chTr, &c);
359    
360      /* Preserve triangularity and unit-triangularity if appropriate;      /* Preserve triangularity and unit-triangularity if appropriate;
361       * see Csparse_Csparse_prod() for comments */       * see Csparse_Csparse_prod() for comments */
# Line 297  Line 368 
368              }              }
369              else diag[0]= 'N';              else diag[0]= 'N';
370          }          }
   
371      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
372                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
373      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
374                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
375        UNPROTECT(1);
376      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
377  }  }
378    
# Line 310  Line 381 
381      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
382      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
383      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
384      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,      CHM_DN chc = cholmod_l_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
385                                          chb->xtype, &c);                                          chb->xtype, &c);
386      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
387      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
388        int nprot = 2;
389      R_CheckStack();      R_CheckStack();
390        /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
391      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);      if(cha->xtype == CHOLMOD_PATTERN) {
392            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
393            /*        " --> slightly inefficient coercion")); */
394    
395            // This *fails* to produce a CHOLMOD_REAL ..
396            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
397            // --> use our Matrix-classes
398            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
399            cha = AS_CHM_SP(da);
400        }
401        cholmod_l_sdmult(cha, 0, one, zero, chb, chc, &c);
402      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
403                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
404      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
405                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
406      UNPROTECT(2);      UNPROTECT(nprot);
407      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
408  }  }
409    
# Line 330  Line 412 
412      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
413      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
414      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
415      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_l_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
416                                          chb->xtype, &c);                                          chb->xtype, &c);
417      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
418      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
419      R_CheckStack();      R_CheckStack();
420    
421      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);      cholmod_l_sdmult(cha, 1, one, zero, chb, chc, &c);
422      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
423                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
424      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
# Line 351  Line 433 
433  {  {
434      int trip = asLogical(triplet),      int trip = asLogical(triplet),
435          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
436    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
437      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
438    #else /* workaround needed:*/
439        SEXP xx = PROTECT(Tsparse_diagU2N(x));
440        CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
441    #endif
442      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
443          chx = (trip ?          chx = (trip ?
444                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_l_triplet_to_sparse(cht, cht->nnz, &c) :
445                 AS_CHM_SP(x));                 AS_CHM_SP(x));
446      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
447      R_CheckStack();      R_CheckStack();
448    
449      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_l_transpose(chx, chx->xtype, &c);
450      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_l_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
451      if(!chcp) {      if(!chcp) {
452          UNPROTECT(1);          UNPROTECT(1);
453          error(_("Csparse_crossprod(): error return from cholmod_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_l_aat()"));
454      }      }
455      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_l_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
456      chcp->stype = 1;      chcp->stype = 1;
457      if (trip) cholmod_free_sparse(&chx, &c);      if (trip) cholmod_l_free_sparse(&chx, &c);
458      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_l_free_sparse(&chxt, &c);
459      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
460                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
461                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
462      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
463    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
464      UNPROTECT(1);      UNPROTECT(1);
465    #else
466        UNPROTECT(2);
467    #endif
468      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
469  }  }
470    
# Line 383  Line 474 
474      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
475      int tr = (cl[1] == 't');      int tr = (cl[1] == 't');
476      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
477      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_l_copy(chx, chx->stype, chx->xtype, &c);
478      double dtol = asReal(tol);      double dtol = asReal(tol);
479      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
480      R_CheckStack();      R_CheckStack();
481    
482      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_l_drop(dtol, ans, &c))
483          error(_("cholmod_drop() failed"));          error(_("cholmod_l_drop() failed"));
484      return chm_sparse_to_SEXP(ans, 1,      return chm_sparse_to_SEXP(ans, 1,
485                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
