Use recommended R_ prefixed versions of Calloc,Realloc,Free (#6382)

* Use recommended R_ prefixed versions of Calloc,Realloc,Free

* Also remove !defined(R_VERSION) guard

inst/tests/tests.Rraw

@@ -13178,7 +13178,7 @@ options(datatable.use.index=FALSE)
 test(1942.10, DT[,sum(v),keyby=id1,verbose=TRUE], data.table(id1=c("D","A","C"), V1=INT(1,6,8), key="id1"), output="Finding groups using forderv")
 options(datatable.use.index=TRUE)
 
-# test coverage in uniqlist.c of Realloc when over initial 1000 uniqs, and use double to cover numeric tolerance (both in one-column case and >1 column branch)
+# test coverage in uniqlist.c of R_Realloc when over initial 1000 uniqs, and use double to cover numeric tolerance (both in one-column case and >1 column branch)
 set.seed(2)
 DT = data.table(real=sample((1:1500)/1000, 10000, replace=TRUE), id=sample(letters, 1000, replace=TRUE), value=1:10000)
 setkey(DT,id,real)

src/bmerge.c

@@ -130,9 +130,9 @@ SEXP bmerge(SEXP idt, SEXP xdt, SEXP icolsArg, SEXP xcolsArg, SEXP xoArg, SEXP r
   if (nqmaxgrp>1 && mult == ALL) {
     // non-equi case with mult=ALL, may need reallocation
     anslen = 1.1 * ((iN > 1000) ? iN : 1000);
-    retFirst = Calloc(anslen, int); // anslen is set above
-    retLength = Calloc(anslen, int);
-    retIndex = Calloc(anslen, int);
+    retFirst = R_Calloc(anslen, int); // anslen is set above
+    retLength = R_Calloc(anslen, int);
+    retIndex = R_Calloc(anslen, int);
     // initialise retIndex here directly, as next loop is meant for both equi and non-equi joins
     for (int j=0; j<anslen; j++) retIndex[j] = j+1;
   } else { // equi joins (or) non-equi join but no multiple matches
@@ -215,9 +215,9 @@ SEXP bmerge(SEXP idt, SEXP xdt, SEXP icolsArg, SEXP xcolsArg, SEXP xoArg, SEXP r
   SET_STRING_ELT(ansnames, 4, char_allGrp1);
   setAttrib(ans, R_NamesSymbol, ansnames);
   if (nqmaxgrp > 1 && mult == ALL) {
-    Free(retFirst);
-    Free(retLength);
-    Free(retIndex);
+    R_Free(retFirst);
+    R_Free(retLength);
+    R_Free(retIndex);
   }
   if (verbose)
     Rprintf("bmerge: took %.3fs\n", omp_get_wtime()-tic);
@@ -416,9 +416,9 @@ void bmerge_r(int xlowIn, int xuppIn, int ilowIn, int iuppIn, int col, int thisg
               ++ctr;
               if (ctr+ilen >= anslen) {
                 anslen = 1.1*anslen;
-                retFirst = Realloc(retFirst, anslen, int);   // if fails, it fails inside Realloc with R error
-                retLength = Realloc(retLength, anslen, int);
-                retIndex = Realloc(retIndex, anslen, int);
+                retFirst = R_Realloc(retFirst, anslen, int);   // if fails, it fails inside R_Realloc with R error
+                retLength = R_Realloc(retLength, anslen, int);
+                retIndex = R_Realloc(retIndex, anslen, int);
               }
             } else if (mult == FIRST) {
               retFirst[k] = (XIND(retFirst[k]-1) > XIND(xlow+1)) ? xlow+2 : retFirst[k];

src/data.table.h

@@ -2,12 +2,15 @@
 #include "dt_stdio.h"  // PRId64 and PRIu64
 #include <R.h>
 #include <Rversion.h>
-#if !defined(R_VERSION) || R_VERSION < R_Version(3, 5, 0)  // R-exts$6.14
+#if R_VERSION < R_Version(3, 5, 0)  // R-exts$6.14
 #  define ALTREP(x) 0     // #2866
 #  define USE_RINTERNALS  // #3301
 #  define DATAPTR_RO(x) ((const void *)DATAPTR(x))
+#  define R_Calloc(x, y) Calloc(x, y)         // #6380
+#  define R_Realloc(x, y, z) Realloc(x, y, z)
+#  define R_Free(x) Free(x)
 #endif
-#if !defined(R_VERSION) || R_VERSION < R_Version(3, 4, 0)
+#if R_VERSION < R_Version(3, 4, 0)
 #  define SET_GROWABLE_BIT(x)  // #3292
 #endif
 #include <Rinternals.h>

src/forder.c

@@ -65,7 +65,7 @@ static char msg[1001];
 /* Using OS realloc() in this file to benefit from (often) in-place realloc() to save copy
  * We have to trap on exit anyway to call savetl_end().
  * NB: R_alloc() would be more convenient (fails within) and robust (auto free) but there is no R_realloc(). Implementing R_realloc() would be an alloc and copy, iiuc.
- *     Calloc/Realloc needs to be Free'd, even before error() [R-exts$6.1.2]. An oom within Calloc causes a previous Calloc to leak so Calloc would still needs to be trapped anyway.
+ *     R_Calloc/R_Realloc needs to be R_Free'd, even before error() [R-exts$6.1.2]. An oom within R_Calloc causes a previous R_Calloc to leak so R_Calloc would still needs to be trapped anyway.
  * Therefore, using <<if (!malloc()) STOP(_("helpful context msg"))>> approach to cleanup() on error.
  */
 

