The interesting part is

configure:3744: gcc    conftest.c  >&5
/tmp/ccr38YUW.s: Assembler messages:
/tmp/ccr38YUW.s:8: Error: unsupported instruction `push'
/tmp/ccr38YUW.s:11: Error: unsupported instruction `movq'
/tmp/ccr38YUW.s:14: Error: unsupported instruction `pop'
configure:3748: $? = 1

I've never seen this, and my best guess is indeed that the compiler setup is broken (emitting assembly for another arch?). Can you try manually building the same thing the same way (e.g. just gcc file.c)?

$ cd /tmp
$ cat > conftest.c <<EOF
/* confdefs.h */
#define PACKAGE_NAME "Geany"
#define PACKAGE_TARNAME "geany"
#define PACKAGE_VERSION "1.35"
#define PACKAGE_STRING "Geany 1.35"
#define PACKAGE_BUGREPORT "https://github.com/geany/geany/issues"
#define PACKAGE_URL ""
#define PACKAGE "geany"
#define VERSION "1.35"
/* end confdefs.h.  */

int
main ()
{

  ;
  return 0;
}
EOF
$ gcc conftest.c

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