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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 2646, Mon Feb 21 10:57:49 2011 UTC revision 2817, Sat Aug 11 23:41:46 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    
# Line 165  Line 166 
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 188  Line 189 
189      if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));      if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
190      int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));      int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
191      SEXP ans;      SEXP ans;
192      char *ncl = strdup(cl_x);      char *ncl = alloca(strlen(cl_x) + 1); /* not much memory required */
193        strcpy(ncl, cl_x);
194      double *dx_x; int *ix_x;      double *dx_x; int *ix_x;
195      ncl[0] = (r_kind == x_double ? 'd' :      ncl[0] = (r_kind == x_double ? 'd' :
196                (r_kind == x_logical ? 'l' :                (r_kind == x_logical ? 'l' :
# Line 230  Line 232 
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 257  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 265  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 282  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 301  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 352  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 381  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};
# Line 398  Line 404 
404          SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;          SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
405          cha = AS_CHM_SP(da);          cha = AS_CHM_SP(da);
406      }      }
407      cholmod_l_sdmult(cha, 0, one, zero, chb, chc, &c);      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,
# Line 412  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)); int nprot = 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};
# Line 422  Line 428 
428          SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;          SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
429          cha = AS_CHM_SP(da);          cha = AS_CHM_SP(da);
430      }      }
431      cholmod_l_sdmult(cha, 1, one, zero, chb, chc, &c);      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,
# Line 445  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 480  Line 486 
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 502  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 515  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 523  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 541  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 565  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            UNPROTECT(1);
583          return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,          return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
584                                    uploT, Rkind, "U",                                    uploT, Rkind, "U",
585                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
# Line 600  Line 608 
608      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
609          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
610    
611      if (chx->stype) /* symmetricMatrix */      if (!chx->stype) {/* non-symmetric Matrix */
612          /* 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,  
613                                  (rsize < 0) ? NULL : INTEGER(i), rsize,                                  (rsize < 0) ? NULL : INTEGER(i), rsize,
614                                  (csize < 0) ? NULL : INTEGER(j), csize,                                  (csize < 0) ? NULL : INTEGER(j), csize,
615                                                    TRUE, TRUE, &c),                                                    TRUE, TRUE, &c),
616                                1, 0, Rkind, "",                                1, 0, Rkind, "",
617                                /* FIXME: drops dimnames */ R_NilValue);                                /* FIXME: drops dimnames */ R_NilValue);
618  }  }
619                                    /* for now, cholmod_submatrix() only accepts "generalMatrix" */
620        CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
621        CHM_SP ans = cholmod_submatrix(tmp,
622                                       (rsize < 0) ? NULL : INTEGER(i), rsize,
623                                       (csize < 0) ? NULL : INTEGER(j), csize,
624                                       TRUE, TRUE, &c);
625        cholmod_free_sparse(&tmp, &c);
626        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
627    }
628    
629    #define _d_Csp_
630    #include "t_Csparse_subassign.c"
631    
632    #define _l_Csp_
633    #include "t_Csparse_subassign.c"
634    
635    #define _i_Csp_
636    #include "t_Csparse_subassign.c"
637    
638    #define _n_Csp_
639    #include "t_Csparse_subassign.c"
640    
641    #define _z_Csp_
642    #include "t_Csparse_subassign.c"
643    
644    
645    
646  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
647  {  {
# Line 619  Line 650 
650      if (!f)      if (!f)
651          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
652                CHAR(asChar(fname)));                CHAR(asChar(fname)));
653      if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),      if (!cholmod_write_sparse(f, AS_CHM_SP(x),
654                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
655          error(_("cholmod_l_write_sparse returned error code"));          error(_("cholmod_write_sparse returned error code"));
656      fclose(f);      fclose(f);
657      return R_NilValue;      return R_NilValue;
658  }  }
# Line 694  Line 725 
725      case diag_backpermuted:      case diag_backpermuted:
726          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
727    
728          warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));          warning(_("%s = '%s' (back-permuted) is experimental"),
729                    "resultKind", "diagBack");
730          /* now back_permute : */          /* now back_permute : */
731          for(i = 0; i < n; i++) {          for(i = 0; i < n; i++) {
732              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 835  Line 867 
867      if (cls[1] != 'g')      if (cls[1] != 'g')
868          error(_("Only 'g'eneral sparse matrix types allowed"));          error(_("Only 'g'eneral sparse matrix types allowed"));
869                                  /* allocate and populate the triplet */                                  /* allocate and populate the triplet */
870      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,
871                                      xtype, &c);                                      xtype, &c);
872      T->x = x;      T->x = x;
873      tri = (int*)T->i;      tri = (int*)T->i;
# Line 845  Line 877 
877          trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);          trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
878      }      }
879                                  /* create the cholmod_sparse structure */                                  /* create the cholmod_sparse structure */
880      A = cholmod_l_triplet_to_sparse(T, nnz, &c);      A = cholmod_triplet_to_sparse(T, nnz, &c);
881      cholmod_l_free_triplet(&T, &c);      cholmod_free_triplet(&T, &c);
882                                  /* copy the information to the SEXP */                                  /* copy the information to the SEXP */
883      ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));      ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
884  /* 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 */
885                                  /* allocate and copy common slots */                                  /* allocate and copy common slots */
886      nnz = cholmod_l_nnz(A, &c);      nnz = cholmod_nnz(A, &c);
887      dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));      dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
888      dims[0] = A->nrow; dims[1] = A->ncol;      dims[0] = A->nrow; dims[1] = A->ncol;
889      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 864  Line 896 
896          error(_("code not yet written for cls = \"lgCMatrix\""));          error(_("code not yet written for cls = \"lgCMatrix\""));
897      }      }
898  /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */  /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
899      cholmod_l_free_sparse(&A, &c);      cholmod_free_sparse(&A, &c);
900      UNPROTECT(1);      UNPROTECT(1);
901      return ans;      return ans;
902  }  }

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