src/ijoin.c

@@ -141,7 +141,7 @@ SEXP lookup(SEXP ux, SEXP xlen, SEXP indices, SEXP gaps, SEXP overlaps, SEXP mul
     Rprintf(_("Second pass on allocation in lookup ... done in %8.3f seconds\n"), 1.0*(pass2)/CLOCKS_PER_SEC);
   // generate lookup
   start = clock();
-  idx = Calloc(uxrows, R_len_t); // resets bits, =0
+  idx = R_Calloc(uxrows, R_len_t); // resets bits, =0
   switch (type) {
   case ANY: case START: case END: case WITHIN:
     for (int i=0; i<xrows; ++i) {
@@ -159,7 +159,7 @@ SEXP lookup(SEXP ux, SEXP xlen, SEXP indices, SEXP gaps, SEXP overlaps, SEXP mul
     break;
   default: error(_("Internal error: unknown type lookup should have been caught earlier: %d"), type); // #nocov
   }
-  Free(idx);
+  R_Free(idx);
   // generate type_lookup
   if (type != WITHIN) {
     switch (mult) {
@@ -249,7 +249,7 @@ SEXP overlaps(SEXP ux, SEXP imatches, SEXP multArg, SEXP typeArg, SEXP nomatchAr
   else if (!strcmp(CHAR(STRING_ELT(typeArg, 0)), "equal")) type = EQUAL;
   else error(_("Internal error: invalid value for 'type'; this should have been caught before. please report to data.table issue tracker")); // # nocov
 
-  // As a first pass get the final length, so that we can allocate up-front and not deal with Calloc + Realloc + size calculation hassle
+  // As a first pass get the final length, so that we can allocate up-front and not deal with R_Calloc + R_Realloc + size calculation hassle
   // Checked the time for this loop on realisitc data (81m reads) and took 0.27 seconds! No excuses ;).
   start = clock();
   if (mult == ALL) {

src/init.c

@@ -352,7 +352,7 @@ SEXP hasOpenMP(void) {
 SEXP beforeR340(void) {
   // used in onAttach.R for message about fread memory leak fix needing R 3.4.0
   // at C level to catch if user upgrades R but does not reinstall data.table
-  #if defined(R_VERSION) && R_VERSION<R_Version(3,4,0)
+  #if R_VERSION < R_Version(3,4,0)
   return ScalarLogical(true);
   #else
   return ScalarLogical(false);

src/uniqlist.c

@@ -22,7 +22,7 @@ SEXP uniqlist(SEXP l, SEXP order)
   unsigned long long *ulv; // for numeric check speed-up
   SEXP v, ans;
   R_len_t len, thisi, previ, isize=1000;
-  int *iidx = Calloc(isize, int); // for 'idx'
+  int *iidx = R_Calloc(isize, int); // for 'idx'
   len = 1;
   iidx[0] = 1; // first row is always the first of the first group
 
@@ -45,7 +45,7 @@ SEXP uniqlist(SEXP l, SEXP order)
           iidx[len++] = i+1;                                                     \
           if (len>=isize) {                                                      \
             isize = MIN(nrow, (size_t)(1.1*(double)isize*((double)nrow/i)));     \
-            iidx = Realloc(iidx, isize, int);                                    \
+            iidx = R_Realloc(iidx, isize, int);                                    \
           }                                                                      \
         }                                                                        \
         prev = elem;                                                             \
@@ -134,14 +134,14 @@ SEXP uniqlist(SEXP l, SEXP order)
         iidx[len++] = i+1;
         if (len >= isize) {
           isize = MIN(nrow, (size_t)(1.1*(double)isize*((double)nrow/i)));
-          iidx = Realloc(iidx, isize, int);
+          iidx = R_Realloc(iidx, isize, int);
         }
       }
     }
   }
   PROTECT(ans = allocVector(INTSXP, len));
   memcpy(INTEGER(ans), iidx, sizeof(int)*len); // sizeof is of type size_t - no integer overflow issues
-  Free(iidx);
+  R_Free(iidx);
   UNPROTECT(1);
   return(ans);
 }
@@ -259,7 +259,7 @@ SEXP nestedid(SEXP l, SEXP cols, SEXP order, SEXP grps, SEXP resetvals, SEXP mul
   R_len_t nrows = length(VECTOR_ELT(l,0)), ncols = length(cols);
   if (nrows==0) return(allocVector(INTSXP, 0));
   R_len_t thisi, previ, ansgrpsize=1000, nansgrp=0;
-  R_len_t *ansgrp = Calloc(ansgrpsize, R_len_t), starts, grplen; // #3401 fix. Needs to be Calloc due to Realloc below .. else segfaults.
+  R_len_t *ansgrp = R_Calloc(ansgrpsize, R_len_t), starts, grplen; // #3401 fix. Needs to be R_Calloc due to R_Realloc below .. else segfaults.
   R_len_t ngrps = length(grps);
   bool *i64 = (bool *)R_alloc(ncols, sizeof(bool));
   if (ngrps==0) error(_("Internal error: nrows[%d]>0 but ngrps==0"), nrows); // # nocov
@@ -335,14 +335,14 @@ SEXP nestedid(SEXP l, SEXP cols, SEXP order, SEXP grps, SEXP resetvals, SEXP mul
     }
     if (nansgrp >= ansgrpsize) {
       ansgrpsize = MIN(nrows, (size_t)(1.1*(double)ansgrpsize*((double)nrows/i)));
-      ansgrp = Realloc(ansgrp, ansgrpsize, int);
+      ansgrp = R_Realloc(ansgrp, ansgrpsize, int);
     }
     for (int j=0; j<grplen; j++) {
       ians[byorder ? INTEGER(order)[igrps[i]-1+j]-1 : igrps[i]-1+j] = tmp+1;
     }
     ansgrp[tmp] = thisi;
   }
-  Free(ansgrp);
+  R_Free(ansgrp);
   UNPROTECT(1);
   return(ans);
 }