Define STRICT_R_HEADERS, use R_{Calloc,Realloc,Free}

src/Makevars

@@ -0,0 +1 @@
+PKG_CPPFLAGS = -DSTRICT_R_HEADERS

src/Makevars.win

@@ -0,0 +1 @@
+PKG_CPPFLAGS = -DSTRICT_R_HEADERS

src/ldc_ad2cp_in_file.cpp

@@ -206,11 +206,11 @@ List do_ldc_ad2cp_in_file(CharacterVector filename, IntegerVector from, IntegerV
  unsigned short header_checksum;
  } header;
  unsigned int dbuflen = 10000; // may be increased later
- unsigned char *dbuf = (unsigned char *)Calloc((size_t)dbuflen, unsigned char);
+ unsigned char *dbuf = (unsigned char *)R_Calloc((size_t)dbuflen, unsigned char);
  unsigned int nchunk = 100000;
- unsigned int *index_buf = (unsigned int*)Calloc((size_t)nchunk, unsigned int);
- unsigned int *length_buf = (unsigned int*)Calloc((size_t)nchunk, unsigned int);
- unsigned int *id_buf = (unsigned int*)Calloc((size_t)nchunk, unsigned int);
+ unsigned int *index_buf = (unsigned int*)R_Calloc((size_t)nchunk, unsigned int);
+ unsigned int *length_buf = (unsigned int*)R_Calloc((size_t)nchunk, unsigned int);
+ unsigned int *id_buf = (unsigned int*)R_Calloc((size_t)nchunk, unsigned int);
  int early_EOF = 0;
  int reset_cindex = 0; // set to 1 if we skipped to find a new header start, after a bad checksum
  while (chunk < to_value) { // FIXME: use whole file here
@@ -220,9 +220,9 @@ List do_ldc_ad2cp_in_file(CharacterVector filename, IntegerVector from, IntegerV
  if (debug)
  Rprintf(" increasing 'index_buf' size from %d", nchunk);
  nchunk = (unsigned int) floor(chunk * 1.4); // increase buffer size by sqrt(2)
- index_buf = (unsigned int*)Realloc(index_buf, nchunk, unsigned int);
- length_buf = (unsigned int*)Realloc(length_buf, nchunk, unsigned int);
- id_buf = (unsigned int*)Realloc(id_buf, nchunk, unsigned int);
+ index_buf = (unsigned int*)R_Realloc(index_buf, nchunk, unsigned int);
+ length_buf = (unsigned int*)R_Realloc(length_buf, nchunk, unsigned int);
+ id_buf = (unsigned int*)R_Realloc(id_buf, nchunk, unsigned int);
  if (debug)
  Rprintf(" to %d\n", nchunk);
  }
@@ -311,7 +311,7 @@ List do_ldc_ad2cp_in_file(CharacterVector filename, IntegerVector from, IntegerV
  Rprintf(" *BUG*: cindex is out of synch with ftell()\n");
 
  dbuflen = header.data_size;
- dbuf = (unsigned char *)Realloc(dbuf, dbuflen, unsigned char);
+ dbuf = (unsigned char *)R_Realloc(dbuf, dbuflen, unsigned char);
  }
  // Read the data
  bytes_read = fread(dbuf, 1, header.data_size, fp);
@@ -402,9 +402,9 @@ List do_ldc_ad2cp_in_file(CharacterVector filename, IntegerVector from, IntegerV
  length[i] = length_buf[i];
  id[i] = id_buf[i];
  }
- Free(index_buf);
- Free(length_buf);
- Free(id_buf);
+ R_Free(index_buf);
+ R_Free(length_buf);
+ R_Free(id_buf);
  if (debug)
  Rprintf("} # do_ldc_ad2cp_in_file()\n");
  return(List::create(Named("index")=index,

src/ldc_rdi_in_file.cpp

@@ -226,7 +226,7 @@ List do_ldc_rdi_in_file(StringVector filename, IntegerVector from, IntegerVector
  // 'obuf' is a growable C buffer to hold the output, which eventually
  // gets saved in the R item "buf".
  unsigned long int nobuf = 100000; // BUFFER SIZE
- unsigned char *obuf = (unsigned char *)Calloc((size_t)nobuf, unsigned char);
+ unsigned char *obuf = (unsigned char *)R_Calloc((size_t)nobuf, unsigned char);
  unsigned long int iobuf = 0;
 
