Add HTS_FORMAT checks to a variety of places.

These are needed in newer clangs with -Wformat=2.

Author: jkbonfield

.cirrus.yml

@@ -113,7 +113,7 @@ ubuntu_task:
     - environment:
        # Cirrus-CI's clang isn't installed with ubsan, so we do that in gcc
        USE_CONFIG: yes
-       CFLAGS: -std=c99 -pedantic -Wformat -g -Wall -O3
+       CFLAGS: -std=c99 -pedantic -Wformat -Wformat=2 -g -Wall -O3
        USE_LIBDEFLATE: yes
 
   # NB: we could consider building a docker image with these

bgzip.c

@@ -48,7 +48,7 @@
 
 static const int WINDOW_SIZE = BGZF_BLOCK_SIZE;
 
-static void error(const char *format, ...)
+static void HTS_FORMAT(HTS_PRINTF_FMT, 1, 2) error(const char *format, ...)
 {
     va_list ap;
     va_start(ap, format);
@@ -689,7 +689,7 @@ int main(int argc, char **argv)
                     if ( bgzf_index_load(fp, argv[optind], ".gzi") < 0 )
                         error("Could not load index: %s.gzi\n", argv[optind]);
                 }
-                if ( bgzf_useek(fp, start, SEEK_SET) < 0 ) error("Could not seek to %d-th (uncompressd) byte\n", start);
+                if ( bgzf_useek(fp, start, SEEK_SET) < 0 ) error("Could not seek to %ld-th (uncompressd) byte\n", start);
             }
 
             if (threads > 1)

htsfile.c

@@ -46,7 +46,7 @@ int show_headers = 1;
 int verbose = 0;
 int status = EXIT_SUCCESS;  /* Exit status from main */
 
-void error(const char *format, ...)
+void HTS_FORMAT(HTS_PRINTF_FMT, 1, 2) error(const char *format, ...)
 {
     int err = errno;
     va_list args;

htslib/vcf.h

@@ -596,7 +596,8 @@ set to one of BCF_ERR* codes and must be checked before calling bcf_write().
     int bcf_hdr_append(bcf_hdr_t *h, const char *line);
 
     HTSLIB_EXPORT
-    int bcf_hdr_printf(bcf_hdr_t *h, const char *format, ...);
+    int bcf_hdr_printf(bcf_hdr_t *h, const char *format, ...)
+    HTS_FORMAT(HTS_PRINTF_FMT, 2, 3);
 
     /** VCF version, e.g. VCFv4.2 */
     HTSLIB_EXPORT

test/hfile.c

@@ -35,7 +35,8 @@ DEALINGS IN THE SOFTWARE.  */
 #include "../htslib/hts_defs.h"
 #include "../htslib/kstring.h"
 
-void HTS_NORETURN fail(const char *format, ...)
+void HTS_FORMAT(HTS_PRINTF_FMT, 1, 2) HTS_NORETURN
+fail(const char *format, ...)
 {
     int err = errno;
     va_list args;

test/test-bcf-sr.c

@@ -40,7 +40,7 @@
 #include "../htslib/hts.h"
 #include "../htslib/vcf.h"
 
-void error(const char *format, ...)
+void HTS_FORMAT(HTS_PRINTF_FMT, 1, 2) error(const char *format, ...)
 {
     va_list ap;
     va_start(ap, format);

test/test-bcf-translate.c

@@ -29,7 +29,7 @@
 
 #include "../htslib/vcf.h"
 
-void error(const char *format, ...)
+void HTS_FORMAT(HTS_PRINTF_FMT, 1, 2) error(const char *format, ...)
 {
     va_list ap;
     va_start(ap, format);

test/test-bcf_set_variant_type.c

@@ -29,7 +29,7 @@ DEALINGS IN THE SOFTWARE.  */
 #include "../htslib/hts.h"
 #include "../vcf.c"
 
-void error(const char *format, ...)
+void HTS_FORMAT(HTS_PRINTF_FMT, 1, 2) error(const char *format, ...)
 {
     va_list ap;
     va_start(ap, format);

test/test-vcf-api.c

@@ -33,7 +33,7 @@ DEALINGS IN THE SOFTWARE.  */
 #include "../htslib/kstring.h"
 #include "../htslib/kseq.h"
 
-void error(const char *format, ...)
+void HTS_FORMAT(HTS_PRINTF_FMT, 1, 2) error(const char *format, ...)
 {
     va_list ap;
     va_start(ap, format);