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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 2834, Mon Sep 3 10:30:03 2012 UTC
# Line 1  Line 1 
1                          /* Sparse matrices in compressed column-oriented form */                          /* Sparse matrices in compressed column-oriented form */
2    
3  #include "Csparse.h"  #include "Csparse.h"
4  #include "Tsparse.h"  #include "Tsparse.h"
5  #include "chm_common.h"  #include "chm_common.h"
# Line 136  Line 137 
137              }              }
138      }      }
139      if (!sorted)      if (!sorted)
140          /* cannot easily use cholmod_l_sort(.) ... -> "error out" :*/          /* cannot easily use cholmod_sort(.) ... -> "error out" :*/
141          return mkString(_("slot j is not increasing inside a column"));          return mkString(_("slot j is not increasing inside a column"));
142      else if(!strictly) /* sorted, but not strictly */      else if(!strictly) /* sorted, but not strictly */
143          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 155 
155      /* This loses the symmetry property, since cholmod_dense has none,      /* This loses the symmetry property, since cholmod_dense has none,
156       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
157       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones : */
158      CHM_DN chxd = cholmod_l_sparse_to_dense(chxs, &c);      CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
159      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
160      R_CheckStack();      R_CheckStack();
161    
162      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));
163  }  }
164    
165    // FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
166  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
167  {  {
168      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
169      CHM_SP chxcp = cholmod_l_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
170      int tr = asLogical(tri);      int tr = asLogical(tri);
171      R_CheckStack();      R_CheckStack();
172    
# Line 174  Line 176 
176                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
177  }  }
178    
179    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
180    SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
181    {
182        return nz2Csparse(x, asInteger(res_kind));
183    }
184    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
185    SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
186    {
187        const char *cl_x = class_P(x);
188        if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));
189        if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
190        int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
191        SEXP ans;
192        char *ncl = alloca(strlen(cl_x) + 1); /* not much memory required */
193        strcpy(ncl, 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 211  Line 267 
267    
268  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
269  {  {
270        int *adims = INTEGER(GET_SLOT(x, Matrix_DimSym)), n = adims[0];
271        if(n != adims[1]) {
272            error(_("Csparse_general_to_symmetric(): matrix is not square!"));
273            return R_NilValue; /* -Wall */
274        }
275      CHM_SP chx = AS_CHM_SP__(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
276      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
277      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
278      R_CheckStack();      R_CheckStack();
279        chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
     chgx = cholmod_l_copy(chx, /* stype: */ uploT, chx->xtype, &c);  
280      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
281      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
282                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 228  Line 288 
288       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
289      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
290      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
291      CHM_SP chxt = cholmod_l_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
292      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
293      int tr = asLogical(tri);      int tr = asLogical(tri);
294      R_CheckStack();      R_CheckStack();
# Line 247  Line 307 
307      CHM_SP      CHM_SP
308          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
309          chb = AS_CHM_SP(b),          chb = AS_CHM_SP(b),
310          chc = cholmod_l_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
311                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
312                                 /*out sorted:*/ 1, &c);                                 /*out sorted:*/ 1, &c);
313      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 358 
358      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
359      R_CheckStack();      R_CheckStack();
360    
361      chTr = cholmod_l_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
362      chc = cholmod_l_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
363                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
364      cholmod_l_free_sparse(&chTr, &c);      cholmod_free_sparse(&chTr, &c);
365    
366      /* Preserve triangularity and unit-triangularity if appropriate;      /* Preserve triangularity and unit-triangularity if appropriate;
367       * see Csparse_Csparse_prod() for comments */       * see Csparse_Csparse_prod() for comments */
# Line 327  Line 387 
387      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
388      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
389      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
390      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,
391                                          chb->xtype, &c);                                          chb->xtype, &c);
392      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
393      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
394        int nprot = 2;
395      R_CheckStack();      R_CheckStack();
396        /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
397      cholmod_l_sdmult(cha, 0, one, zero, chb, chc, &c);      if(cha->xtype == CHOLMOD_PATTERN) {
398            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
399            /*        " --> slightly inefficient coercion")); */
400    
401            // This *fails* to produce a CHOLMOD_REAL ..
