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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 1960, Fri Jul 6 16:54:43 2007 UTC pkg/Matrix/src/Csparse.c revision 3018, Sat Oct 11 17:52:10 2014 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"
5  #include "chm_common.h"  #include "chm_common.h"
6    
7  SEXP Csparse_validate(SEXP x)  /** "Cheap" C version of  Csparse_validate() - *not* sorting : */
8    Rboolean isValid_Csparse(SEXP x)
9  {  {
10      /* NB: we do *NOT* check a potential 'x' slot here, at all */      /* NB: we do *NOT* check a potential 'x' slot here, at all */
11      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
12          islot = GET_SLOT(x, Matrix_iSym);          islot = GET_SLOT(x, Matrix_iSym);
13      Rboolean sorted, strictly;      int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)), j,
     int j, k,  
         *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),  
14          nrow = dims[0],          nrow = dims[0],
15          ncol = dims[1],          ncol = dims[1],
16          *xp = INTEGER(pslot),          *xp = INTEGER(pslot),
17          *xi = INTEGER(islot);          *xi = INTEGER(islot);
18    
19      if (length(pslot) != dims[1] + 1)      if (length(pslot) != dims[1] + 1)
20          return mkString(_("slot p must have length = ncol(.) + 1"));          return FALSE;
21      if (xp[0] != 0)      if (xp[0] != 0)
22          return mkString(_("first element of slot p must be zero"));          return FALSE;
23      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
24          return          return FALSE;
25              mkString(_("last element of slot p must match length of slots i and x"));      for (j = 0; j < xp[ncol]; j++) {
     for (j = 0; j < length(islot); j++) {  
26          if (xi[j] < 0 || xi[j] >= nrow)          if (xi[j] < 0 || xi[j] >= nrow)
27              return mkString(_("all row indices must be between 0 and nrow-1"));              return FALSE;
28      }      }
     sorted = TRUE; strictly = TRUE;  
29      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
30          if (xp[j] > xp[j+1])          if (xp[j] > xp[j+1])
31                return FALSE;
32        }
33        return TRUE;
34    }
35    
36    SEXP Csparse_validate(SEXP x) {
37        return Csparse_validate_(x, FALSE);
38    }
39    
40    
41    #define _t_Csparse_validate
42    #include "t_Csparse_validate.c"
43    
44    #define _t_Csparse_sort
45    #include "t_Csparse_validate.c"
46    
47    // R: .validateCsparse(x, sort.if.needed = FALSE) :
48    SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
49        return Csparse_validate_(x, asLogical(maybe_modify));
50    }
51    
52    // R: Matrix:::.sortCsparse(x) :
53    SEXP Csparse_sort (SEXP x) {
54       int ok = Csparse_sort_2(x, TRUE); // modifying x directly
55       if(!ok) warning(_("Csparse_sort(x): x is not a valid (apart from sorting) CsparseMatrix"));
56       return x;
57    }
58    
59    SEXP Rsparse_validate(SEXP x)
60    {
61        /* NB: we do *NOT* check a potential 'x' slot here, at all */
62        SEXP pslot = GET_SLOT(x, Matrix_pSym),
63            jslot = GET_SLOT(x, Matrix_jSym);
64        Rboolean sorted, strictly;
65        int i, k,
66            *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
67            nrow = dims[0],
68            ncol = dims[1],
69            *xp = INTEGER(pslot),
70            *xj = INTEGER(jslot);
71    
72        if (length(pslot) != dims[0] + 1)
73            return mkString(_("slot p must have length = nrow(.) + 1"));
74        if (xp[0] != 0)
75            return mkString(_("first element of slot p must be zero"));
76        if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
77            return
78                mkString(_("last element of slot p must match length of slots j and x"));
79        for (i = 0; i < length(jslot); i++) {
80            if (xj[i] < 0 || xj[i] >= ncol)
81                return mkString(_("all column indices must be between 0 and ncol-1"));
82        }
83        sorted = TRUE; strictly = TRUE;
84        for (i = 0; i < nrow; i++) {
85            if (xp[i] > xp[i+1])
86              return mkString(_("slot p must be non-decreasing"));              return mkString(_("slot p must be non-decreasing"));
87          if(sorted)          if(sorted)
88              for (k = xp[j] + 1; k < xp[j + 1]; k++) {              for (k = xp[i] + 1; k < xp[i + 1]; k++) {
89                  if (xi[k] < xi[k - 1])                  if (xj[k] < xj[k - 1])
90                      sorted = FALSE;                      sorted = FALSE;
