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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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revision 2586, Sun Jul 25 02:32:06 2010 UTC 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"  #include "Tsparse.h"
6  #include "chm_common.h"  #include "chm_common.h"
# Line 136  Line 138 
138              }              }
139      }      }
140      if (!sorted)      if (!sorted)
141          /* cannot easily use cholmod_l_sort(.) ... -> "error out" :*/          /* cannot easily use cholmod_sort(.) ... -> "error out" :*/
142          return mkString(_("slot j is not increasing inside a column"));          return mkString(_("slot j is not increasing inside a column"));
143      else if(!strictly) /* sorted, but not strictly */      else if(!strictly) /* sorted, but not strictly */
144          return mkString(_("slot j is not *strictly* increasing inside a column"));          return mkString(_("slot j is not *strictly* increasing inside a column"));
# Line 154  Line 156 
156      /* This loses the symmetry property, since cholmod_dense has none,      /* This loses the symmetry property, since cholmod_dense has none,
157       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
158       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones : */
159      CHM_DN chxd = cholmod_l_sparse_to_dense(chxs, &c);      CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
160      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
161      R_CheckStack();      R_CheckStack();
162    
163      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));
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)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
168  {  {
169      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
170      CHM_SP chxcp = cholmod_l_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
171      int tr = asLogical(tri);      int tr = asLogical(tri);
172      R_CheckStack();      R_CheckStack();
173    
# Line 174  Line 177 
177                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
178  }  }
179    
180    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
181    SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
182    {
183        return nz2Csparse(x, asInteger(res_kind));
184    }
185    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
186    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      return chm_dense_to_matrix(cholmod_l_sparse_to_dense(AS_CHM_SP__(x), &c),      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),
236                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, 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      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
242      CHM_TR chxt = cholmod_l_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
243      int tr = asLogical(tri);      int tr = asLogical(tri);
244      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
245      R_CheckStack();      R_CheckStack();
# Line 203  Line 259 
259    
260      if (!(chx->stype))      if (!(chx->stype))
261          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
262      chgx = cholmod_l_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      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
265                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 216  Line 272 
272      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
273      R_CheckStack();      R_CheckStack();
274    
275      chgx = cholmod_l_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
276      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
277      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
278                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 228  Line 284 
284       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
285      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
286      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
287      CHM_SP chxt = cholmod_l_transpose(chx, chx->xtype, &c);      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 tr = asLogical(tri);      int tr = asLogical(tri);
290      R_CheckStack();      R_CheckStack();
# Line 247  Line 303 
303      CHM_SP      CHM_SP
304          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
305          chb = AS_CHM_SP(b),          chb = AS_CHM_SP(b),
306          chc = cholmod_l_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
307                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
308                                 /*out sorted:*/ 1, &c);                                 /*out sorted:*/ 1, &c);
309      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
# Line 298  Line 354 
354      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
355      R_CheckStack();      R_CheckStack();
356    
357      chTr = cholmod_l_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
358      chc = cholmod_l_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
359                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
360      cholmod_l_free_sparse(&chTr, &c);      cholmod_free_sparse(&chTr, &c);
361    
362      /* Preserve triangularity and unit-triangularity if appropriate;      /* Preserve triangularity and unit-triangularity if appropriate;
363       * see Csparse_Csparse_prod() for comments */       * see Csparse_Csparse_prod() for comments */
# Line 327  Line 383 
383      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
384      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
385      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
386      CHM_DN chc = cholmod_l_allocate_dense(cha->nrow, chb->ncol, cha->nrow,      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
387                                          chb->xtype, &c);                                          chb->xtype, &c);
388      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
389      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
390        int nprot = 2;
391      R_CheckStack();      R_CheckStack();
392        /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
393      cholmod_l_sdmult(cha, 0, one, zero, chb, chc, &c);      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 */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
405                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
406      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
407                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
408      UNPROTECT(2);      UNPROTECT(nprot);
409      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
410  }  }
411    
# Line 347  Line 414 
414      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
415      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
416      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
417      CHM_DN chc = cholmod_l_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
418                                          chb->xtype, &c);                                          chb->xtype, &c);
419      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
420      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
421      R_CheckStack();      R_CheckStack();
422        // -- see Csparse_dense_prod() above :
423      cholmod_l_sdmult(cha, 1, one, zero, chb, chc, &c);      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 */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
429                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
430      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
431                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
432      UNPROTECT(2);      UNPROTECT(nprot);
433      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
434  }  }
435    
# Line 376  Line 447 
447  #endif  #endif
448      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
449          chx = (trip ?          chx = (trip ?
