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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 2144, Tue Mar 18 23:08:12 2008 UTC pkg/Matrix/src/Csparse.c revision 2646, Mon Feb 21 10:57:49 2011 UTC
# Line 3  Line 3 
3  #include "Tsparse.h"  #include "Tsparse.h"
4  #include "chm_common.h"  #include "chm_common.h"
5    
6  SEXP Csparse_validate(SEXP x)  /** "Cheap" C version of  Csparse_validate() - *not* sorting : */
7    Rboolean isValid_Csparse(SEXP x)
8    {
9        /* NB: we do *NOT* check a potential 'x' slot here, at all */
10        SEXP pslot = GET_SLOT(x, Matrix_pSym),
11            islot = GET_SLOT(x, Matrix_iSym);
12        int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)), j,
13            nrow = dims[0],
14            ncol = dims[1],
15            *xp = INTEGER(pslot),
16            *xi = INTEGER(islot);
17    
18        if (length(pslot) != dims[1] + 1)
19            return FALSE;
20        if (xp[0] != 0)
21            return FALSE;
22        if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
23            return FALSE;
24        for (j = 0; j < xp[ncol]; j++) {
25            if (xi[j] < 0 || xi[j] >= nrow)
26                return FALSE;
27        }
28        for (j = 0; j < ncol; j++) {
29            if (xp[j] > xp[j + 1])
30                return FALSE;
31        }
32        return TRUE;
33    }
34    
35    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 23  Line 60 
60      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
61          return          return
62              mkString(_("last element of slot p must match length of slots i and x"));              mkString(_("last element of slot p must match length of slots i and x"));
63      for (j = 0; j < length(islot); j++) {      for (j = 0; j < xp[ncol]; j++) {
64          if (xi[j] < 0 || xi[j] >= nrow)          if (xi[j] < 0 || xi[j] >= nrow)
65              return mkString(_("all row indices must be between 0 and nrow-1"));              return mkString(_("all row indices must be between 0 and nrow-1"));
66      }      }
# Line 31  Line 68 
68      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
69          if (xp[j] > xp[j+1])          if (xp[j] > xp[j+1])
70              return mkString(_("slot p must be non-decreasing"));              return mkString(_("slot p must be non-decreasing"));
71          if(sorted)          if(sorted) /* only act if >= 2 entries in column j : */
72              for (k = xp[j] + 1; k < xp[j + 1]; k++) {              for (k = xp[j] + 1; k < xp[j + 1]; k++) {
73                  if (xi[k] < xi[k - 1])                  if (xi[k] < xi[k - 1])
74                      sorted = FALSE;                      sorted = FALSE;
# Line 40  Line 77 
77              }              }
78      }      }
79      if (!sorted) {      if (!sorted) {
80          CHM_SP chx = AS_CHM_SP(x);          if(maybe_modify) {
81                CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
82          R_CheckStack();          R_CheckStack();
83                as_cholmod_sparse(chx, x, FALSE, TRUE);/*-> cholmod_l_sort() ! */
84                /* as chx = AS_CHM_SP__(x)  but  ^^^^ sorting x in_place !!! */
85    
         cholmod_sort(chx, &c);  
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 95  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 109  Line 150 
150   * FIXME: replace by non-CHOLMOD code ! */   * FIXME: replace by non-CHOLMOD code ! */
151  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
152  {  {
153      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
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 133  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 156  Line 251 
251  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
252  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
253  {  {
254      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
255      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
256      R_CheckStack();      R_CheckStack();
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 170  Line 265 
265    
266  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
267  {  {
268      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
269      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
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 185  Line 280 
280  {  {
281      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
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 204  Line 299 
299  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
300  {  {
301      CHM_SP      CHM_SP
302          cha = AS_CHM_SP(Csparse_diagU2N(a)),          cha = AS_CHM_SP(a),
303          chb = AS_CHM_SP(Csparse_diagU2N(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 235  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 242  Line 343 
343  {  {
344      int tr = asLogical(trans);      int tr = asLogical(trans);
345      CHM_SP      CHM_SP
346          cha = AS_CHM_SP(Csparse_diagU2N(a)),          cha = AS_CHM_SP(a),
347          chb = AS_CHM_SP(Csparse_diagU2N(b)),          chb = AS_CHM_SP(b),
348          chTr, chc;          chTr, chc;
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 267  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    
379  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
380  {  {
381      CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(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    
410  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
411  {  {
412      CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(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)); int nprot = 2;
418      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
419      R_CheckStack();      R_CheckStack();
420        // -- see Csparse_dense_prod() above :
421      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);      if(cha->xtype == CHOLMOD_PATTERN) {
422            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
423            cha = AS_CHM_SP(da);
424        }
425        cholmod_l_sdmult(cha, 1, one, zero, chb, chc, &c);
426      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
427                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
