Replace strdup with xrl_strdup

src/Makefile.am

@@ -48,7 +48,9 @@ libprdata_la_SOURCES = \
 		 radrate.c \
 		 auger_trans.c \
 		 kissel_pe.c \
-	         cross_sections.c
+	         cross_sections.c \
+		 xraylib-aux.c \
+		 xraylib-aux.h 
 
 if !OS_WINDOWS
 libprdata_la_LIBADD = -lm

src/crystal_diffraction.c

@@ -156,7 +156,7 @@ Crystal_Struct* Crystal_MakeCopy (Crystal_Struct *crystal, xrl_error **error) {
   }
 
   *crystal_out = *crystal;
-  crystal_out->name = strdup(crystal->name);
+  crystal_out->name = xrl_strdup(crystal->name);
   n = crystal->n_atom * sizeof(Crystal_Atom);
   crystal_out->atom = malloc(n);
   if (crystal_out->atom == NULL) {
@@ -195,7 +195,7 @@ char** Crystal_GetCrystalsList(Crystal_Array *c_array, int *nCrystals, xrl_error
     return NULL;
   }
   for (i = 0 ; i < c_array->n_crystal ; i++)
-    rv[i] = strdup(c_array->crystal[i].name);
+    rv[i] = xrl_strdup(c_array->crystal[i].name);
 
   rv[c_array->n_crystal] = NULL;
 
@@ -587,7 +587,7 @@ int Crystal_ReadFile(const char* file_name, Crystal_Array* c_array, xrl_error **
     }
     crystal = &(c_array->crystal[c_array->n_crystal++]);
 
-    crystal->name = strdup(compound);
+    crystal->name = xrl_strdup(compound);
 
     /*
      * Parse lines of the crystal definition before list of atom positions.

src/xrayfiles.c

@@ -54,7 +54,7 @@ void XRayInit(void)
 
 
   for (i = 0 ; i < MENDEL_MAX ; i++) {
-		MendelArraySorted[i].name = strdup(MendelArray[i].name); 
+		MendelArraySorted[i].name = xrl_strdup(MendelArray[i].name); 
 		MendelArraySorted[i].Zatom = MendelArray[i].Zatom; 
 	}
 
@@ -296,7 +296,7 @@ void XRayInit(void)
         if (nerror_lines == 0) {
 	    	fprintf(stderr, "%s is not present in the linenames database: adjust xraylib-lines.h and xrayvars.c/h\n",line_name);
 		error_lines = malloc(sizeof(char *) * ++nerror_lines);
-		error_lines[0] = strdup(line_name);
+		error_lines[0] = xrl_strdup(line_name);
 	}
 	else {
 		found_error_line = 0;
@@ -309,7 +309,7 @@ void XRayInit(void)
 		if (!found_error_line) {
 	    		fprintf(stderr, "%s is not present in the linenames database: adjust xraylib-lines.h and xrayvars.c/h\n",line_name);
 			error_lines= (char **) realloc((char **) error_lines,sizeof(char *)*++nerror_lines);
-			error_lines[nerror_lines-1] = strdup(line_name);
+			error_lines[nerror_lines-1] = xrl_strdup(line_name);
 		}
 	}
     }
@@ -345,7 +345,7 @@ void XRayInit(void)
         if (nerror_lines == 0) {
 	    	fprintf(stderr,"%s is not present in the shellnames database: adjust xraylib-shells.h and xrayvars.c/h\n",shell_name);
 		error_lines = malloc(sizeof(char *) * ++nerror_lines);
-		error_lines[0] = strdup(shell_name);
+		error_lines[0] = xrl_strdup(shell_name);
 	}
 	else {
 		found_error_line = 0;
@@ -358,7 +358,7 @@ void XRayInit(void)
 		if (!found_error_line) {
 	    		fprintf(stderr,"%s is not present in the shellnames database: adjust xraylib-shells.h and xrayvars.c/h\n",shell_name);
 			error_lines= (char **) realloc((char **) error_lines,sizeof(char *)*++nerror_lines);
-			error_lines[nerror_lines-1] = strdup(shell_name);
+			error_lines[nerror_lines-1] = xrl_strdup(shell_name);
 		}
 	}
     }
@@ -456,7 +456,7 @@ void XRayInit(void)
         if (nerror_lines == 0) {
 	    	fprintf(stderr, "%s is not present in the linenames database: adjust xraylib-lines.h and xrayvars.c/h\n",line_name);
 		error_lines = malloc(sizeof(char *) * ++nerror_lines);
-		error_lines[0] = strdup(line_name);
+		error_lines[0] = xrl_strdup(line_name);
 	}
 	else {
 		found_error_line = 0;
@@ -469,7 +469,7 @@ void XRayInit(void)
 		if (!found_error_line) {
 	    		fprintf(stderr, "%s is not present in the linenames database: adjust xraylib-lines.h and xrayvars.c/h\n",line_name);
 			error_lines= (char **) realloc((char **) error_lines,sizeof(char *)*++nerror_lines);
-			error_lines[nerror_lines-1] = strdup(line_name);
+			error_lines[nerror_lines-1] = xrl_strdup(line_name);
 		}
 	}
     }
@@ -512,7 +512,7 @@ void XRayInit(void)
         if (nerror_lines == 0) {
 	    	fprintf(stderr, "%s is not present in the Auger transition names database: adjust xraylib-auger.h and xrayvars.c/h\n",auger_name);
 		error_lines = malloc(sizeof(char *) * ++nerror_lines);
-		error_lines[0] = strdup(auger_name);
+		error_lines[0] = xrl_strdup(auger_name);
 	}
 	else {
 		found_error_line = 0;
@@ -525,7 +525,7 @@ void XRayInit(void)
 		if (!found_error_line) {
 	    		fprintf(stderr, "%s is not present in the Auger transition names database: adjust xraylib-auger.h and xrayvars.c/h\n",auger_name);
 			error_lines= (char **) realloc((char **) error_lines,sizeof(char *)*++nerror_lines);
-			error_lines[nerror_lines-1] = strdup(auger_name);
+			error_lines[nerror_lines-1] = xrl_strdup(auger_name);
 		}
 	}
     }