486                                Rkind, tr ? diag_P(x) : "",                                Rkind, tr ? diag_P(x) : "",
# Line 399  Line 490 
490  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
491  {  {
492      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
493      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
494            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
495            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
496      R_CheckStack();      R_CheckStack();
497    
498      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
499      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_horzcat(chx, chy, 1, &c),
500                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
501  }  }
502    
503  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
504  {  {
505      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
506      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
507            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
508            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
509      R_CheckStack();      R_CheckStack();
510    
511      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
512      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_vertcat(chx, chy, 1, &c),
513                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
514  }  }
515    
# Line 422  Line 517 
517  {  {
518      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
519      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
520      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      CHM_SP ans = cholmod_l_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
521      R_CheckStack();      R_CheckStack();
522    
523      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
# Line 440  Line 535 
535      }      }
536      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
537          CHM_SP chx = AS_CHM_SP__(x);          CHM_SP chx = AS_CHM_SP__(x);
538          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_l_speye(chx->nrow, chx->ncol, chx->xtype, &c);
539          double one[] = {1, 0};          double one[] = {1, 0};
540          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_l_add(chx, eye, one, one, TRUE, TRUE, &c);
541          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
542          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
543    
544          R_CheckStack();          R_CheckStack();
545          cholmod_free_sparse(&eye, &c);          cholmod_l_free_sparse(&eye, &c);
546          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
547                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
548      }      }
# Line 477  Line 572 
572      }      }
573  }  }
574    
575    /**
576     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
577     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
578     * @param x CsparseMatrix
579     * @param i row     indices (0-origin), or NULL (R's)
580     * @param j columns indices (0-origin), or NULL
581     *
582     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
583     */
584  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
585  {  {
586      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
587      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
588          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
589      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 490  Line 594 
594      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
595          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
596    
597      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      if (chx->stype) /* symmetricMatrix */
598                                                  INTEGER(j), csize,          /* for now, cholmod_submatrix() only accepts "generalMatrix" */
599            chx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);
600    
601        return chm_sparse_to_SEXP(cholmod_l_submatrix(chx,
602                                    (rsize < 0) ? NULL : INTEGER(i), rsize,
603                                    (csize < 0) ? NULL : INTEGER(j), csize,
604                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
605                                1, 0, Rkind, "",                                1, 0, Rkind, "",
606                                /* FIXME: drops dimnames */ R_NilValue);                                /* FIXME: drops dimnames */ R_NilValue);
# Line 504  Line 613 
613      if (!f)      if (!f)
614          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
615                CHAR(asChar(fname)));                CHAR(asChar(fname)));
616      if (!cholmod_write_sparse(f, AS_CHM_SP(x),      if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),
617                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
618          error(_("cholmod_write_sparse returned error code"));          error(_("cholmod_l_write_sparse returned error code"));
619      fclose(f);      fclose(f);
620      return R_NilValue;      return R_NilValue;
621  }  }
# Line 588  Line 697 
697          break;          break;
698    
699      default: /* -1 from above */      default: /* -1 from above */
700          error("diag_tC(): invalid 'resultKind'");          error(_("diag_tC(): invalid 'resultKind'"));
701          /* Wall: */ ans = R_NilValue; v = REAL(ans);          /* Wall: */ ans = R_NilValue; v = REAL(ans);
702      }      }
703    
# Line 618  Line 727 
727    
728      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
729  }  }
730    
731    /**
732     * Create a Csparse matrix object from indices and/or pointers.
733     *
734     * @param cls name of actual class of object to create
735     * @param i optional integer vector of length nnz of row indices
736     * @param j optional integer vector of length nnz of column indices
737     * @param p optional integer vector of length np of row or column pointers
738     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
739     * @param x optional vector of values
740     * @param nnz length of vectors i, j and/or x, whichever is to be used
741     * @param dims optional integer vector of length 2 to be used as
742     *     dimensions.  If dims == (int*)NULL then the maximum row and column
743     *     index are used as the dimensions.
744     * @param dimnames optional list of length 2 to be used as dimnames
745     * @param index1 indicator of 1-based indices
746     *
747     * @return an SEXP of class cls inheriting from CsparseMatrix.
