MUSL build fails on OSX

[edmundlth]

Hello,

I have been trying cargo build on rust-htslib:

$ git clone --recursive https://github.com/rust-bio/rust-htslib.git
$ cd rust-htslib 
$ cargo build

which output a whole lot warning on the c source code and a fatal

    error occurred: Command "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c" with args "cc" did not execute successfully (status code exit code: 1).

I have also tried

$ brew install FiloSottile/musl-cross/musl-cross
$ brew install bzip2 zlib xz curl-openssl
$ cross build

with the same result.

However, cross build --target x86_64-unknown-linux-musl does work.

Other info:

• OS: MacOS Catalina 10.15.6

$ cc --version
Apple clang version 12.0.0 (clang-1200.0.31.1)
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

[brainstorm]

Thanks @edmundlth, can you post a full backtrace?

[edmundlth]

$ cross build
   Compiling hts-sys v1.10.3 (/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/hts-sys)
The following warnings were emitted during compilation:

warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/kstring.c:158:12: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
warning:         if (l + 1 > s->m - s->l) {
warning:             ~~~~~ ^ ~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/knetfile.c:380:55: warning: unused parameter 'mode' [-Wunused-parameter]
warning: knetFile *khttp_parse_url(const char *fn, const char *mode)
warning:                                                       ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/knetfile.c:518:42: warning: unused parameter 'mode' [-Wunused-parameter]
warning: knetFile *knet_dopen(int fd, const char *mode)
warning:                                          ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bcf_sr_sort.c:55:16: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:     for (i=0; i<dst->n; i++) dst->b[i] |= src->b[i];
warning:               ~^~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bcf_sr_sort.c:351:17: warning: comparison of integers of different signs: 'int' and 'khint_t' (aka 'unsigned int') [-Wsign-compare]
warning:     for (k=0; k < kh_end(hash); k++)
warning:               ~ ^ ~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bcf_sr_sort.c:354:17: warning: comparison of integers of different signs: 'int' and 'khint_t' (aka 'unsigned int') [-Wsign-compare]
warning:     for (k=0; k < kh_end(hash); k++)
warning:               ~ ^ ~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bcf_sr_sort.c:629:43: warning: unused parameter 'readers' [-Wunused-parameter]
warning: void bcf_sr_sort_remove_reader(bcf_srs_t *readers, sr_sort_t *srt, int i)
warning:                                           ^
warning: 1 warning generated.
warning: 2 warnings generated.
warning: In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:46:
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:         if (fp->limit - fp->begin < nbytes){
warning:             ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:583:101: warning: unused parameter 'level' [-Wunused-parameter]
warning: static int bgzf_gzip_compress(BGZF *fp, void *_dst, size_t *dlen, const void *src, size_t slen, int level)
warning:                                                                                                     ^
warning: In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/faidx.c:41:
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:         if (fp->limit - fp->begin < nbytes){
warning:             ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:1113:23: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:     while (bytes_read < length) {
warning:            ~~~~~~~~~~ ^ ~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:1126:43: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
warning:         copy_length = length - bytes_read < available? length - bytes_read : available;
warning:                       ~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:1289:55: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:         if (hwrite(fp->fp, j->comp_data, j->comp_len) != j->comp_len)
warning:             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:1630:42: warning: unused parameter 'n_sub_blks' [-Wunused-parameter]
warning: int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks)
warning:                                          ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:1870:41: warning: comparison of integers of different signs: 'unsigned long long' and 'int' [-Wsign-compare]
warning:         ublock_size = current_block + 1 < fp->idx->moffs ? fp->idx->offs[current_block+1].uaddr-fp->idx->offs[current_block].uaddr : BGZF_MAX_BLOCK_SIZE;
warning:                       ~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:1878:30: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare]
warning:         if (fp->block_offset == ublock_size) {
warning:             ~~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/faidx.c:727:15: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'long long' [-Wsign-compare]
warning:     while ( l < end - beg && (c=bgzf_getc(fai->bgzf))>=0 )
warning:             ~ ^ ~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/faidx.c:763:13: warning: comparison of integers of different signs: 'hts_pos_t' (aka 'long long') and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare]
warning:     if (beg >= val->len) beg = val->len;
warning:         ~~~ ^  ~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/faidx.c:764:13: warning: comparison of integers of different signs: 'hts_pos_t' (aka 'long long') and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare]
warning:     if (end >= val->len) end = val->len;
warning:         ~~~ ^  ~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/faidx.c:855:22: warning: comparison of integers of different signs: 'uint64_t' (aka 'unsigned long long') and 'hts_pos_t' (aka 'long long') [-Wsign-compare]
warning:     else if(val->len <= *p_beg_i)
warning:             ~~~~~~~~ ^  ~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/faidx.c:860:22: warning: comparison of integers of different signs: 'uint64_t' (aka 'unsigned long long') and 'hts_pos_t' (aka 'long long') [-Wsign-compare]
warning:     else if(val->len <= *p_end_i)
warning:             ~~~~~~~~ ^  ~~~~~~~~
warning: 4 warnings generated.
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:2391:22: warning: comparison of integers of different signs: 'off_t' (aka 'long long') and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare]
warning:         if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1;