  // 'ensembles', 'times' and 'sec100s' are growable buffers of equal length, with one
@@ -237,12 +237,12 @@ List do_ldc_rdi_in_file(StringVector filename, IntegerVector from, IntegerVector
  // Note that we do not check the Calloc() results because the R docs say that
  // Calloc() performs its won tests, and that R will handle any problems.
  unsigned long int nensembles = 100000; // BUFFER SIZE
- unsigned int *ensemble_in_files = (unsigned int *)Calloc((size_t)nensembles, unsigned int);
- int *ensembles = (int *)Calloc((size_t)nensembles, int);
- int *times = (int *)Calloc((size_t)nensembles, int);
- int *sec100s = (int *)Calloc((size_t)nensembles, int);
+ unsigned int *ensemble_in_files = (unsigned int *)R_Calloc((size_t)nensembles, unsigned int);
+ int *ensembles = (int *)R_Calloc((size_t)nensembles, int);
+ int *times = (int *)R_Calloc((size_t)nensembles, int);
+ int *sec100s = (int *)R_Calloc((size_t)nensembles, int);
  unsigned long int nebuf = 50000; // BUFFER SIZE
- unsigned char *ebuf = (unsigned char *)Calloc((size_t)nebuf, unsigned char);
+ unsigned char *ebuf = (unsigned char *)R_Calloc((size_t)nebuf, unsigned char);
 
  unsigned long int in_ensemble = 1, out_ensemble = 0;
  int b1, b2;
@@ -291,10 +291,10 @@ List do_ldc_rdi_in_file(StringVector filename, IntegerVector from, IntegerVector
  if (debug_value > 0)
  Rprintf("\nbytes_to_check=%d based on b1=%d(0x%02x) and b2=%d(0x%02x)\n", bytes_to_check, b1, b1, b2, b2);
  if (bytes_to_check < 5) { // this will only happen in error; we check so bytes_to_read won't be crazy
- Free(ensembles);
- Free(times);
- Free(sec100s);
- Free(ebuf);
+ R_Free(ensembles);
+ R_Free(times);
+ R_Free(sec100s);
+ R_Free(ebuf);
  ::Rf_error("cannot decode the length of ensemble number %d", in_ensemble);
  }
  if (bytes_to_check < 4)
@@ -305,7 +305,7 @@ List do_ldc_rdi_in_file(StringVector filename, IntegerVector from, IntegerVector
  if (bytes_to_read > nebuf) {
  if (debug_value > 0)
  Rprintf("Increasing 'ebuf' buffer size from %d bytes to %d bytes\n", nebuf, bytes_to_read);
- ebuf = (unsigned char *)Realloc(ebuf, bytes_to_read, unsigned char);
+ ebuf = (unsigned char *)R_Realloc(ebuf, bytes_to_read, unsigned char);
  nebuf = bytes_to_read;
  }
  // Read the bytes in one operation, because fgetc() is too slow.
@@ -351,10 +351,10 @@ List do_ldc_rdi_in_file(StringVector filename, IntegerVector from, IntegerVector
  nensembles = 3 * nensembles / 2;
  if (debug_value > -1)
  Rprintf("Increasing ensembles,times,sec100s storage to %d elements ...\n", nensembles);
- ensemble_in_files = (unsigned int *) Realloc(ensemble_in_files, nensembles, unsigned int);
- ensembles = (int *) Realloc(ensembles, nensembles, int);
- times = (int *) Realloc(times, nensembles, int);
- sec100s = (int *)Realloc(sec100s, nensembles, int);
+ ensemble_in_files = (unsigned int *) R_Realloc(ensemble_in_files, nensembles, unsigned int);
+ ensembles = (int *) R_Realloc(ensembles, nensembles, int);
+ times = (int *) R_Realloc(times, nensembles, int);
+ sec100s = (int *)R_Realloc(sec100s, nensembles, int);
  }
  // We will decide whether to keep this ensemble, based on ensemble
  // number, if mode_value==0 or on time, if mode_value==1. That
@@ -407,7 +407,7 @@ List do_ldc_rdi_in_file(StringVector filename, IntegerVector from, IntegerVector
  nobuf = nobuf + 100 + bytes_to_read + nobuf / 2;
  if (debug_value > 0)
  Rprintf("about to enlarge obuf storage to %d elements ...\n", nobuf);
- obuf = (unsigned char *)Realloc(obuf, nobuf, unsigned char);
+ obuf = (unsigned char *)R_Realloc(obuf, nobuf, unsigned char);
  if (debug_value > 0)
  Rprintf(" ... allocation was successful\n");
  }
@@ -540,15 +540,15 @@ List do_ldc_rdi_in_file(StringVector filename, IntegerVector from, IntegerVector
  sec100[i] = sec100s[i];
  //Rprintf("i=%d ensemble=%d time=%d sec100=%d\n", i, ensemble[i], time[i], (int)sec100[i]);
  }
- Free(ensemble_in_files);
- Free(ensembles);
- Free(times);
- Free(sec100s);
- Free(ebuf);
+ R_Free(ensemble_in_files);
+ R_Free(ensembles);
+ R_Free(times);
+ R_Free(sec100s);
+ R_Free(ebuf);
  for (unsigned long int i = 0; i < iobuf; i++) {
  buf[i] = obuf[i];
  }
- Free(obuf);
+ R_Free(obuf);
  if (debug_value > 0)
  Rprintf("Returning from C++ function named do_ldc_rdi_in_file.\n");
  return(List::create(Named("ensembleStart")=ensemble, Named("time")=time,