428      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
429                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
430      UNPROTECT(2);      UNPROTECT(nprot);
431      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
432  }  }
433    
# Line 321  Line 437 
437  {  {
438      int trip = asLogical(triplet),      int trip = asLogical(triplet),
439          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
440      CHM_TR cht = trip ? AS_CHM_TR(Tsparse_diagU2N(x)) : (CHM_TR) NULL;  #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
441        CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
442    #else /* workaround needed:*/
443        SEXP xx = PROTECT(Tsparse_diagU2N(x));
444        CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
445    #endif
446      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
447          chx = (trip ?          chx = (trip ?
448                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_l_triplet_to_sparse(cht, cht->nnz, &c) :
449                 AS_CHM_SP(Csparse_diagU2N(x)));                 AS_CHM_SP(x));
450      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
451      R_CheckStack();      R_CheckStack();
452    
453      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_l_transpose(chx, chx->xtype, &c);
454      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);
455      if(!chcp) {      if(!chcp) {
456          UNPROTECT(1);          UNPROTECT(1);
457          error(_("Csparse_crossprod(): error return from cholmod_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_l_aat()"));
458      }      }
459      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_l_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
460      chcp->stype = 1;      chcp->stype = 1;
461      if (trip) cholmod_free_sparse(&chx, &c);      if (trip) cholmod_l_free_sparse(&chx, &c);
462      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_l_free_sparse(&chxt, &c);
463      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
464                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
465                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
466      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
467    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
468      UNPROTECT(1);      UNPROTECT(1);
469    #else
470        UNPROTECT(2);
471    #endif
472      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
473  }  }
474    
475    /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
476    *  at least all "explicit" zeros */
477  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
478  {  {
479      CHM_SP chx = AS_CHM_SP(x);      const char *cl = class_P(x);
480      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
481        int tr = (cl[1] == 't');
482        CHM_SP chx = AS_CHM_SP__(x);
483        CHM_SP ans = cholmod_l_copy(chx, chx->stype, chx->xtype, &c);
484      double dtol = asReal(tol);      double dtol = asReal(tol);
485      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
486      R_CheckStack();      R_CheckStack();
487    
488      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_l_drop(dtol, ans, &c))
489          error(_("cholmod_drop() failed"));          error(_("cholmod_l_drop() failed"));
490      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1,
491                                  tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
492                                  Rkind, tr ? diag_P(x) : "",
493                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
494  }  }
495    
496  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
497  {  {
498      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
499      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
500            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
501            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
502      R_CheckStack();      R_CheckStack();
503    
504      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
505      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_horzcat(chx, chy, 1, &c),
506                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
507  }  }
508    
509  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
510  {  {
511      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
512      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
513            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
514            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
515      R_CheckStack();      R_CheckStack();
516    
517      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
518      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_vertcat(chx, chy, 1, &c),
519                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
520  }  }
521    
522  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
523  {  {
524      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
525      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
526      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);
527      R_CheckStack();      R_CheckStack();
528    
529      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
# Line 404  Line 540 
540          return (x);          return (x);
541      }      }
542      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
543          CHM_SP chx = AS_CHM_SP(x);          CHM_SP chx = AS_CHM_SP__(x);
544          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);
545          double one[] = {1, 0};          double one[] = {1, 0};
546          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);
547          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
548          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
549    
550          R_CheckStack();          R_CheckStack();
551          cholmod_free_sparse(&eye, &c);          cholmod_l_free_sparse(&eye, &c);
552          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
553                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
554      }      }
# Line 429  Line 565 
565      }      }