warning:              ~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:2392:27: warning: comparison of integers of different signs: 'off_t' (aka 'long long') and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare]
warning:         else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1;
warning:                   ~~~~~~~ ^  ~~~~~~~~~~~~~~~~~~~~~~
warning: 6 warnings generated.
warning: In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:44:
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:         if (fp->limit - fp->begin < nbytes){
warning:             ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/header.c:59:19: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:     for (j = 0; j < len && line[j] != '\n'; j++)
warning:                 ~ ^ ~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:211:16: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'ptrdiff_t' (aka 'long') [-Wsign-compare]
warning:     if (bufsiz < curr_used)
warning:         ~~~~~~ ^ ~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:452:35: warning: comparison of integers of different signs: 'off_t' (aka 'long long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:         if (offset > 0 || -offset > length) {
warning:                           ~~~~~~~ ^ ~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:570:28: warning: unused parameter 'fpv' [-Wunused-parameter]
warning: static int fd_flush(hFILE *fpv)
warning:                            ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:760:30: warning: unused parameter 'fpv' [-Wunused-parameter]
warning: static off_t mem_seek(hFILE *fpv, off_t offset, int whence)
warning:                              ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:760:41: warning: unused parameter 'offset' [-Wunused-parameter]
warning: static off_t mem_seek(hFILE *fpv, off_t offset, int whence)
warning:                                         ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:760:53: warning: unused parameter 'whence' [-Wunused-parameter]
warning: static off_t mem_seek(hFILE *fpv, off_t offset, int whence)
warning:                                                     ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:766:29: warning: unused parameter 'fpv' [-Wunused-parameter]
warning: static int mem_close(hFILE *fpv)
warning:                             ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:828:38: warning: unused parameter 'filename' [-Wunused-parameter]
warning: static hFILE *hopenv_mem(const char *filename, const char *mode, va_list args)
warning:                                      ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:946:51: warning: unused parameter 'scheme' [-Wunused-parameter]
warning: static int try_exe_add_scheme_handler(const char *scheme,
warning:                                                   ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:947:74: warning: unused parameter 'handler' [-Wunused-parameter]
warning:                                       const struct hFILE_scheme_handler *handler)
warning:                                                                          ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:998:64: warning: missing field 'vopen' initializer [-Wmissing-field-initializers]
warning:         data = { hopen_mem, hfile_always_local, "built-in", 80 },
warning:                                                                ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:999:71: warning: missing field 'vopen' initializer [-Wmissing-field-initializers]
warning:         file = { hopen_fd_fileuri, hfile_always_local, "built-in", 80 },
warning:                                                                       ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:1000:74: warning: missing field 'vopen' initializer [-Wmissing-field-initializers]
warning:         preload = { hopen_preload, is_preload_url_remote, "built-in", 80 };
warning:                                                                          ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:1061:67: warning: missing field 'vopen' initializer [-Wmissing-field-initializers]
warning:         { hopen_unknown_scheme, hfile_always_local, "built-in", 0 };
warning:                                                                   ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:1066:19: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
warning:     for (i = 0; i < sizeof scheme; i++)
warning:                 ~ ^ ~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:1073:21: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
warning:     if (i <= 1 || i >= sizeof scheme) return NULL;
warning:                   ~ ^  ~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:1107:37: warning: unused parameter 'fname' [-Wunused-parameter]
warning: int hfile_always_local (const char *fname) { return 0; }
warning:                                     ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:1110:37: warning: unused parameter 'fname' [-Wunused-parameter]
warning: int hfile_always_remote(const char *fname) { return 1; }
warning:                                     ^
warning: In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile_net.c:30:
warning: In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile_internal.h:31:
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:         if (fp->limit - fp->begin < nbytes){
warning:             ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile_net.c:106:57: warning: missing field 'vopen' initializer [-Wmissing-field-initializers]
warning:         { hopen_net, hfile_always_remote, "knetfile", 0 };
warning:                                                         ^
warning: 2 warnings generated.
warning: 19 warnings generated.
warning: 10 warnings generated.
warning: In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:44:
warning: In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/cram/cram.h:52:
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/cram/cram_codecs.h:164:20: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int32_t' (aka 'int') [-Wsign-compare]
warning:         (blk->byte >= blk->uncomp_size && nbits > 0) ||
warning:          ~~~~~~~~~ ^  ~~~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/cram/cram_codecs.h:166:60: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
warning:          (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
warning:          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~
warning: In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:45:
