Fix more warnings and adjust Cirrus CI rules

Change hts_close() to hts_close_abruptly() in bgzip, to fix an
empty body warning, allowing removal of -Wno-empty-body in CI
tests.

Fix signed compare in htslib/bgzf.h, which caused a warning in
the maintainer-check usepublic.cpp check.  It appears that -Wall
does not allow signed-compare in c++.

Make CFLAGS settings more consistent in .cirrus.yml, and ensure
$MAKE_OPTS is consistently applied in all make invocations.  The
latter is necessary because "make cc-version" and
"make maintainer-check" can trigger production of some .mk files,
and we want them to be made in the same way as if we ran the full
build.

Switch MacOS build to Sonoma as Ventura is no longer supported
by Cirrus.

.cirrus.yml

@@ -35,22 +35,22 @@ compile_template: &COMPILE
     if test "$USE_CONFIG" = "yes"; then
       MAKE_OPTS=
       autoreconf -i
-      eval ./configure --enable-plugins --enable-werror $CONFIG_OPTS CFLAGS=\"-g -O3 $CFLAGS\" || \
+      eval ./configure --enable-plugins --enable-werror $CONFIG_OPTS CFLAGS=\"$CFLAGS\" || \
         ( cat config.log; false )
     else
       MAKE_OPTS=-e
     fi
-    make cc-version
+    make cc-version $MAKE_OPTS
     if test "x$DO_MAINTAINER_CHECKS" = "xyes"; then
-      make maintainer-check
+      make maintainer-check $MAKE_OPTS
     fi
     make -j 4 $MAKE_OPTS
 
 test_template: &TEST
   test_script: |
-    make test-shlib-exports
-    make test
-    if test "x$DO_UNTRACKED_FILE_CHECK" = "xyes"; then make check-untracked ; fi
+    make test-shlib-exports $MAKE_OPTS
+    make test $MAKE_OPTS
+    if test "x$DO_UNTRACKED_FILE_CHECK" = "xyes"; then make check-untracked $MAKE_OPTS ; fi
 
 #--------------------------------------------------
 # Task: linux builds.
@@ -76,7 +76,7 @@ gcc_task:
     - environment:
        USE_CONFIG: yes
        # ubsan is incompatible with some -Wformat opts so we do that on clang.
-       CFLAGS: -fsanitize=address,undefined -DHTS_ALLOW_UNALIGNED=0 -Wno-format-truncation -Wno-format-overflow
+       CFLAGS: -g -O3 -fsanitize=address,undefined -DHTS_ALLOW_UNALIGNED=0 -Wno-format-truncation -Wno-format-overflow
        LDFLAGS: -fsanitize=address,undefined
        USE_LIBDEFLATE: yes
        UBSAN_OPTIONS: print_stacktrace=1:halt_on_error=1
@@ -110,11 +110,12 @@ ubuntu_task:
   matrix:
     - environment:
        USE_CONFIG: yes
+       CFLAGS: -g -O3
        DO_UNTRACKED_FILE_CHECK: yes
     - environment:
        # Cirrus-CI's clang isn't installed with ubsan, so we do that in gcc
        USE_CONFIG: yes
-       CFLAGS: -std=c99 -pedantic -Wformat -Wformat=2 -g -Wall -O3
+       CFLAGS: -g -O3 -std=c99 -pedantic -Wall -Wformat -Wformat=2
        USE_LIBDEFLATE: yes
 
   # NB: we could consider building a docker image with these
@@ -142,7 +143,7 @@ rocky_task:
     LC_ALL: C
     CIRRUS_CLONE_DEPTH: 1
     USE_CONFIG: yes
-    CFLAGS: -g -O3 -std=gnu90 -Wformat -Wformat=2 -Wextra -Wno-sign-compare -Wno-unused-parameter -Wno-missing-field-initializers -Wno-empty-body
+    CFLAGS: -g -O3 -std=gnu90 -Wall -Wformat -Wformat=2 -Wextra -Wno-sign-compare -Wno-unused-parameter -Wno-missing-field-initializers
 
   # NB: we could consider building a docker image with these
   # preinstalled and specifying that instead, to speed up testing.
@@ -187,11 +188,10 @@ arm_ubuntu_task:
 macosx_task:
   name: macosx + clang
   macos_instance:
-    image: ghcr.io/cirruslabs/macos-ventura-base:latest
+    image: ghcr.io/cirruslabs/macos-sonoma-base:latest
 
   environment:
     CC: clang
-    CFLAGS: "-Wall -arch arm64 -arch x86_64"
     LDFLAGS: "-arch arm64 -arch x86_64"
     LIBDEFLATE_CFLAGS: "-arch arm64 -arch x86_64"
     LC_ALL: C
@@ -200,9 +200,11 @@ macosx_task:
   matrix:
     - environment:
        USE_CONFIG: no
+       CFLAGS: "-g -O3 -Wall -Werror -arch arm64 -arch x86_64"
     - environment:
        USE_CONFIG: yes
        USE_LIBDEFLATE: yes
+       CFLAGS: "-g -O3 -Wall -arch arm64 -arch x86_64"
 
   package_install_script: |
     HOMEBREW_NO_AUTO_UPDATE=1 brew install autoconf automake libtool xz git \

bgzip.c

@@ -362,8 +362,7 @@ int main(int argc, char **argv)
                         }
                         else {
                             ret = 2;                        //explicit N - no overwrite, continue and return 2
-                            if (hclose(f_src) < 0)
-                                ;                           //ignoring return value
+                            hclose_abruptly(f_src);
                             free(name);
                             continue;
                         }

htslib/bgzf.h

@@ -182,7 +182,8 @@ static inline ssize_t bgzf_read_small(BGZF *fp, void *data, size_t length) {
  */
 static inline
 ssize_t bgzf_write_small(BGZF *fp, const void *data, size_t length) {
-    if (fp->is_compressed && BGZF_BLOCK_SIZE - fp->block_offset > length) {
+    if (fp->is_compressed
+        && (size_t) (BGZF_BLOCK_SIZE - fp->block_offset) > length) {
         // Short cut the common and easy mode
         memcpy((uint8_t *)fp->uncompressed_block + fp->block_offset,
                data, length);