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.

.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
@@ -114,7 +114,7 @@ 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 -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 +142,7 @@ 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.
@@ -191,7 +191,6 @@ macosx_task:
 
   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 +199,11 @@ 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);