91                  else if (xi[k] == xi[k - 1])                  else if (xj[k] == xj[k - 1])
92                      strictly = FALSE;                      strictly = FALSE;
93              }              }
94      }      }
95      if (!sorted) {      if (!sorted)
96          CHM_SP chx = AS_CHM_SP(x);          /* cannot easily use cholmod_sort(.) ... -> "error out" :*/
97          R_CheckStack();          return mkString(_("slot j is not increasing inside a column"));
98        else if(!strictly) /* sorted, but not strictly */
99          cholmod_sort(chx, &c);          return mkString(_("slot j is not *strictly* increasing inside a column"));
         /* Now re-check that row indices are *strictly* increasing  
          * (and not just increasing) within each column : */  
         for (j = 0; j < ncol; j++) {  
             for (k = xp[j] + 1; k < xp[j + 1]; k++)  
                 if (xi[k] == xi[k - 1])  
                     return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_sort)"));  
         }  
100    
     } else if(!strictly) {  /* sorted, but not strictly */  
         return mkString(_("slot i is not *strictly* increasing inside a column"));  
     }  
101      return ScalarLogical(1);      return ScalarLogical(1);
102  }  }
103    
104    
105  /* Called from ../R/Csparse.R : */  /* Called from ../R/Csparse.R : */
106  /* Can only return [dln]geMatrix (no symm/triang);  /* Can only return [dln]geMatrix (no symm/triang);
107   * FIXME: replace by non-CHOLMOD code ! */   * FIXME: replace by non-CHOLMOD code ! */
108  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
109  {  {
110      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
111      /* This loses the symmetry property, since cholmod_dense has none,      /* This loses the symmetry property, since cholmod_dense has none,
112       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
113       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones : */
# Line 73  Line 118 
118      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));
119  }  }
120    
121    // FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
122  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
123  {  {
124      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
125      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
126      int tr = asLogical(tri);      int tr = asLogical(tri);
127      R_CheckStack();      R_CheckStack();
# Line 86  Line 132 
132                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
133  }  }
134    
135  SEXP Csparse_to_matrix(SEXP x)  // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
136    SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
137    {
138        return nz2Csparse(x, asInteger(res_kind));
139    }
140    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
141    SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
142    {
143        const char *cl_x = class_P(x);
144        if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));
145        if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
146        int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
147        SEXP ans;
148        char *ncl = alloca(strlen(cl_x) + 1); /* not much memory required */
149        strcpy(ncl, cl_x);
150        double *dx_x; int *ix_x;
151        ncl[0] = (r_kind == x_double ? 'd' :
152                  (r_kind == x_logical ? 'l' :
153                   /* else (for now):  r_kind == x_integer : */ 'i'));
154        PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
155        // create a correct 'x' slot:
156        switch(r_kind) {
157            int i;
158        case x_double: // 'd'
159            dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
160            for (i=0; i < nnz; i++) dx_x[i] = 1.;
161            break;
162        case x_logical: // 'l'
163            ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
164            for (i=0; i < nnz; i++) ix_x[i] = TRUE;
165            break;
166        case x_integer: // 'i'
167            ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
168            for (i=0; i < nnz; i++) ix_x[i] = 1;
169            break;
170    
171        default:
172            error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
173                  r_kind);
174        }
175    
176        // now copy all other slots :
177        slot_dup(ans, x, Matrix_iSym);
178        slot_dup(ans, x, Matrix_pSym);
179        slot_dup(ans, x, Matrix_DimSym);
180        slot_dup(ans, x, Matrix_DimNamesSym);
181        if(ncl[1] != 'g') { // symmetric or triangular ...