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:         if (fp->limit - fp->begin < nbytes){
warning:             ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
warning: In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.c:35:
warning: In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile_internal.h:31:
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:         if (fp->limit - fp->begin < nbytes){
warning:             ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.c:114:39: warning: unused parameter 'fpv' [-Wunused-parameter]
warning: static ssize_t multipart_write(hFILE *fpv, const void *buffer, size_t nbytes)
warning:                                       ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.c:114:56: warning: unused parameter 'buffer' [-Wunused-parameter]
warning: static ssize_t multipart_write(hFILE *fpv, const void *buffer, size_t nbytes)
warning:                                                        ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.c:114:71: warning: unused parameter 'nbytes' [-Wunused-parameter]
warning: static ssize_t multipart_write(hFILE *fpv, const void *buffer, size_t nbytes)
warning:                                                                       ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.c:120:36: warning: unused parameter 'fpv' [-Wunused-parameter]
warning: static off_t multipart_seek(hFILE *fpv, off_t offset, int whence)
warning:                                    ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.c:120:47: warning: unused parameter 'offset' [-Wunused-parameter]
warning: static off_t multipart_seek(hFILE *fpv, off_t offset, int whence)
warning:                                               ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.c:120:59: warning: unused parameter 'whence' [-Wunused-parameter]
warning: static off_t multipart_seek(hFILE *fpv, off_t offset, int whence)
warning:                                                           ^
warning: 1 warning generated.
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/probaln.c:179:28: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
warning:             if (u < 3 || u >= i_dim - 3) continue;
warning:                          ~ ^  ~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/probaln.c:203:24: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
warning:         if (u < 3 || u >= i_dim - 3) continue;
warning:                      ~ ^  ~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/probaln.c:241:28: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
warning:             if (u < 3 || u >= i_dim - 3) continue;
warning:                          ~ ^  ~~~~~~~~~
warning: 7 warnings generated.
warning: 3 warnings generated.
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:1667:34: warning: comparison of integers of different signs: 'khint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
warning:             if ( kh_key(bidx, k) < idx->n_bins )
warning:                  ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:1694:55: warning: comparison of integers of different signs: 'khint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
warning:             if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue;
warning:                                       ~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:1724:51: warning: comparison of integers of different signs: 'khint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
warning:         if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue;
warning:                                   ~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:2121:60: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:             if (bgzf_read(fp, p->list, ((size_t) p->n)<<4) != ((size_t) p->n)<<4) return -1;
warning:                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/realn.c:49:35: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:     for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
warning:                                 ~ ^ ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/realn.c:98:24: warning: comparison of integers of different signs: 'const int32_t' (aka 'const int') and 'unsigned long' [-Wsign-compare]
warning:     if (b->core.l_qseq != strlen((const char *) tg + 1)) {
warning:         ~~~~~~~~~~~~~~ ^  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/realn.c:161:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:     for (k = 0; k < c->n_cigar; ++k) {
warning:                 ~ ^ ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/realn.c:191:32: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int32_t' (aka 'int') [-Wsign-compare]
warning:         if (extend_baq && lref < c->l_qseq)
warning:                           ~~~~ ^ ~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/realn.c:224:46: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
warning:                                            ~ ^ ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/realn.c:251:46: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
warning:                                            ~ ^ ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:153:14: warning: comparison of integers of different signs: 'hts_pos_t' (aka 'long long') and 'unsigned long long' [-Wsign-compare]
warning:     if ( beg > MAX_COOR_0 ) beg = MAX_COOR_0;
warning:          ~~~ ^ ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:154:14: warning: comparison of integers of different signs: 'hts_pos_t' (aka 'long long') and 'unsigned long long' [-Wsign-compare]
warning:     if ( end > MAX_COOR_0 ) end = MAX_COOR_0;
warning:          ~~~ ^ ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:184:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:         if ( mreg != list->mreg ) {
warning:              ~~~~ ^  ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:318:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             for (j=0; j<list->nreg; j++)
warning:                       ~^~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:342:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             for (i=0; i<list->nreg; i++) ptr[i] = list->reg + i;
warning:                       ~^~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:347:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             for (i=0; i<list->nreg; i++) {
warning:                       ~^~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:358:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             for (i=0; i<list->nreg; i++) {
warning:                       ~^~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:376:18: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
