@@ -118,7 +118,7 @@ configure:2948: result: yes

 configure:2948: checking for pow

 configure:2948: gcc -o conftest -g -O2   conftest.c -lz  >&5

 conftest.c:35: warning: conflicting types for built-in function 'pow'

-/tmp/ccxSNas5.o: In function `main':

+/tmp/cc2oJinr.o: In function `main':

 /home/dcjones/bio/seqbias/conftest.c:46: undefined reference to `pow'

 collect2: ld returned 1 exit status

 configure:2948: $? = 1

@@ -176,7 +176,7 @@ configure:2948: result: no

 configure:2948: checking for sqrt

 configure:2948: gcc -o conftest -g -O2   conftest.c -lz  >&5

 conftest.c:35: warning: conflicting types for built-in function 'sqrt'

-/tmp/ccFZLqEa.o: In function `main':

+/tmp/ccFdFAsw.o: In function `main':

 /home/dcjones/bio/seqbias/conftest.c:46: undefined reference to `sqrt'

 collect2: ld returned 1 exit status

 configure:2948: $? = 1

@@ -3,6 +3,7 @@

 #include "common.hpp"

 #include "miscmath.hpp"

 #include "logger.h"

+#include "snprintf.h"

 #include <string>

 #include <cstring>

@@ -1,6 +1,6 @@

-

 #include "logger.h"

+#include "snprintf.h"

 #include <R.h>

 #include <R_ext/Print.h>

@@ -11,6 +11,7 @@

 #include <stdarg.h>

 #include <stdbool.h>

+

 const char* INDENT = "  ";

 struct logger

@@ -6,6 +6,7 @@ extern "C" {

 #include "samtools/faidx.h"

 #include "samtools/faidx_t.h"

 #include "samtools/sam.h"

+#include "snprintf.h"

 #include <R.h>

 #include <Rinternals.h>

@@ -4,23 +4,23 @@

 #define PORTABLE_SNPRINTF_VERSION_MAJOR 2

 #define PORTABLE_SNPRINTF_VERSION_MINOR 2

-#ifdef HAVE_SNPRINTF

-#include <stdio.h>

-#else

-extern int snprintf(char *, size_t, const char *, /*args*/ ...);

-extern int vsnprintf(char *, size_t, const char *, va_list);

+#ifdef __cplusplus

+extern "C" {

 #endif

-#if defined(HAVE_SNPRINTF) && defined(PREFER_PORTABLE_SNPRINTF)

-extern int portable_snprintf(char *str, size_t str_m, const char *fmt, /*args*/ ...);

-extern int portable_vsnprintf(char *str, size_t str_m, const char *fmt, va_list ap);

-#define snprintf  portable_snprintf

-#define vsnprintf portable_vsnprintf

-#endif

+#include <stdarg.h>

+#include <stdio.h>

+#ifndef _GNU_SOURCE 

 extern int asprintf  (char **ptr, const char *fmt, /*args*/ ...);

 extern int vasprintf (char **ptr, const char *fmt, va_list ap);

 extern int asnprintf (char **ptr, size_t str_m, const char *fmt, /*args*/ ...);

 extern int vasnprintf(char **ptr, size_t str_m, const char *fmt, va_list ap);

+#endif

+

+

+#ifdef __cplusplus

+}

+#endif

 #endif