revert to c memory

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: raer
 Type: Package
 Title: RNA editing tools in R
-Version: 1.1.1
+Version: 1.1.2
 Authors@R: c(
     person("Kent", "Riemondy", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0750-1273")),

src/regfile.c

@@ -4,25 +4,16 @@
 
 static inline void free_regidx(void* payload) {
   payload_t* pld = *((payload_t**)payload);
-  if (pld->alt) R_Free(pld->alt); 
-  if (pld->ref) R_Free(pld->ref);
-  R_Free(pld);
+  if (pld->alt) free(pld->alt); 
+  if (pld->ref) free(pld->ref);
+  free(pld);
 }
 
-// use R memory handling for strdup
-static inline char * rstrdup(const char *x) {
-    char *buf;
-    size_t l = strlen(x) + 1;
-    buf = R_Calloc(l, char);
-    strcpy(buf, x);
-    return buf;
-} 
-
 static void load_payload(payload_t* pld, int strand, char* ref,
                          char* alt, int rowidx) {
   pld->strand = strand;
-  pld->alt = rstrdup(alt);
-  pld->ref = rstrdup(ref);
+  pld->alt = strdup(alt);
+  pld->ref = strdup(ref);
   pld->idx = rowidx;
 }
 
@@ -39,12 +30,14 @@ static regidx_t* regidx_load_payload(char** chroms, int* pos, int* strand,
   payload_t* pld;
   for (i = 0; i < n_sites; ++i) {
     chr_beg = chroms[i];
-    // use R memory management to avoid memory leak if index build has an error
-    pld = (payload_t*) R_Calloc(1, payload_t);
+    pld = (payload_t*) calloc(1, sizeof(payload_t));
     load_payload(pld, strand[i], ref[i], alt[i], rowidx[i]);
     hts_pos_t p = (hts_pos_t) pos[i] - 1; // convert 1 to 0 based
     ret = regidx_push(idx, chr_beg, chr_beg + strlen(chr_beg) - 1, p, p, &pld);
-    if (ret < 0) Rf_error("[raer internal] index push failed\n");
+    if (ret < 0) {
+        if(idx) regidx_destroy(idx);
+        Rf_error("[raer internal] index push failed\n");
+    }
   }
   return idx;
 }
@@ -61,7 +54,10 @@ static regidx_t* regidx_load_simple(char** chroms, int* start, int* end, int n_s
     hts_pos_t s = (hts_pos_t) start[i] - 1; // convert to 0 based
     hts_pos_t e = (hts_pos_t) end[i] - 1; // inclusive
     ret = regidx_push(idx, chr_beg, chr_beg + strlen(chr_beg) - 1, s, e, NULL);
-    if (ret < 0) Rf_error("[raer internal] index push failed\n");
+    if (ret < 0) {
+        if(idx) regidx_destroy(idx);
+        Rf_error("[raer internal] index push failed\n");
+    }
   }
   return idx;
 }