src/xraylib-aux.c

@@ -1,5 +1,5 @@
 /*
-Copyright (c) 2010, Tom Schoonjans
+Copyright (c) 2010-2020, Tom Schoonjans
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -17,20 +17,28 @@ THIS SOFTWARE IS PROVIDED BY Tom Schoonjans ''AS IS'' AND ANY EXPRESS OR IMPLIED
 #include <string.h>
 
 #ifndef HAVE_STRDUP
-char *strdup(const char *str) {
+char *xrl_strdup(const char *str) {
 	char *dup= (char *)malloc( strlen(str)+1 );
 	if (dup) strcpy(dup,str);
 	return dup;
 }
+#else
+char *xrl_strdup(const char *str) {
+	return strdup(str);
+}
 #endif
 
 #ifndef HAVE_STRNDUP
-char *strndup(const char *str, size_t len) {
+char *xrl_strndup(const char *str, size_t len) {
 	char *dup= (char *)malloc( len+1 );
 	if (dup) {
 		strncpy(dup,str,len);
 		dup[len]= '\0';
 	}
 	return dup;
 }
+#else
+char *xrl_strndup(const char *str, size_t len) {
+	return strndup(str, len);
+}
 #endif

src/xraylib-aux.h

@@ -1,5 +1,5 @@
 /*
-Copyright (c) 2010, Tom Schoonjans
+Copyright (c) 2010-2020, Tom Schoonjans
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
@@ -14,25 +14,10 @@ THIS SOFTWARE IS PROVIDED BY Tom Schoonjans ''AS IS'' AND ANY EXPRESS OR IMPLIED
 #ifndef _XRAYLIB_AUX_H
 #define _XRAYLIB_AUX_H
 
-#include "config.h"
 #include <stddef.h>
 
-/*
- *
- *  The following two functions are ISO C extensions and are not available on all platforms.
- *  We will use our own functions if they are absent from libc.
- *
- */
-
-
-#ifndef HAVE_STRDUP
-extern char *strdup(const char *str);
-#endif
-
-#ifndef HAVE_STRNDUP
-extern char *strndup(const char *str, size_t len);
-#endif
-
+char *xrl_strdup(const char *str);
 
+char *xrl_strndup(const char *str, size_t len);
 
 #endif

src/xraylib-error.c

@@ -11,6 +11,7 @@ THIS SOFTWARE IS PROVIDED BY Tom Schoonjans 'AS IS' AND ANY EXPRESS OR IMPLIED W
 */
 
 #include "config.h"
+#include "xraylib-aux.h"
 #include "xraylib-error-private.h"
 #include <stdio.h>
 #include <stdlib.h>
@@ -77,7 +78,7 @@ xrl_error* xrl_error_new_literal(xrl_error_code code, const char *message) {
 
 	error = malloc(sizeof(xrl_error));
 	error->code = code;
-	error->message = strdup(message);
+	error->message = xrl_strdup(message);
 
 	return error;
 }
@@ -104,7 +105,7 @@ xrl_error* xrl_error_copy(const xrl_error *error) {
 
 	copy->message = NULL;
 	if (error->message)
-		copy->message = strdup(error->message);
+		copy->message = xrl_strdup(error->message);
 
 	return copy;
 }

src/xraylib-nist-compounds.c

@@ -48,7 +48,7 @@ struct compoundDataNIST *GetCompoundDataNISTByName(const char compoundString[],
 		xrl_set_error_literal(error, XRL_ERROR_INVALID_ARGUMENT, "compoundString cannot be NULL");
 		return NULL;
 	}
-	key->name = strdup(compoundString);
+	key->name = xrl_strdup(compoundString);
 