warning:         if (midx <= iend) midx = iend;
warning:             ~~~~ ^  ~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:391:27: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
warning:             for (k=ibeg; k<=iend; k++)
warning:                          ~^ ~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:2589:23: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             for(j=0; j<curr_reg->count; j++) {
warning:                      ~^~~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:422:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:         if ( ibeg >= list->nidx ) return 0;     // beg is too big
warning:              ~~~~ ^  ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:429:23: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             if ( iend > list->nidx ) iend = list->nidx;
warning:                  ~~~~ ^ ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:430:27: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
warning:             for (i=ibeg; i<=iend; i++)
warning:                          ~^ ~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:432:19: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
warning:             if ( i>iend ) return 0;
warning:                  ~^~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:435:28: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:         for (ireg=i-1; ireg<list->nreg; ireg++)
warning:                        ~~~~^~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:441:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:         if ( ireg >= list->nreg ) return 0;   // no match
warning:              ~~~~ ^  ~~~~~~~~~~
warning: 6 warnings generated.
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:464:110: warning: unused parameter 'payload' [-Wunused-parameter]
warning: int regidx_parse_bed(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr)
warning:                                                                                                              ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:464:125: warning: unused parameter 'usr' [-Wunused-parameter]
warning: int regidx_parse_bed(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr)
warning:                                                                                                                             ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:496:110: warning: unused parameter 'payload' [-Wunused-parameter]
warning: int regidx_parse_tab(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr)
warning:                                                                                                              ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:496:125: warning: unused parameter 'usr' [-Wunused-parameter]
warning: int regidx_parse_tab(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr)
warning:                                                                                                                             ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:543:110: warning: unused parameter 'payload' [-Wunused-parameter]
warning: int regidx_parse_reg(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr)
warning:                                                                                                              ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:543:125: warning: unused parameter 'usr' [-Wunused-parameter]
warning: int regidx_parse_reg(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr)
warning:                                                                                                                             ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:2701:25: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             for (j=0; j < curr_reg->count; j++) {
warning:                       ~ ^ ~~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:626:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:     for (i=itr->ireg; i<list->nreg; i++)
warning:                       ~^~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:632:12: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:     if ( i >= list->nreg ) return 0;   // no match
warning:          ~ ^  ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:658:15: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
warning:     if ( iseq >= regidx->nseq ) return 0;
warning:          ~~~~ ^  ~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:663:19: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
warning:         if ( iseq >= regidx->nseq ) return 0; // no more sequences, done
warning:              ~~~~ ^  ~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:3340:17: warning: comparison of integers of different signs: 'hts_pos_t' (aka 'long long') and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare]
warning:         if (beg >  iter->off[iter->i].max) {
warning:             ~~~ ^  ~~~~~~~~~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:3347:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:         for (i = ci; i < iter->reg_list[cr].count; i++) {
warning:                      ~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:3429:49: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
warning:                 if (fwrite(buf, 1, l, local_fp) != l) {
warning:                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^  ~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:3740:62: warning: unused parameter 'func' [-Wunused-parameter]
warning:                           int clear, void **ptr, const char *func) {
warning:                                                              ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:3891:18: warning: comparison of integers of different signs: 'enum htsLogLevel' and 'int' [-Wsign-compare]
warning:     if (severity <= hts_verbose) {
warning:         ~~~~~~~~ ^  ~~~~~~~~~~~
warning: 25 warnings generated.
warning: In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:46:
warning: In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/cram/cram.h:52:
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/cram/cram_codecs.h:164:20: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int32_t' (aka 'int') [-Wsign-compare]
warning:         (blk->byte >= blk->uncomp_size && nbits > 0) ||
warning:          ~~~~~~~~~ ^  ~~~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/cram/cram_codecs.h:166:60: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
warning:          (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