402            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
403            // --> use our Matrix-classes
404            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
405            cha = AS_CHM_SP(da);
406        }
407        cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
408      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
409                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
410      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
411                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
412      UNPROTECT(2);      UNPROTECT(nprot);
413      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
414  }  }
415    
# Line 347  Line 418 
418      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
419      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
420      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
421      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,
422                                          chb->xtype, &c);                                          chb->xtype, &c);
423      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
424      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
425      R_CheckStack();      R_CheckStack();
426        // -- see Csparse_dense_prod() above :
427      cholmod_l_sdmult(cha, 1, one, zero, chb, chc, &c);      if(cha->xtype == CHOLMOD_PATTERN) {
428            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
429            cha = AS_CHM_SP(da);
430        }
431        cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
432      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
433                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
434      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
435                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
436      UNPROTECT(2);      UNPROTECT(nprot);
437      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
438  }  }
439    
# Line 376  Line 451 
451  #endif  #endif
452      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
453          chx = (trip ?          chx = (trip ?
454                 cholmod_l_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
455                 AS_CHM_SP(x));                 AS_CHM_SP(x));
456      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
457      R_CheckStack();      R_CheckStack();
458    
459      if (!tr) chxt = cholmod_l_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
460      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);
461      if(!chcp) {      if(!chcp) {
462          UNPROTECT(1);          UNPROTECT(1);
463          error(_("Csparse_crossprod(): error return from cholmod_l_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_aat()"));
464      }      }
465      cholmod_l_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
466      chcp->stype = 1;      chcp->stype = 1;
467      if (trip) cholmod_l_free_sparse(&chx, &c);      if (trip) cholmod_free_sparse(&chx, &c);
468      if (!tr) cholmod_l_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
469      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
470                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
471                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
# Line 403  Line 478 
478      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
479  }  }
480    
481    /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
482    *  at least all "explicit" zeros */
483  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
484  {  {
485      const char *cl = class_P(x);      const char *cl = class_P(x);
486      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
487      int tr = (cl[1] == 't');      int tr = (cl[1] == 't');
488      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
489      CHM_SP ans = cholmod_l_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
490      double dtol = asReal(tol);      double dtol = asReal(tol);
491      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
492      R_CheckStack();      R_CheckStack();
493    
494      if(!cholmod_l_drop(dtol, ans, &c))      if(!cholmod_drop(dtol, ans, &c))
495          error(_("cholmod_l_drop() failed"));          error(_("cholmod_drop() failed"));
496      return chm_sparse_to_SEXP(ans, 1,      return chm_sparse_to_SEXP(ans, 1,
497                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
498                                Rkind, tr ? diag_P(x) : "",                                Rkind, tr ? diag_P(x) : "",
# Line 431  Line 508 
508      R_CheckStack();      R_CheckStack();
509    
510      /* TODO: currently drops dimnames - and we fix at R level */      /* TODO: currently drops dimnames - and we fix at R level */
511      return chm_sparse_to_SEXP(cholmod_l_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
512                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
513  }  }
514    
# Line 444  Line 521 
521      R_CheckStack();      R_CheckStack();
522    
523      /* TODO: currently drops dimnames - and we fix at R level */      /* TODO: currently drops dimnames - and we fix at R level */
524      return chm_sparse_to_SEXP(cholmod_l_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
525                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
526  }  }
527    
# Line 452  Line 529 
529  {  {
530      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
531      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
532      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);
533      R_CheckStack();      R_CheckStack();
534    
535      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
# Line 470  Line 547 
547      }      }
548      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
549          CHM_SP chx = AS_CHM_SP__(x);          CHM_SP chx = AS_CHM_SP__(x);
550          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);
551          double one[] = {1, 0};          double one[] = {1, 0};
552          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);
553          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
554          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
555    
556          R_CheckStack();          R_CheckStack();
557          cholmod_l_free_sparse(&eye, &c);          cholmod_free_sparse(&eye, &c);
558          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
559                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
560      }      }
# Line 494  Line 571 
571      }      }
572      else { /* triangular with diag='N'): now drop the diagonal */      else { /* triangular with diag='N'): now drop the diagonal */
573          /* duplicate, since chx will be modified: */          /* duplicate, since chx will be modified: */
574          CHM_SP chx = AS_CHM_SP__(duplicate(x));          SEXP xx = PROTECT(duplicate(x));
575            CHM_SP chx = AS_CHM_SP__(xx);
576          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
577              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
578          R_CheckStack();          R_CheckStack();
579    
580          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
581    
582          return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,          SEXP ans = chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
583                                    uploT, Rkind, "U",                                    uploT, Rkind, "U",