src/map.c

@@ -242,8 +242,8 @@ SEXP map_check_polygons(SEXP x, SEXP y, SEXP z, SEXP xokspan, SEXP usr) // retur
  if (j > (clen - 2)) { \
  /*Rprintf("INCREASE storage from %d to %d [a]\n", clen, (int)(100 + clen));*/ \
  clen += 100; \
- xbp = (double*)Realloc(xbp, clen, double); \
- ybp = (double*)Realloc(ybp, clen, double); \
+ xbp = (double*)R_Realloc(xbp, clen, double); \
+ ybp = (double*)R_Realloc(ybp, clen, double); \
  } \
  j++;
 
@@ -268,8 +268,8 @@ SEXP map_clip_xy_OLD_BROKEN(SEXP x, SEXP y, SEXP usr) // returns list with new x
  error("must have at least two 'x' and 'y' pairs");
  // xbp and xbp are growable buffers
  int clen = xlen + 100; // the 100 may save reallocs
- double *xbp = (double*)Calloc((size_t)clen, double);
- double *ybp = (double*)Calloc((size_t)clen, double);
+ double *xbp = (double*)R_Calloc((size_t)clen, double);
+ double *ybp = (double*)R_Calloc((size_t)clen, double);
 #ifdef DEBUG
  double distMIN = 10e6; // FIXME: temporary to find problem in Greenland
 #endif
@@ -388,8 +388,8 @@ SEXP map_clip_xy(SEXP x, SEXP y, SEXP usr) // returns list with new x and y vect
  error("must have at least two 'x' and 'y' pairs");
  // xb and yb are growable buffers; we copy to xc and yc near the end.
  int clen = xlen + 100; // the 100 may save reallocs
- double *xbp = (double*)Calloc((size_t)clen, double);
- double *ybp = (double*)Calloc((size_t)clen, double);
+ double *xbp = (double*)R_Calloc((size_t)clen, double);
+ double *ybp = (double*)R_Calloc((size_t)clen, double);
 #ifdef DEBUG
  double distMIN = 10e6; // FIXME: temporary to find problem in Greenland
 #endif