warning:          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~
warning: In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:49:
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:         if (fp->limit - fp->begin < nbytes){
warning:             ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/vcf_sweep.c:169:53: warning: comparison of integers of different signs: 'unsigned long long' and 'int' [-Wsign-compare]
warning:         if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size )
warning:                           ~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:255:15: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:     if (bytes != h->l_text) goto read_err;
warning:         ~~~~~ ^  ~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:425:34: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:                        b->l_data < b->m_data ? b->l_data : b->m_data);
warning:                        ~~~~~~~~~ ^ ~~~~~~~~~
warning: /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/secure/_string.h:63:33: note: expanded from macro 'memcpy'
warning:                 __builtin___memcpy_chk (dest, __VA_ARGS__, __darwin_obsz0 (dest))
warning:                                               ^~~~~~~~~~~
warning: 1 warning generated.
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:569:49: warning: unused parameter 'l_data' [-Wunused-parameter]
warning: static void swap_data(const bam1_core_t *c, int l_data, uint8_t *data, int is_host)
warning:                                                 ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:569:76: warning: unused parameter 'is_host' [-Wunused-parameter]
warning: static void swap_data(const bam1_core_t *c, int l_data, uint8_t *data, int is_host)
warning:                                                                            ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:947:30: warning: unused parameter 'ignored' [-Wunused-parameter]
warning: static int sam_readrec(BGZF *ignored, void *fpv, void *bv, int *tid, hts_pos_t *beg, hts_pos_t *end)
warning:                              ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:962:35: warning: unused parameter 'ignored' [-Wunused-parameter]
warning: static int sam_readrec_rest(BGZF *ignored, void *fpv, void *bv, int *tid, hts_pos_t *beg, hts_pos_t *end)
warning:                                   ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:962:70: warning: unused parameter 'tid' [-Wunused-parameter]
warning: static int sam_readrec_rest(BGZF *ignored, void *fpv, void *bv, int *tid, hts_pos_t *beg, hts_pos_t *end)
warning:                                                                      ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:962:86: warning: unused parameter 'beg' [-Wunused-parameter]
warning: static int sam_readrec_rest(BGZF *ignored, void *fpv, void *bv, int *tid, hts_pos_t *beg, hts_pos_t *end)
warning:                                                                                      ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:962:102: warning: unused parameter 'end' [-Wunused-parameter]
warning: static int sam_readrec_rest(BGZF *ignored, void *fpv, void *bv, int *tid, hts_pos_t *beg, hts_pos_t *end)
warning:                                                                                                      ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:971:31: warning: unused parameter 'ignored' [-Wunused-parameter]
warning: static int cram_readrec(BGZF *ignored, void *fpv, void *bv, int *tid, hts_pos_t *beg, hts_pos_t *end)
warning:                               ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:989:53: warning: unused parameter 'whence' [-Wunused-parameter]
warning: static int cram_pseek(void *fp, int64_t offset, int whence)
warning:                                                     ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:1622:19: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:         if (bytes != l_text)
warning:             ~~~~~ ^  ~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:1642:27: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:                 if (bytes != fp->line.l)
warning:                     ~~~~~ ^  ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:1684:36: warning: comparison of integers of different signs: 'unsigned long' and 'long' [-Wsign-compare]
warning:                     && strlen(val) == end - beg - 4)
warning:                        ~~~~~~~~~~~ ^  ~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:2015:23: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:         for (i = 0; i < c->n_cigar; ++i) {
warning:                     ~ ^ ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:2067:18: warning: comparison of integers of different signs: 'unsigned int' and 'int32_t' (aka 'int') [-Wsign-compare]
warning:         for (; i < c->l_qseq; ++i)
warning:                ~ ^ ~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:2077:38: warning: comparison of integers of different signs: 'unsigned long' and 'int32_t' (aka 'int') [-Wsign-compare]
warning:         _parse_err(s->l - (p - s->s) < c->l_qseq
warning:                    ~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:1950:40: note: expanded from macro '_parse_err'
warning: #define _parse_err(cond, msg) do { if (cond) { hts_log_error(msg); goto err_ret; } } while (0)
warning:                                        ^~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:2080:9: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int32_t' (aka 'int') [-Wsign-compare]
warning:         COPY_MINUS_N(t, p, 33, c->l_qseq, failed);
warning:         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:1928:23: note: expanded from macro 'COPY_MINUS_N'
warning:         for (i<<=3; i < (l); ++i) {                             \
warning:                     ~ ^  ~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:2331:21: error: implicit declaration of function 'usleep' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
warning:                     usleep(10000);
warning:                     ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:2477:34: warning: unused parameter 'arg' [-Wunused-parameter]
warning: static void *sam_parse_eof(void *arg) {
warning:                                  ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3010:23: warning: comparison of integers of different signs: 'int' and 'const uint32_t' (aka 'const unsigned int') [-Wsign-compare]
warning:         for (i = 0; i < c->n_cigar; ++i) {