 
 #ifndef _WIN32
@@ -64,7 +64,7 @@ struct compoundDataNIST *GetCompoundDataNISTByName(const char compoundString[],
 	free(key->name);
 
 	if (rv != NULL) {
-		key->name = strdup(rv->name);
+		key->name = xrl_strdup(rv->name);
 		key->nElements = rv->nElements; 
 		key->Elements = malloc(sizeof(int)*rv->nElements);
 		memcpy(key->Elements, rv->Elements, sizeof(int)*rv->nElements);
@@ -93,7 +93,7 @@ struct compoundDataNIST *GetCompoundDataNISTByIndex(int compoundIndex, xrl_error
 		xrl_set_error(error, XRL_ERROR_MEMORY, MALLOC_ERROR, strerror(errno));
 		return NULL;
 	}
-	key->name = strdup(compoundDataNISTList[compoundIndex].name);
+	key->name = xrl_strdup(compoundDataNISTList[compoundIndex].name);
 	key->nElements = compoundDataNISTList[compoundIndex].nElements; 
 	key->Elements = malloc(sizeof(int)*compoundDataNISTList[compoundIndex].nElements);
 	memcpy(key->Elements, compoundDataNISTList[compoundIndex].Elements, sizeof(int)*compoundDataNISTList[compoundIndex].nElements);
@@ -118,7 +118,7 @@ char **GetCompoundDataNISTList(int *nCompounds, xrl_error **error) {
 	}
 
 	for (i = 0 ; i < nCompoundDataNISTList; i++)
-		rv[i] = strdup(compoundDataNISTList[i].name);
+		rv[i] = xrl_strdup(compoundDataNISTList[i].name);
 
 	rv[nCompoundDataNISTList] = NULL;
 

src/xraylib-parser.c

@@ -124,7 +124,7 @@ static int CompoundParserSimple(char compoundString[], struct compoundAtoms *ca,
 	for (i = 0 ; i < nuppers ; i++) {
 		if (islower(upper_locs[i][1]) && !islower(upper_locs[i][2])) {
 			/*second letter is lowercase and third one isn't -> valid */
-			tempElement = strndup(upper_locs[i],2);
+			tempElement = xrl_strndup(upper_locs[i],2);
 			/*get corresponding atomic number */
 			res = bsearch(tempElement, MendelArraySorted, MENDEL_MAX, sizeof(struct MendelElement), matchMendelElement);
 			if (res == NULL) {
@@ -147,7 +147,7 @@ static int CompoundParserSimple(char compoundString[], struct compoundAtoms *ca,
 				tempnAtoms = 1.0;
 			}
 			else {
-				tempSubstring = strndup(upper_locs[i] + 2, j - 2);
+				tempSubstring = xrl_strndup(upper_locs[i] + 2, j - 2);
 				tempnAtoms =  strtod(tempSubstring, &endPtr);
 				if (endPtr != tempSubstring+strlen(tempSubstring)) {
 					xrl_set_error(error, XRL_ERROR_INVALID_ARGUMENT, "Invalid chemical formula: could not convert subscript %s to a real number", tempSubstring);
@@ -165,7 +165,7 @@ static int CompoundParserSimple(char compoundString[], struct compoundAtoms *ca,
 		}
 		else if (!islower(upper_locs[i][1])) {
 			/*second letter is not lowercase -> valid */
-			tempElement = strndup(upper_locs[i], 1);
+			tempElement = xrl_strndup(upper_locs[i], 1);
 			/*get corresponding atomic number */
 			res = bsearch(tempElement, MendelArraySorted, MENDEL_MAX, sizeof(struct MendelElement), matchMendelElement);
 			if (res == NULL) {
@@ -188,7 +188,7 @@ static int CompoundParserSimple(char compoundString[], struct compoundAtoms *ca,
 				tempnAtoms = 1.0;
 			}
 			else {
-				tempSubstring = strndup(upper_locs[i] + 1, j - 1);
+				tempSubstring = xrl_strndup(upper_locs[i] + 1, j - 1);
 				tempnAtoms =  strtod(tempSubstring, &endPtr);
 				if (endPtr != tempSubstring + strlen(tempSubstring)) {
 					xrl_set_error(error, XRL_ERROR_INVALID_ARGUMENT, "Invalid chemical formula: could not convert subscript %s to a real number", tempSubstring);
@@ -241,7 +241,7 @@ static int CompoundParserSimple(char compoundString[], struct compoundAtoms *ca,
 	/*handle the brackets... */
 	for (i = 0 ; i < nbracket_pairs ; i++) {
 		tempBracketAtoms = malloc(sizeof(struct compoundAtoms));
-		tempBracketString = strndup(brackets_begin_locs[i]+1,(size_t) (brackets_end_locs[i]-brackets_begin_locs[i]-1));
+		tempBracketString = xrl_strndup(brackets_begin_locs[i]+1,(size_t) (brackets_end_locs[i]-brackets_begin_locs[i]-1));
 		tempBracketAtoms->nElements = 0;
 		tempBracketAtoms->singleElements = NULL;
 		/*recursive call */
@@ -265,7 +265,7 @@ static int CompoundParserSimple(char compoundString[], struct compoundAtoms *ca,
 			tempnAtoms = 1.0;
 		}
 		else {
-			tempSubstring = strndup(brackets_end_locs[i]+1,j-1);
+			tempSubstring = xrl_strndup(brackets_end_locs[i]+1,j-1);
 			tempnAtoms =  strtod(tempSubstring,&endPtr);
 			if (endPtr != tempSubstring+strlen(tempSubstring)) {
 				xrl_set_error(error, XRL_ERROR_INVALID_ARGUMENT, "Invalid chemical formula: could not convert subscript %s to a real number", tempSubstring);
@@ -337,7 +337,7 @@ struct compoundData* CompoundParser(const char compoundString[], xrl_error **err
 	/* the locale is changed to default locale because we'll be using strtod later on */
 	backup_locale = setlocale(LC_NUMERIC, "C");
 