182            slot_dup_if_has(ans, x, Matrix_uploSym);
183            slot_dup_if_has(ans, x, Matrix_diagSym);
184        }
185        UNPROTECT(1);
186        return ans;
187    }
188    
189    SEXP Csparse_to_matrix(SEXP x, SEXP chk)
190  {  {
191      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP(x), &c),      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP2(x, asLogical(chk)), &c),
192                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
193  }  }
194    SEXP Csparse_to_vector(SEXP x)
195    {
196        return chm_dense_to_vector(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c), 1);
197    }
198    
199  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
200  {  {
201      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
202      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
203      int tr = asLogical(tri);      int tr = asLogical(tri);
204      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 109  Line 213 
213  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
214  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
215  {  {
216      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
217      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
218      R_CheckStack();      R_CheckStack();
219    
# Line 123  Line 227 
227    
228  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
229  {  {
230      CHM_SP chx = AS_CHM_SP(x), chgx;      int *adims = INTEGER(GET_SLOT(x, Matrix_DimSym)), n = adims[0];
231      int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;      if(n != adims[1]) {
232            error(_("Csparse_general_to_symmetric(): matrix is not square!"));
233            return R_NilValue; /* -Wall */
234        }
235        CHM_SP chx = AS_CHM_SP__(x), chgx;
236        int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
237      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
238      R_CheckStack();      R_CheckStack();
   
239      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
240      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
241      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
# Line 138  Line 246 
246  {  {
247      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
248       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
249      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
250      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
251      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
252      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
# Line 156  Line 264 
264    
265  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
266  {  {
267      CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b);      CHM_SP
268      CHM_SP chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);          cha = AS_CHM_SP(a),
269      SEXP dn = allocVector(VECSXP, 2);          chb = AS_CHM_SP(b),
270            chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
271                                   /* values:= is_numeric (T/F) */ cha->xtype > 0,
272                                   /*out sorted:*/ 1, &c);
273        const char *cl_a = class_P(a), *cl_b = class_P(b);
274        char diag[] = {'\0', '\0'};
275        int uploT = 0;
276        SEXP dn = PROTECT(allocVector(VECSXP, 2));
277      R_CheckStack();      R_CheckStack();
278    
279    #ifdef DEBUG_Matrix_verbose
280        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
281    #endif
282    
283        /* Preserve triangularity and even unit-triangularity if appropriate.
284         * Note that in that case, the multiplication itself should happen
285         * faster.  But there's no support for that in CHOLMOD */
286    
287        /* UGLY hack -- rather should have (fast!) C-level version of
288         *       is(a, "triangularMatrix") etc */
289        if (cl_a[1] == 't' && cl_b[1] == 't')
290            /* FIXME: fails for "Cholesky","BunchKaufmann"..*/
291            if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
292                uploT = (*uplo_P(a) == 'U') ? 1 : -1;
293                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
294                    /* "remove the diagonal entries": */
295                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
296                    diag[0]= 'U';
297                }
298                else diag[0]= 'N';
299            }
300      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
301                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
302      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
303                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
304      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      UNPROTECT(1);
305        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
306  }  }
307    
308  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
309  {  {
310      int tr = asLogical(trans);      int tr = asLogical(trans);
311      CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b), chTr, chc;      CHM_SP
312      SEXP dn = allocVector(VECSXP, 2);          cha = AS_CHM_SP(a),
313            chb = AS_CHM_SP(b),
314            chTr, chc;
315        const char *cl_a = class_P(a), *cl_b = class_P(b);
316        char diag[] = {'\0', '\0'};
317        int uploT = 0;
318        SEXP dn = PROTECT(allocVector(VECSXP, 2));
319      R_CheckStack();      R_CheckStack();
320    
321      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
322      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
323                           0, cha->xtype, 1, &c);                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
324      cholmod_free_sparse(&chTr, &c);      cholmod_free_sparse(&chTr, &c);
325    
326        /* Preserve triangularity and unit-triangularity if appropriate;
327         * see Csparse_Csparse_prod() for comments */
328        if (cl_a[1] == 't' && cl_b[1] == 't')
329            if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
330                uploT = (*uplo_P(b) == 'U') ? 1 : -1;
331                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
332                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
333                    diag[0]= 'U';
334                }
335                else diag[0]= 'N';
336            }
337      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
338                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
339      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
340                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
341      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      UNPROTECT(1);
342        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
343  }  }
344    
345  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
346  {  {
347      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
348      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix2(b, // transpose_if_vector =
349                                                 cha->ncol == 1));
350      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
351      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
352                                          chb->xtype, &c);                                          chb->xtype, &c);
353      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
354      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
355        int nprot = 2;
356      R_CheckStack();      R_CheckStack();
357        /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
358        if(cha->xtype == CHOLMOD_PATTERN) {
359            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
360            /*        " --> slightly inefficient coercion")); */
361    
362            // This *fails* to produce a CHOLMOD_REAL ..