warning:                     ~ ^ ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3125:31: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:                 for (i = 0; i < n; ++i) {r |= kputc_(',', str); r |= kputw(*(int8_t*)s, str); ++s;}
warning:                             ~ ^ ~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3129:31: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:                 for (i = 0; i < n; ++i) {r |= kputc_(',', str); r |= kputw(*(uint8_t*)s, str); ++s;}
warning:                             ~ ^ ~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3133:31: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:                 for (i = 0; i < n; ++i) {r |= kputc_(',', str); r |= kputw(le_to_i16(s), str); s += 2; }
warning:                             ~ ^ ~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3137:31: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:                 for (i = 0; i < n; ++i) {r |= kputc_(',', str); r |= kputw(le_to_u16(s), str); s += 2; }
warning:                             ~ ^ ~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3141:31: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:                 for (i = 0; i < n; ++i) {r |= kputc_(',', str); r |= kputw(le_to_i32(s), str); s += 4; }
warning:                             ~ ^ ~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3145:31: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:                 for (i = 0; i < n; ++i) {r |= kputc_(',', str); r |= kputuw(le_to_u32(s), str); s += 4; }
warning:                             ~ ^ ~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3149:31: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:                 for (i = 0; i < n; ++i) {r |= kputc_(',', str); r |= kputd(le_to_float(s), str); s += 4; }
warning:                             ~ ^ ~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3281:70: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:                 if ( bgzf_write(fp->fp.bgzf, fp->line.s, fp->line.l) != fp->line.l ) return -1;
warning:                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3283:67: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:                 if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1;
warning:                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3367:40: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
warning:     if (new_len > INT32_MAX || new_len < b->l_data) goto nomem;
warning:                                ~~~~~~~ ^ ~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3980:52: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) {
warning:                                                  ~ ^ ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3987:22: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             assert(k < c->n_cigar);
warning:                    ~ ^ ~~~~~~~~~~
warning: /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/assert.h:93:25: note: expanded from macro 'assert'
warning:     (__builtin_expect(!(e), 0) ? __assert_rtn(__func__, __FILE__, __LINE__, #e) : (void)0)
warning:                         ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3993:25: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             assert(s->k < c->n_cigar); // otherwise a bug: this function should not be called in this case
warning:                    ~~~~ ^ ~~~~~~~~~~
warning: /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/assert.h:93:25: note: expanded from macro 'assert'
warning:     (__builtin_expect(!(e), 0) ? __assert_rtn(__func__, __FILE__, __LINE__, #e) : (void)0)
warning:                         ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4002:38: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:                 for (k = s->k + 1; k < c->n_cigar; ++k) {
warning:                                    ~ ^ ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4009:25: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             assert(s->k < c->n_cigar); // otherwise a bug
warning:                    ~~~~ ^ ~~~~~~~~~~
warning: /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/assert.h:93:25: note: expanded from macro 'assert'
warning:     (__builtin_expect(!(e), 0) ? __assert_rtn(__func__, __FILE__, __LINE__, #e) : (void)0)
warning:                         ^
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4016:45: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:         if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation
warning:                                    ~~~~~~~~ ^ ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4021:50: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding
warning:                                         ~~~~~~~~ ^ ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4023:38: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:                 for (k = s->k + 2; k < c->n_cigar; ++k) {
warning:                                    ~ ^ ~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4073:14: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:     while (k < p->b->core.n_cigar) {
warning:            ~ ^ ~~~~~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4093:14: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:     while (k < p->b->core.n_cigar) {
warning:            ~ ^ ~~~~~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4097:27: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             for (l = 0; l < (cigar[k]>>BAM_CIGAR_SHIFT); l++)
warning:                         ~ ^  ~~~~~~~~~~~~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4101:27: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             for (l = 0; l < (cigar[k]>>BAM_CIGAR_SHIFT); l++, j++) {
warning:                         ~ ^  ~~~~~~~~~~~~~~~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4672:30: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             if (iter->tid[i] < new_min_tid) {
warning:                 ~~~~~~~~~~~~ ^ ~~~~~~~~~~~
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4675:37: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
warning:             } else if (iter->tid[i] == new_min_tid && iter->pos[i] < new_min_pos) {
warning:                        ~~~~~~~~~~~~ ^  ~~~~~~~~~~~
warning: 47 warnings and 1 error generated.
warning: In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/textutils.c:31:
warning: /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
warning:         if (fp->limit - fp->begin < nbytes){
warning:             ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
warning: 14 warnings generated.
warning: 1 warning generated.