584                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
585            UNPROTECT(1);// only now !
586            return ans;
587      }      }
588  }  }
589    
# Line 529  Line 609 
609      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
610          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
611    
612      if (chx->stype) /* symmetricMatrix */      if (!chx->stype) {/* non-symmetric Matrix */
613          /* for now, cholmod_submatrix() only accepts "generalMatrix" */          return chm_sparse_to_SEXP(cholmod_submatrix(chx,
         chx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);  
   
     return chm_sparse_to_SEXP(cholmod_l_submatrix(chx,  
614                                  (rsize < 0) ? NULL : INTEGER(i), rsize,                                  (rsize < 0) ? NULL : INTEGER(i), rsize,
615                                  (csize < 0) ? NULL : INTEGER(j), csize,                                  (csize < 0) ? NULL : INTEGER(j), csize,
616                                                    TRUE, TRUE, &c),                                                    TRUE, TRUE, &c),
617                                1, 0, Rkind, "",                                1, 0, Rkind, "",
618                                /* FIXME: drops dimnames */ R_NilValue);                                /* FIXME: drops dimnames */ R_NilValue);
619  }  }
620                                    /* for now, cholmod_submatrix() only accepts "generalMatrix" */
621        CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
622        CHM_SP ans = cholmod_submatrix(tmp,
623                                       (rsize < 0) ? NULL : INTEGER(i), rsize,
624                                       (csize < 0) ? NULL : INTEGER(j), csize,
625                                       TRUE, TRUE, &c);
626        cholmod_free_sparse(&tmp, &c);
627        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
628    }
629    
630    #define _d_Csp_
631    #include "t_Csparse_subassign.c"
632    
633    #define _l_Csp_
634    #include "t_Csparse_subassign.c"
635    
636    #define _i_Csp_
637    #include "t_Csparse_subassign.c"
638    
639    #define _n_Csp_
640    #include "t_Csparse_subassign.c"
641    
642    #define _z_Csp_
643    #include "t_Csparse_subassign.c"
644    
645    
646    
647  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
648  {  {
# Line 548  Line 651 
651      if (!f)      if (!f)
652          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
653                CHAR(asChar(fname)));                CHAR(asChar(fname)));
654      if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),      if (!cholmod_write_sparse(f, AS_CHM_SP(x),
655                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
656          error(_("cholmod_l_write_sparse returned error code"));          error(_("cholmod_write_sparse returned error code"));
657      fclose(f);      fclose(f);
658      return R_NilValue;      return R_NilValue;
659  }  }
# Line 623  Line 726 
726      case diag_backpermuted:      case diag_backpermuted:
727          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
728    
729          warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));          warning(_("%s = '%s' (back-permuted) is experimental"),
730                    "resultKind", "diagBack");
731          /* now back_permute : */          /* now back_permute : */
732          for(i = 0; i < n; i++) {          for(i = 0; i < n; i++) {
733              double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;              double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
# Line 764  Line 868 
868      if (cls[1] != 'g')      if (cls[1] != 'g')
869          error(_("Only 'g'eneral sparse matrix types allowed"));          error(_("Only 'g'eneral sparse matrix types allowed"));
870                                  /* allocate and populate the triplet */                                  /* allocate and populate the triplet */
871      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,
872                                      xtype, &c);                                      xtype, &c);
873      T->x = x;      T->x = x;
874      tri = (int*)T->i;      tri = (int*)T->i;
# Line 774  Line 878 
878          trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);          trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
879      }      }
880                                  /* create the cholmod_sparse structure */                                  /* create the cholmod_sparse structure */
881      A = cholmod_l_triplet_to_sparse(T, nnz, &c);      A = cholmod_triplet_to_sparse(T, nnz, &c);
882      cholmod_l_free_triplet(&T, &c);      cholmod_free_triplet(&T, &c);
883                                  /* copy the information to the SEXP */                                  /* copy the information to the SEXP */
884      ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));      ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
885  /* 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 */
886                                  /* allocate and copy common slots */                                  /* allocate and copy common slots */
887      nnz = cholmod_l_nnz(A, &c);      nnz = cholmod_nnz(A, &c);
888      dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));      dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
889      dims[0] = A->nrow; dims[1] = A->ncol;      dims[0] = A->nrow; dims[1] = A->ncol;
890      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 896 
896      case 'l':      case 'l':
897          error(_("code not yet written for cls = \"lgCMatrix\""));          error(_("code not yet written for cls = \"lgCMatrix\""));
898      }      }
899      cholmod_l_free_sparse(&A, &c);  /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
900        cholmod_free_sparse(&A, &c);
901      UNPROTECT(1);      UNPROTECT(1);
902      return ans;      return ans;
903  }  }

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