363            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
364            // --> use our Matrix-classes
365            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
366            cha = AS_CHM_SP(da);
367        }
368      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
369      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
370                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
371      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
372                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
373      UNPROTECT(2);      UNPROTECT(nprot);
374      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
375  }  }
376    
377  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
378  {  {
379      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
380      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix2(b, // transpose_if_vector =
381                                                 cha->nrow == 1));
382      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
383      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
384                                          chb->xtype, &c);                                          chb->xtype, &c);
385      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
386      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
387      R_CheckStack();      R_CheckStack();
388        // -- see Csparse_dense_prod() above :
389        if(cha->xtype == CHOLMOD_PATTERN) {
390            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
391            cha = AS_CHM_SP(da);
392        }
393      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
394      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
395                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
396      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
397                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
398      UNPROTECT(2);      UNPROTECT(nprot);
399      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
400  }  }
401    
402  /* Computes   x'x  or  x x'  -- see Csparse_Csparse_crossprod above for  x'y and x y' */  /* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
403       see Csparse_Csparse_crossprod above for  x'y and x y' */
404  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
405  {  {
406      int trip = asLogical(triplet),      int trip = asLogical(triplet),
407          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
408    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
409      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
410    #else /* workaround needed:*/
411        SEXP xx = PROTECT(Tsparse_diagU2N(x));
412        CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
413    #endif
414      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
415          chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c) : AS_CHM_SP(x);          chx = (trip ?
416                   cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
417                   AS_CHM_SP(x));
418      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
419      R_CheckStack();      R_CheckStack();
420    
421      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
422      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
423      if(!chcp) error(_("Csparse_crossprod(): error return from cholmod_aat()"));      if(!chcp) {
424            UNPROTECT(1);
425            error(_("Csparse_crossprod(): error return from cholmod_aat()"));
426        }
427      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
428      chcp->stype = 1;      chcp->stype = 1;
429      if (trip) cholmod_free_sparse(&chx, &c);      if (trip) cholmod_free_sparse(&chx, &c);
# Line 249  Line 432 
432                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
433                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
434      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
435    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
436      UNPROTECT(1);      UNPROTECT(1);
437    #else
438        UNPROTECT(2);
439    #endif
440      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
441  }  }
442    
443    /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
444    *  at least all "explicit" zeros */
445  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
446  {  {
447      CHM_SP chx = AS_CHM_SP(x);      const char *cl = class_P(x);
448        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
449        int tr = (cl[1] == 't');
450        CHM_SP chx = AS_CHM_SP__(x);
451      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
452      double dtol = asReal(tol);      double dtol = asReal(tol);
453      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 263  Line 455 
455    
456      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_drop(dtol, ans, &c))
457          error(_("cholmod_drop() failed"));          error(_("cholmod_drop() failed"));
458      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",     return chm_sparse_to_SEXP(ans, 1,
459                                  tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
460                                  Rkind, tr ? diag_P(x) : "",
461                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
462  }  }
463    
464  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
465  {  {
466      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
467      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
468            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
469            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
470      R_CheckStack();      R_CheckStack();
471    
472      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
473      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
474                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
475  }  }
476    
477  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
478  {  {
479      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
480      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
481            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
482            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
483      R_CheckStack();      R_CheckStack();
484    
485      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
486      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
487                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
488  }  }
489    
490  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
491  {  {
492      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
493      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
494      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
495      R_CheckStack();      R_CheckStack();
# Line 302  Line 500 
500    
501  SEXP Csparse_diagU2N(SEXP x)  SEXP Csparse_diagU2N(SEXP x)
502  {  {
503      if (*diag_P(x) != 'U') {/* "trivially fast" when there's no 'diag' slot at all */      const char *cl = class_P(x);
504        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
505        if (cl[1] != 't' || *diag_P(x) != 'U') {
506            /* "trivially fast" when not triangular (<==> no 'diag' slot),
507               or not *unit* triangular */
508          return (x);          return (x);
509      }      }
510      else {      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
511          CHM_SP chx = AS_CHM_SP(x);          CHM_SP chx = AS_CHM_SP__(x);
512          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
513          double one[] = {1, 0};          double one[] = {1, 0};
514          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
# Line 320  Line 522 
522      }      }
523  }  }
524    
525    SEXP Csparse_diagN2U(SEXP x)
526    {
527        const char *cl = class_P(x);
528        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
529        if (cl[1] != 't' || *diag_P(x) != 'N') {
530            /* "trivially fast" when not triangular (<==> no 'diag' slot),
531               or already *unit* triangular */
532            return (x);