error: failed to run custom build command for `hts-sys v1.10.3 (/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/hts-sys)`

Caused by:
  process didn't exit successfully: `/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-1eac3856cfb36bd5/build-script-build` (exit code: 1)
  --- stdout
  cargo:rerun-if-changed=htslib/kfunc.c
  cargo:rerun-if-changed=htslib/knetfile.c
  cargo:rerun-if-changed=htslib/kstring.c
  cargo:rerun-if-changed=htslib/bcf_sr_sort.c
  cargo:rerun-if-changed=htslib/bgzf.c
  cargo:rerun-if-changed=htslib/errmod.c
  cargo:rerun-if-changed=htslib/faidx.c
  cargo:rerun-if-changed=htslib/header.c
  cargo:rerun-if-changed=htslib/hfile.c
  cargo:rerun-if-changed=htslib/hfile_net.c
  cargo:rerun-if-changed=htslib/hts.c
  cargo:rerun-if-changed=htslib/hts_os.c
  cargo:rerun-if-changed=htslib/md5.c
  cargo:rerun-if-changed=htslib/multipart.c
  cargo:rerun-if-changed=htslib/probaln.c
  cargo:rerun-if-changed=htslib/realn.c
  cargo:rerun-if-changed=htslib/regidx.c
  cargo:rerun-if-changed=htslib/region.c
  cargo:rerun-if-changed=htslib/sam.c
  cargo:rerun-if-changed=htslib/synced_bcf_reader.c
  cargo:rerun-if-changed=htslib/vcf_sweep.c
  cargo:rerun-if-changed=htslib/tbx.c
  cargo:rerun-if-changed=htslib/textutils.c
  cargo:rerun-if-changed=htslib/thread_pool.c
  cargo:rerun-if-changed=htslib/vcf.c
  cargo:rerun-if-changed=htslib/vcfutils.c
  cargo:rerun-if-changed=htslib/cram/cram_codecs.c
  cargo:rerun-if-changed=htslib/cram/cram_decode.c
  cargo:rerun-if-changed=htslib/cram/cram_encode.c
  cargo:rerun-if-changed=htslib/cram/cram_external.c
  cargo:rerun-if-changed=htslib/cram/cram_index.c
  cargo:rerun-if-changed=htslib/cram/cram_io.c
  cargo:rerun-if-changed=htslib/cram/cram_samtools.c
  cargo:rerun-if-changed=htslib/cram/cram_stats.c
  cargo:rerun-if-changed=htslib/cram/mFILE.c
  cargo:rerun-if-changed=htslib/cram/open_trace_file.c
  cargo:rerun-if-changed=htslib/cram/pooled_alloc.c
  cargo:rerun-if-changed=htslib/cram/rANS_static.c
  cargo:rerun-if-changed=htslib/cram/string_alloc.c
  cargo:rerun-if-changed=htslib/hfile_libcurl.c
  TARGET = Some("x86_64-apple-darwin")
  OPT_LEVEL = Some("0")
  HOST = Some("x86_64-apple-darwin")
  CC_x86_64-apple-darwin = None
  CC_x86_64_apple_darwin = None
  HOST_CC = None
  CC = None
  CFLAGS_x86_64-apple-darwin = None
  CFLAGS_x86_64_apple_darwin = None
  HOST_CFLAGS = None
  CFLAGS = None
  CRATE_CC_NO_DEFAULTS = None
  DEBUG = Some("true")
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/kfunc.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/kfunc.c"
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/knetfile.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/knetfile.c"
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/kstring.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/kstring.c"
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bcf_sr_sort.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bcf_sr_sort.c"
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/kstring.c:158:12: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
  cargo:warning=        if (l + 1 > s->m - s->l) {
  cargo:warning=            ~~~~~ ^ ~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/knetfile.c:380:55: warning: unused parameter 'mode' [-Wunused-parameter]
  cargo:warning=knetFile *khttp_parse_url(const char *fn, const char *mode)
  cargo:warning=                                                      ^
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c"
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/knetfile.c:518:42: warning: unused parameter 'mode' [-Wunused-parameter]
  cargo:warning=knetFile *knet_dopen(int fd, const char *mode)
  cargo:warning=                                         ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bcf_sr_sort.c:55:16: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=    for (i=0; i<dst->n; i++) dst->b[i] |= src->b[i];
  cargo:warning=              ~^~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bcf_sr_sort.c:351:17: warning: comparison of integers of different signs: 'int' and 'khint_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=    for (k=0; k < kh_end(hash); k++)