-	compoundStringCopy = strdup(compoundString);
+	compoundStringCopy = xrl_strdup(compoundString);
 
 	rvCPS = CompoundParserSimple(compoundStringCopy, &ca, error);
 
@@ -458,7 +458,7 @@ char *AtomicNumberToSymbol(int Z, xrl_error **error) {
 		return NULL;
 	}
 
-	return strdup(MendelArray[Z-1].name);
+	return xrl_strdup(MendelArray[Z-1].name);
 }
 
 int SymbolToAtomicNumber(const char *symbol, xrl_error **error) {

src/xraylib-radionuclides.c

@@ -52,7 +52,7 @@ struct radioNuclideData *GetRadioNuclideDataByName(const char radioNuclideString
 		xrl_set_error_literal(error, XRL_ERROR_INVALID_ARGUMENT, "radioNuclideString cannot be NULL");
 		return NULL;
 	}
-	key->name = strdup(radioNuclideString);
+	key->name = xrl_strdup(radioNuclideString);
 
 #ifndef _WIN32
 	nelp = nNuclideDataList;
@@ -66,7 +66,7 @@ struct radioNuclideData *GetRadioNuclideDataByName(const char radioNuclideString
 	free(key->name);
 
 	if (rv != NULL) {
-		key->name = strdup(rv->name);
+		key->name = xrl_strdup(rv->name);
 		key->Z = rv->Z; 
 		key->A = rv->A; 
 		key->N = rv->N; 
@@ -104,7 +104,7 @@ struct radioNuclideData *GetRadioNuclideDataByIndex(int radioNuclideIndex, xrl_e
 		xrl_set_error(error, XRL_ERROR_MEMORY, MALLOC_ERROR, strerror(errno));
 		return NULL;
 	}
-	key->name = strdup(nuclideDataList[radioNuclideIndex].name);
+	key->name = xrl_strdup(nuclideDataList[radioNuclideIndex].name);
 	key->Z = nuclideDataList[radioNuclideIndex].Z; 
 	key->A = nuclideDataList[radioNuclideIndex].A; 
 	key->N = nuclideDataList[radioNuclideIndex].N; 
@@ -137,7 +137,7 @@ char **GetRadioNuclideDataList(int *nRadioNuclides, xrl_error **error) {
 	}
 
 	for (i = 0 ; i < nNuclideDataList; i++)
-		rv[i] = strdup(nuclideDataList[i].name);
+		rv[i] = xrl_strdup(nuclideDataList[i].name);
 
 	rv[nNuclideDataList] = NULL;
 

tests/test-crystal_diffraction.c

@@ -13,6 +13,7 @@ THIS SOFTWARE IS PROVIDED BY Tom Schoonjans ''AS IS'' AND ANY EXPRESS OR IMPLIED
 
 #include <config.h>
 #include "xraylib.h"
+#include "xraylib-aux.h"
 #include "xraylib-error-private.h"
 #ifdef NDEBUG
   #undef NDEBUG
@@ -119,7 +120,7 @@ int main(int argc, char **argv) {
 	assert(error == NULL);
 	assert(cs_copy != NULL);
 	free(cs_copy->name);
-	cs_copy->name = strdup("Diamond-copy");
+	cs_copy->name = xrl_strdup("Diamond-copy");
 
 	rv = Crystal_AddCrystal(cs, NULL, &error);
 	assert(rv == 0);