533        }
534        else { /* triangular with diag='N'): now drop the diagonal */
535            /* duplicate, since chx will be modified: */
536            SEXP xx = PROTECT(duplicate(x));
537            CHM_SP chx = AS_CHM_SP__(xx);
538            int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
539                Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
540            R_CheckStack();
541    
542            chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
543    
544            SEXP ans = chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
545                                          uploT, Rkind, "U",
546                                          GET_SLOT(x, Matrix_DimNamesSym));
547            UNPROTECT(1);// only now !
548            return ans;
549        }
550    }
551    
552    /**
553     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
554     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
555     * @param x CsparseMatrix
556     * @param i row     indices (0-origin), or NULL (R's)
557     * @param j columns indices (0-origin), or NULL
558     *
559     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
560     */
561  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
562  {  {
563      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
564      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
565          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
566      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 333  Line 571 
571      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
572          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
573    
574      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,  #define CHM_SUB(_M_, _i_, _j_)                                  \
575                                                  INTEGER(j), csize,      cholmod_submatrix(_M_,                                      \
576                                                  TRUE, TRUE, &c),                        (rsize < 0) ? NULL : INTEGER(_i_), rsize, \
577                                1, 0, Rkind, "",                        (csize < 0) ? NULL : INTEGER(_j_), csize, \
578                                /* FIXME: drops dimnames */ R_NilValue);                        TRUE, TRUE, &c)
579        CHM_SP ans;
580        if (!chx->stype) {/* non-symmetric Matrix */
581            ans = CHM_SUB(chx, i, j);
582        }
583        else {
584            /* for now, cholmod_submatrix() only accepts "generalMatrix" */
585            CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
586            ans = CHM_SUB(tmp, i, j);
587            cholmod_free_sparse(&tmp, &c);
588        }
589    
590        // "FIXME": currently dropping dimnames, and adding them afterwards in R :
591        /* // dimnames: */
592        /* SEXP x_dns = GET_SLOT(x, Matrix_DimNamesSym), */
593        /*  dn = PROTECT(allocVector(VECSXP, 2)); */
594        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", /* dimnames: */ R_NilValue);
595    }
596    
597    #define _d_Csp_
598    #include "t_Csparse_subassign.c"
599    
600    #define _l_Csp_
601    #include "t_Csparse_subassign.c"
602    
603    #define _i_Csp_
604    #include "t_Csparse_subassign.c"
605    
606    #define _n_Csp_
607    #include "t_Csparse_subassign.c"
608    
609    #define _z_Csp_
610    #include "t_Csparse_subassign.c"
611    
612    
613    
614    SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
615    {
616        FILE *f = fopen(CHAR(asChar(fname)), "w");
617    
618        if (!f)
619            error(_("failure to open file \"%s\" for writing"),
620                  CHAR(asChar(fname)));
621        if (!cholmod_write_sparse(f, AS_CHM_SP(x),
622                                  (CHM_SP)NULL, (char*) NULL, &c))
623            error(_("cholmod_write_sparse returned error code"));
624        fclose(f);
625        return R_NilValue;
626    }
627    
628    
629    /**
630     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
631     * cholmod_sparse factor (LDL = TRUE).
632     *
633     * @param n  dimension of the matrix.
634     * @param x_p  'p' (column pointer) slot contents
635     * @param x_x  'x' (non-zero entries) slot contents
636     * @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
637     * @param resultKind a (SEXP) string indicating which kind of result is desired.