748     */
749    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
750                        void* x, int nnz, int* dims, SEXP dimnames,
751                        int index1)
752    {
753        SEXP ans;
754        int *ij = (int*)NULL, *tri, *trj,
755            mi, mj, mp, nrow = -1, ncol = -1;
756        int xtype = -1;             /* -Wall */
757        CHM_TR T;
758        CHM_SP A;
759    
760        if (np < 0 || nnz < 0)
761            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
762                  np, nnz);
763        if (1 != ((mi = (i == (int*)NULL)) +
764                  (mj = (j == (int*)NULL)) +
765                  (mp = (p == (int*)NULL))))
766            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
767        if (mp) {
768            if (np) error(_("np = %d, must be zero when p is NULL"), np);
769        } else {
770            if (np) {               /* Expand p to form i or j */
771                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
772                for (int ii = 0; ii < np; ii++)
773                    if (p[ii] > p[ii + 1])
774                        error(_("p must be non-decreasing"));
775                if (p[np] != nnz)
776                    error("p[np] = %d != nnz = %d", p[np], nnz);
777                ij = Calloc(nnz, int);
778                if (mi) {
779                    i = ij;
780                    nrow = np;
781                } else {
782                    j = ij;
783                    ncol = np;
784                }
785                                    /* Expand p to 0-based indices */
786                for (int ii = 0; ii < np; ii++)
787                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
788            } else {
789                if (nnz)
790                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
791                          nnz);
792            }
793        }
794                                    /* calculate nrow and ncol */
795        if (nrow < 0) {
796            for (int ii = 0; ii < nnz; ii++) {
797                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
798                if (i1 < 1) error(_("invalid row index at position %d"), ii);
799                if (i1 > nrow) nrow = i1;
800            }
801        }
802        if (ncol < 0) {
803            for (int jj = 0; jj < nnz; jj++) {
804                int j1 = j[jj] + (index1 ? 0 : 1);
805                if (j1 < 1) error(_("invalid column index at position %d"), jj);
806                if (j1 > ncol) ncol = j1;
807            }
808        }
809        if (dims != (int*)NULL) {
810            if (dims[0] > nrow) nrow = dims[0];
811            if (dims[1] > ncol) ncol = dims[1];
812        }
813                                    /* check the class name */
814        if (strlen(cls) != 8)
815            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
816        if (!strcmp(cls + 2, "CMatrix"))
817            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
818        switch(cls[0]) {
819        case 'd':
820        case 'l':
821               xtype = CHOLMOD_REAL;
822               break;
823        case 'n':
824               xtype = CHOLMOD_PATTERN;
825               break;
826        default:
827               error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
828        }
829        if (cls[1] != 'g')
830            error(_("Only 'g'eneral sparse matrix types allowed"));
831                                    /* allocate and populate the triplet */
832        T = cholmod_l_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
833                                        xtype, &c);
834        T->x = x;
835        tri = (int*)T->i;
836        trj = (int*)T->j;
837        for (int ii = 0; ii < nnz; ii++) {
838            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
839            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
840        }
841                                    /* create the cholmod_sparse structure */
842        A = cholmod_l_triplet_to_sparse(T, nnz, &c);
843        cholmod_l_free_triplet(&T, &c);
844                                    /* copy the information to the SEXP */
845        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
846    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
847                                    /* allocate and copy common slots */
848        nnz = cholmod_l_nnz(A, &c);
849        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
850        dims[0] = A->nrow; dims[1] = A->ncol;
851        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
852        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
853        switch(cls[1]) {
854        case 'd':
855            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
856            break;
857        case 'l':
858            error(_("code not yet written for cls = \"lgCMatrix\""));
859        }
860        cholmod_l_free_sparse(&A, &c);
861        UNPROTECT(1);
862        return ans;
863    }

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