error: ‘str2int’ undeclared (first use in this function)

[grenaud]

I am getting the following error while building htslib:

      |         ^~~~~~~~
test/test_khash.c:53:18: error: ‘str2int’ undeclared (first use in this function)
   53 |     if (kh_stats(str2int, h, &empty, &deleted, &hist_size, &hist) == 0) {
      |                  ^~

But the rest seems to build.

[whitwham]

Could we have some more details? Like the compiler you are using, the version of htslib and the operating system?

[grenaud]

sure! It was a git clone done 3 days ago, c++ is c++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
Linux 6.8.0-51-generic
Ubuntu 24.04.1

[jkbonfield]

This looks like a missing khash init macro, possibly caused by forgetting to include htslib/kash_str2int.h. str2int here isn't a variable or a type, but a preprocessor token which is appended to the various khash functions.

#include "khash.h"

KHASH_MAP_INIT_STR(str2int, int)

/*
 *  Wrappers for khash dictionaries used by mpileup.
 */

static inline void *khash_str2int_init(void)
{
    return kh_init(str2int);
}
...

The KHASH_MAP_INIT_STR creates functions like kh_init_str2int which is what the kh_init(str2int) expands to.