638     *
639     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
640     */
641    SEXP diag_tC_ptr(int n, int *x_p, double *x_x, Rboolean is_U, int *perm,
642    /*                                ^^^^^^ FIXME[Generalize] to int / ... */
643                     SEXP resultKind)
644    {
645        const char* res_ch = CHAR(STRING_ELT(resultKind,0));
646        enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log, min, max, range
647        } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
648                      ((!strcmp(res_ch, "sumLog")) ? sum_log :
649                       ((!strcmp(res_ch, "prod")) ? prod :
650                        ((!strcmp(res_ch, "min")) ? min :
651                         ((!strcmp(res_ch, "max")) ? max :
652                          ((!strcmp(res_ch, "range")) ? range :
653                           ((!strcmp(res_ch, "diag")) ? diag :
654                            ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
655                             -1))))))));
656        int i, n_x, i_from;
657        SEXP ans = PROTECT(allocVector(REALSXP,
658    /*                                 ^^^^  FIXME[Generalize] */
659                                       (res_kind == diag ||
660                                        res_kind == diag_backpermuted) ? n :
661                                       (res_kind == range ? 2 : 1)));
662        double *v = REAL(ans);
663    /*  ^^^^^^      ^^^^  FIXME[Generalize] */
664    
665        i_from = (is_U ? -1 : 0);
666    
667    #define for_DIAG(v_ASSIGN)                                      \
668        for(i = 0; i < n; i++) {                                    \
669            /* looking at i-th column */                            \
670            n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
671            if( is_U) i_from += n_x;                                \
672            v_ASSIGN;                                               \
673            if(!is_U) i_from += n_x;                                \
674        }
675    
676        /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
677         *            for uplo = "U" (makes sense with a "dtCMatrix" !),
678         *            should use  x_x[i_from + (n_x - 1)] instead of x_x[i_from],
679         *            where n_x = (x_p[i+1] - x_p[i])
680         */
681    
682        switch(res_kind) {
683        case trace: // = sum
684            v[0] = 0.;
685            for_DIAG(v[0] += x_x[i_from]);
686            break;
687    
688        case sum_log:
689            v[0] = 0.;
690            for_DIAG(v[0] += log(x_x[i_from]));
691            break;
692    
693        case prod:
694            v[0] = 1.;
695            for_DIAG(v[0] *= x_x[i_from]);
696            break;
697    
698        case min:
699            v[0] = R_PosInf;
700            for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from]);
701            break;
702    
703        case max:
704            v[0] = R_NegInf;
705            for_DIAG(if(v[0] < x_x[i_from]) v[0] = x_x[i_from]);
706            break;
707    
708        case range:
709            v[0] = R_PosInf;
710            v[1] = R_NegInf;
711            for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from];
712                     if(v[1] < x_x[i_from]) v[1] = x_x[i_from]);
713            break;
714    
715        case diag:
716            for_DIAG(v[i] = x_x[i_from]);
717            break;
718    
719        case diag_backpermuted:
720            for_DIAG(v[i] = x_x[i_from]);
721    
722            warning(_("%s = '%s' (back-permuted) is experimental"),
723                    "resultKind", "diagBack");
724            /* now back_permute : */
725            for(i = 0; i < n; i++) {
726                double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
727                /*^^^^ FIXME[Generalize] */
728            }
729            break;
730    
731        default: /* -1 from above */
732            error(_("diag_tC(): invalid 'resultKind'"));
733            /* Wall: */ ans = R_NilValue; v = REAL(ans);
734        }
735    
736        UNPROTECT(1);
737        return ans;
738    }
739    
740    /**
741     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
742     * cholmod_sparse factor (LDL = TRUE).
743     *
744     * @param obj -- now a cholmod_sparse factor or a dtCMatrix
745     * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
746     * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
747     * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
748     *                   only used for "diagBack"
749     * @param resultKind a (SEXP) string indicating which kind of result is desired.
750     *
751     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
752     */
753    SEXP diag_tC(SEXP obj, SEXP resultKind)
754    {
755    
756        SEXP
757            pslot = GET_SLOT(obj, Matrix_pSym),
758            xslot = GET_SLOT(obj, Matrix_xSym);
759        Rboolean is_U = (R_has_slot(obj, Matrix_uploSym) &&
760                         *CHAR(asChar(GET_SLOT(obj, Matrix_uploSym))) == 'U');
761        int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
762            *x_p  = INTEGER(pslot), pp = -1, *perm;
763        double *x_x = REAL(xslot);
764    /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
765    
766        if(R_has_slot(obj, Matrix_permSym))
767            perm = INTEGER(GET_SLOT(obj, Matrix_permSym));
768        else perm = &pp;
769    
770        return diag_tC_ptr(n, x_p, x_x, is_U, perm, resultKind);
771    }
772    
773    
774    /**
775     * Create a Csparse matrix object from indices and/or pointers.