566      else { /* triangular with diag='N'): now drop the diagonal */      else { /* triangular with diag='N'): now drop the diagonal */
567          /* duplicate, since chx will be modified: */          /* duplicate, since chx will be modified: */
568          CHM_SP chx = AS_CHM_SP(duplicate(x));          CHM_SP chx = AS_CHM_SP__(duplicate(x));
569          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
570              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
571          R_CheckStack();          R_CheckStack();
# Line 442  Line 578 
578      }      }
579  }  }
580    
581    /**
582     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
583     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
584     * @param x CsparseMatrix
585     * @param i row     indices (0-origin), or NULL (R's)
586     * @param j columns indices (0-origin), or NULL
587     *
588     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
589     */
590  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
591  {  {
592      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
593      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
594          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
595      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 455  Line 600 
600      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
601          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
602    
603      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      if (chx->stype) /* symmetricMatrix */
604                                                  INTEGER(j), csize,          /* for now, cholmod_submatrix() only accepts "generalMatrix" */
605            chx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);
606    
607        return chm_sparse_to_SEXP(cholmod_l_submatrix(chx,
608                                    (rsize < 0) ? NULL : INTEGER(i), rsize,
609                                    (csize < 0) ? NULL : INTEGER(j), csize,
610                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
611                                1, 0, Rkind, "",                                1, 0, Rkind, "",
612                                /* FIXME: drops dimnames */ R_NilValue);                                /* FIXME: drops dimnames */ R_NilValue);
# Line 469  Line 619 
619      if (!f)      if (!f)
620          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
621                CHAR(asChar(fname)));                CHAR(asChar(fname)));
622      if (!cholmod_write_sparse(f, AS_CHM_SP(Csparse_diagU2N(x)),      if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),
623                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
624          error(_("cholmod_write_sparse returned error code"));          error(_("cholmod_l_write_sparse returned error code"));
625      fclose(f);      fclose(f);
626      return R_NilValue;      return R_NilValue;
627  }  }
# Line 484  Line 634 
634   * @param n  dimension of the matrix.   * @param n  dimension of the matrix.
635   * @param x_p  'p' (column pointer) slot contents   * @param x_p  'p' (column pointer) slot contents
636   * @param x_x  'x' (non-zero entries) slot contents   * @param x_x  'x' (non-zero entries) slot contents
637   * @param perm 'perm' (= permutation vector) slot contents   * @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
638   * @param resultKind a (SEXP) string indicating which kind of result is desired.   * @param resultKind a (SEXP) string indicating which kind of result is desired.
639   *   *
640   * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries   * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
# Line 544  Line 694 
694      case diag_backpermuted:      case diag_backpermuted:
695          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
696    
697          error(_("resultKind = 'diagBack' (back-permuted) is not yet implemented"));          warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));
698          /* now back_permute : */          /* now back_permute : */
699          for(i = 0; i < n; i++) {          for(i = 0; i < n; i++) {
700              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 553  Line 703 
703          break;          break;
704    
705      default: /* -1 from above */      default: /* -1 from above */
706          error("diag_tC(): invalid 'resultKind'");          error(_("diag_tC(): invalid 'resultKind'"));
707          /* Wall: */ ans = R_NilValue; v = REAL(ans);          /* Wall: */ ans = R_NilValue; v = REAL(ans);
708      }      }
709    
# Line 567  Line 717 
717   *   *
718   * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor   * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
719   * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor   * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
720   * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor   * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
721     *                   only used for "diagBack"
722   * @param resultKind a (SEXP) string indicating which kind of result is desired.   * @param resultKind a (SEXP) string indicating which kind of result is desired.
723   *   *
724   * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries   * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
# Line 582  Line 733 
733    
734      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
735  }  }
736    
737    /**
738     * Create a Csparse matrix object from indices and/or pointers.
739     *
740     * @param cls name of actual class of object to create
741     * @param i optional integer vector of length nnz of row indices
742     * @param j optional integer vector of length nnz of column indices
743     * @param p optional integer vector of length np of row or column pointers
744     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
745     * @param x optional vector of values
746     * @param nnz length of vectors i, j and/or x, whichever is to be used
747     * @param dims optional integer vector of length 2 to be used as
748     *     dimensions.  If dims == (int*)NULL then the maximum row and column
749     *     index are used as the dimensions.