450                 cholmod_l_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
451                 AS_CHM_SP(x));                 AS_CHM_SP(x));
452      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
453      R_CheckStack();      R_CheckStack();
454    
455      if (!tr) chxt = cholmod_l_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
456      chcp = cholmod_l_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          UNPROTECT(1);          UNPROTECT(1);
459          error(_("Csparse_crossprod(): error return from cholmod_l_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_aat()"));
460      }      }
461      cholmod_l_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) cholmod_l_free_sparse(&chx, &c);      if (trip) cholmod_free_sparse(&chx, &c);
464      if (!tr) cholmod_l_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
465      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
466                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
467                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
# Line 403  Line 474 
474      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      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)  SEXP Csparse_drop(SEXP x, SEXP tol)
480  {  {
481      const char *cl = class_P(x);      const char *cl = class_P(x);
482      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
483      int tr = (cl[1] == 't');      int tr = (cl[1] == 't');
484      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
485      CHM_SP ans = cholmod_l_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
486      double dtol = asReal(tol);      double dtol = asReal(tol);
487      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
488      R_CheckStack();      R_CheckStack();
489    
490      if(!cholmod_l_drop(dtol, ans, &c))      if(!cholmod_drop(dtol, ans, &c))
491          error(_("cholmod_l_drop() failed"));          error(_("cholmod_drop() failed"));
492      return chm_sparse_to_SEXP(ans, 1,      return chm_sparse_to_SEXP(ans, 1,
493                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
494                                Rkind, tr ? diag_P(x) : "",                                Rkind, tr ? diag_P(x) : "",
# Line 431  Line 504 
504      R_CheckStack();      R_CheckStack();
505    
506      /* TODO: currently drops dimnames - and we fix at R level */      /* TODO: currently drops dimnames - and we fix at R level */
507      return chm_sparse_to_SEXP(cholmod_l_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
508                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
509  }  }
510    
# Line 444  Line 517 
517      R_CheckStack();      R_CheckStack();
518    
519      /* TODO: currently drops dimnames - and we fix at R level */      /* TODO: currently drops dimnames - and we fix at R level */
520      return chm_sparse_to_SEXP(cholmod_l_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
521                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
522  }  }
523    
# Line 452  Line 525 
525  {  {
526      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
527      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
528      CHM_SP ans = cholmod_l_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
529      R_CheckStack();      R_CheckStack();
530    
531      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
# Line 470  Line 543 
543      }      }
544      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
545          CHM_SP chx = AS_CHM_SP__(x);          CHM_SP chx = AS_CHM_SP__(x);
546          CHM_SP eye = cholmod_l_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
547          double one[] = {1, 0};          double one[] = {1, 0};
548          CHM_SP ans = cholmod_l_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
549          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
550          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
551    
552          R_CheckStack();          R_CheckStack();
553          cholmod_l_free_sparse(&eye, &c);          cholmod_free_sparse(&eye, &c);
554          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
555                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
556      }      }
# Line 531  Line 604 
604    
605      if (chx->stype) /* symmetricMatrix */      if (chx->stype) /* symmetricMatrix */
606          /* for now, cholmod_submatrix() only accepts "generalMatrix" */          /* for now, cholmod_submatrix() only accepts "generalMatrix" */
607          chx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);          chx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
608    
609      return chm_sparse_to_SEXP(cholmod_l_submatrix(chx,      return chm_sparse_to_SEXP(cholmod_submatrix(chx,
610                                  (rsize < 0) ? NULL : INTEGER(i), rsize,                                  (rsize < 0) ? NULL : INTEGER(i), rsize,
611                                  (csize < 0) ? NULL : INTEGER(j), csize,                                  (csize < 0) ? NULL : INTEGER(j), csize,
612                                                    TRUE, TRUE, &c),                                                    TRUE, TRUE, &c),
# Line 541  Line 614 
614                                /* FIXME: drops dimnames */ R_NilValue);                                /* 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)  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
635  {  {
636      FILE *f = fopen(CHAR(asChar(fname)), "w");      FILE *f = fopen(CHAR(asChar(fname)), "w");
# Line 548  Line 638 
638      if (!f)      if (!f)
639          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
640                CHAR(asChar(fname)));                CHAR(asChar(fname)));
641      if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),      if (!cholmod_write_sparse(f, AS_CHM_SP(x),
642                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
643          error(_("cholmod_l_write_sparse returned error code"));          error(_("cholmod_write_sparse returned error code"));
644      fclose(f);      fclose(f);
645      return R_NilValue;      return R_NilValue;
646  }  }
# Line 764  Line 854 
854      if (cls[1] != 'g')      if (cls[1] != 'g')
855          error(_("Only 'g'eneral sparse matrix types allowed"));          error(_("Only 'g'eneral sparse matrix types allowed"));
856                                  /* allocate and populate the triplet */                                  /* allocate and populate the triplet */
857      T = cholmod_l_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,      T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
858                                      xtype, &c);                                      xtype, &c);
859      T->x = x;      T->x = x;
860      tri = (int*)T->i;      tri = (int*)T->i;
# Line 774  Line 864 
864          trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);          trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
865      }      }
866                                  /* create the cholmod_sparse structure */                                  /* create the cholmod_sparse structure */
867      A = cholmod_l_triplet_to_sparse(T, nnz, &c);      A = cholmod_triplet_to_sparse(T, nnz, &c);
868      cholmod_l_free_triplet(&T, &c);      cholmod_free_triplet(&T, &c);
869                                  /* copy the information to the SEXP */                                  /* copy the information to the SEXP */
870      ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));      ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
871  /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */  /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
872                                  /* allocate and copy common slots */                                  /* allocate and copy common slots */
873      nnz = cholmod_l_nnz(A, &c);      nnz = cholmod_nnz(A, &c);
874      dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));      dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
875      dims[0] = A->nrow; dims[1] = A->ncol;      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);      Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
# Line 792  Line 882 
882      case 'l':      case 'l':
883          error(_("code not yet written for cls = \"lgCMatrix\""));          error(_("code not yet written for cls = \"lgCMatrix\""));
884      }      }
885      cholmod_l_free_sparse(&A, &c);  /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
886        cholmod_free_sparse(&A, &c);
887      UNPROTECT(1);      UNPROTECT(1);
888      return ans;      return ans;
889  }  }

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