776     *
777     * @param cls name of actual class of object to create
778     * @param i optional integer vector of length nnz of row indices
779     * @param j optional integer vector of length nnz of column indices
780     * @param p optional integer vector of length np of row or column pointers
781     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
782     * @param x optional vector of values
783     * @param nnz length of vectors i, j and/or x, whichever is to be used
784     * @param dims optional integer vector of length 2 to be used as
785     *     dimensions.  If dims == (int*)NULL then the maximum row and column
786     *     index are used as the dimensions.
787     * @param dimnames optional list of length 2 to be used as dimnames
788     * @param index1 indicator of 1-based indices
789     *
790     * @return an SEXP of class cls inheriting from CsparseMatrix.
791     */
792    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
793                        void* x, int nnz, int* dims, SEXP dimnames,
794                        int index1)
795    {
796        SEXP ans;
797        int *ij = (int*)NULL, *tri, *trj,
798            mi, mj, mp, nrow = -1, ncol = -1;
799        int xtype = -1;             /* -Wall */
800        CHM_TR T;
801        CHM_SP A;
802    
803        if (np < 0 || nnz < 0)
804            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
805                  np, nnz);
806        if (1 != ((mi = (i == (int*)NULL)) +
807                  (mj = (j == (int*)NULL)) +
808                  (mp = (p == (int*)NULL))))
809            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
810        if (mp) {
811            if (np) error(_("np = %d, must be zero when p is NULL"), np);
812        } else {
813            if (np) {               /* Expand p to form i or j */
814                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
815                for (int ii = 0; ii < np; ii++)
816                    if (p[ii] > p[ii + 1])
817                        error(_("p must be non-decreasing"));
818                if (p[np] != nnz)
819                    error("p[np] = %d != nnz = %d", p[np], nnz);
820                ij = Calloc(nnz, int);
821                if (mi) {
822                    i = ij;
823                    nrow = np;
824                } else {
825                    j = ij;
826                    ncol = np;
827                }
828                /* Expand p to 0-based indices */
829                for (int ii = 0; ii < np; ii++)
830                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
831            } else {
832                if (nnz)
833                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
834                          nnz);
835            }
836        }
837        /* calculate nrow and ncol */
838        if (nrow < 0) {
839            for (int ii = 0; ii < nnz; ii++) {
840                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
841                if (i1 < 1) error(_("invalid row index at position %d"), ii);
842                if (i1 > nrow) nrow = i1;
843            }
844        }
845        if (ncol < 0) {
846            for (int jj = 0; jj < nnz; jj++) {
847                int j1 = j[jj] + (index1 ? 0 : 1);
848                if (j1 < 1) error(_("invalid column index at position %d"), jj);
849                if (j1 > ncol) ncol = j1;
850            }
851        }
852        if (dims != (int*)NULL) {
853            if (dims[0] > nrow) nrow = dims[0];
854            if (dims[1] > ncol) ncol = dims[1];
855        }
856        /* check the class name */
857        if (strlen(cls) != 8)
858            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
859        if (!strcmp(cls + 2, "CMatrix"))
860            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
861        switch(cls[0]) {
862        case 'd':
863        case 'l':
864            xtype = CHOLMOD_REAL;
865        break;
866        case 'n':
867            xtype = CHOLMOD_PATTERN;
868            break;
869        default:
870            error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
871        }
872        if (cls[1] != 'g')
873            error(_("Only 'g'eneral sparse matrix types allowed"));
874        /* allocate and populate the triplet */
875        T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
876                                     xtype, &c);
877        T->x = x;
878        tri = (int*)T->i;
879        trj = (int*)T->j;
880        for (int ii = 0; ii < nnz; ii++) {
881            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
882            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
883        }
884        /* create the cholmod_sparse structure */
885        A = cholmod_triplet_to_sparse(T, nnz, &c);
886        cholmod_free_triplet(&T, &c);
887        /* copy the information to the SEXP */
888        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
889    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
890        /* allocate and copy common slots */
891        nnz = cholmod_nnz(A, &c);
892        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
893        dims[0] = A->nrow; dims[1] = A->ncol;
894        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
895        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
896        switch(cls[1]) {
897        case 'd':
898            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
899            break;
900        case 'l':
901            error(_("code not yet written for cls = \"lgCMatrix\""));
902        }
903    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
904        cholmod_free_sparse(&A, &c);
905        UNPROTECT(1);
906        return ans;
907  }  }

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