From 6afcb53f89132c3859029b21f915846237911286 Mon Sep 17 00:00:00 2001
From: James Bonfield <jkb@sanger.ac.uk>
Date: Thu, 15 Aug 2024 16:14:56 +0100
Subject: [PATCH] Add HTS_FORMAT checks to a variety of places.

These are needed in newer clangs with -Wformat=2.
---
 .cirrus.yml                      | 2 +-
 htsfile.c                        | 2 +-
 htslib/vcf.h                     | 3 ++-
 test/hfile.c                     | 3 ++-
 test/test-bcf-sr.c               | 2 +-
 test/test-bcf-translate.c        | 2 +-
 test/test-bcf_set_variant_type.c | 2 +-
 test/test-vcf-api.c              | 2 +-
 8 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/.cirrus.yml b/.cirrus.yml
index 9d80ea07df..61f094c2b1 100644
--- a/.cirrus.yml
+++ b/.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
diff --git a/htsfile.c b/htsfile.c
index 9af4ae31bc..25af3f5846 100644
--- a/htsfile.c
+++ b/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;
diff --git a/htslib/vcf.h b/htslib/vcf.h
index e60911ab5e..9a36cab058 100644
--- a/htslib/vcf.h
+++ b/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
diff --git a/test/hfile.c b/test/hfile.c
index 8f06a971f3..741cf7a8dc 100644
--- a/test/hfile.c
+++ b/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;
diff --git a/test/test-bcf-sr.c b/test/test-bcf-sr.c
index 80daf04230..b4943b5eff 100644
--- a/test/test-bcf-sr.c
+++ b/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);
diff --git a/test/test-bcf-translate.c b/test/test-bcf-translate.c
index c2f069e398..263e71eb86 100644
--- a/test/test-bcf-translate.c
+++ b/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);
diff --git a/test/test-bcf_set_variant_type.c b/test/test-bcf_set_variant_type.c
index 3688609f6c..eb12ecde37 100644
--- a/test/test-bcf_set_variant_type.c
+++ b/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);
diff --git a/test/test-vcf-api.c b/test/test-vcf-api.c
index ff16fa1941..b86b71d992 100644
--- a/test/test-vcf-api.c
+++ b/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);