750     * @param dimnames optional list of length 2 to be used as dimnames
751     * @param index1 indicator of 1-based indices
752     *
753     * @return an SEXP of class cls inheriting from CsparseMatrix.
754     */
755    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
756                        void* x, int nnz, int* dims, SEXP dimnames,
757                        int index1)
758    {
759        SEXP ans;
760        int *ij = (int*)NULL, *tri, *trj,
761            mi, mj, mp, nrow = -1, ncol = -1;
762        int xtype = -1;             /* -Wall */
763        CHM_TR T;
764        CHM_SP A;
765    
766        if (np < 0 || nnz < 0)
767            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
768                  np, nnz);
769        if (1 != ((mi = (i == (int*)NULL)) +
770                  (mj = (j == (int*)NULL)) +
771                  (mp = (p == (int*)NULL))))
772            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
773        if (mp) {
774            if (np) error(_("np = %d, must be zero when p is NULL"), np);
775        } else {
776            if (np) {               /* Expand p to form i or j */
777                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
778                for (int ii = 0; ii < np; ii++)
779                    if (p[ii] > p[ii + 1])
780                        error(_("p must be non-decreasing"));
781                if (p[np] != nnz)
782                    error("p[np] = %d != nnz = %d", p[np], nnz);
783                ij = Calloc(nnz, int);
784                if (mi) {
785                    i = ij;
786                    nrow = np;
787                } else {
788                    j = ij;
789                    ncol = np;
790                }
791                                    /* Expand p to 0-based indices */
792                for (int ii = 0; ii < np; ii++)
793                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
794            } else {
795                if (nnz)
796                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
797                          nnz);
798            }
799        }
800                                    /* calculate nrow and ncol */
801        if (nrow < 0) {
802            for (int ii = 0; ii < nnz; ii++) {
803                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
804                if (i1 < 1) error(_("invalid row index at position %d"), ii);
805                if (i1 > nrow) nrow = i1;
806            }
807        }
808        if (ncol < 0) {
809            for (int jj = 0; jj < nnz; jj++) {
810                int j1 = j[jj] + (index1 ? 0 : 1);
811                if (j1 < 1) error(_("invalid column index at position %d"), jj);
812                if (j1 > ncol) ncol = j1;
813            }
814        }
815        if (dims != (int*)NULL) {
816            if (dims[0] > nrow) nrow = dims[0];
817            if (dims[1] > ncol) ncol = dims[1];
818        }
819                                    /* check the class name */
820        if (strlen(cls) != 8)
821            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
822        if (!strcmp(cls + 2, "CMatrix"))
823            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
824        switch(cls[0]) {
825        case 'd':
826        case 'l':
827               xtype = CHOLMOD_REAL;
828               break;
829        case 'n':
830               xtype = CHOLMOD_PATTERN;
831               break;
832        default:
833               error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
834        }
835        if (cls[1] != 'g')
836            error(_("Only 'g'eneral sparse matrix types allowed"));
837                                    /* allocate and populate the triplet */
838        T = cholmod_l_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
839                                        xtype, &c);
840        T->x = x;
841        tri = (int*)T->i;
842        trj = (int*)T->j;
843        for (int ii = 0; ii < nnz; ii++) {
844            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
845            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
846        }
847                                    /* create the cholmod_sparse structure */
848        A = cholmod_l_triplet_to_sparse(T, nnz, &c);
849        cholmod_l_free_triplet(&T, &c);
850                                    /* copy the information to the SEXP */
851        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
852    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
853                                    /* allocate and copy common slots */
854        nnz = cholmod_l_nnz(A, &c);
855        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
856        dims[0] = A->nrow; dims[1] = A->ncol;
857        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
858        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
859        switch(cls[1]) {
860        case 'd':
861            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
862            break;
863        case 'l':
864            error(_("code not yet written for cls = \"lgCMatrix\""));
865        }
866    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
867        cholmod_l_free_sparse(&A, &c);
868        UNPROTECT(1);
869        return ans;
870    }

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