  cargo:warning=              ~ ^ ~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bcf_sr_sort.c:354:17: warning: comparison of integers of different signs: 'int' and 'khint_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=    for (k=0; k < kh_end(hash); k++)
  cargo:warning=              ~ ^ ~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bcf_sr_sort.c:629:43: warning: unused parameter 'readers' [-Wunused-parameter]
  cargo:warning=void bcf_sr_sort_remove_reader(bcf_srs_t *readers, sr_sort_t *srt, int i)
  cargo:warning=                                          ^
  cargo:warning=1 warning generated.
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/errmod.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/errmod.c"
  cargo:warning=2 warnings generated.
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/faidx.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/faidx.c"
  cargo:warning=In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:46:
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=        if (fp->limit - fp->begin < nbytes){
  cargo:warning=            ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:583:101: warning: unused parameter 'level' [-Wunused-parameter]
  cargo:warning=static int bgzf_gzip_compress(BGZF *fp, void *_dst, size_t *dlen, const void *src, size_t slen, int level)
  cargo:warning=                                                                                                    ^
  cargo:warning=In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/faidx.c:41:
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=        if (fp->limit - fp->begin < nbytes){
  cargo:warning=            ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:1113:23: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=    while (bytes_read < length) {
  cargo:warning=           ~~~~~~~~~~ ^ ~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:1126:43: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
  cargo:warning=        copy_length = length - bytes_read < available? length - bytes_read : available;
  cargo:warning=                      ~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:1289:55: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=        if (hwrite(fp->fp, j->comp_data, j->comp_len) != j->comp_len)
  cargo:warning=            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:1630:42: warning: unused parameter 'n_sub_blks' [-Wunused-parameter]
  cargo:warning=int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks)
  cargo:warning=                                         ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:1870:41: warning: comparison of integers of different signs: 'unsigned long long' and 'int' [-Wsign-compare]
  cargo:warning=        ublock_size = current_block + 1 < fp->idx->moffs ? fp->idx->offs[current_block+1].uaddr-fp->idx->offs[current_block].uaddr : BGZF_MAX_BLOCK_SIZE;
  cargo:warning=                      ~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:1878:30: warning: comparison of integers of different signs: 'int' and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare]
  cargo:warning=        if (fp->block_offset == ublock_size) {
  cargo:warning=            ~~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/faidx.c:727:15: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'long long' [-Wsign-compare]
  cargo:warning=    while ( l < end - beg && (c=bgzf_getc(fai->bgzf))>=0 )
  cargo:warning=            ~ ^ ~~~~~~~~~
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/header.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/header.c"
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/faidx.c:763:13: warning: comparison of integers of different signs: 'hts_pos_t' (aka 'long long') and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare]
  cargo:warning=    if (beg >= val->len) beg = val->len;
  cargo:warning=        ~~~ ^  ~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/faidx.c:764:13: warning: comparison of integers of different signs: 'hts_pos_t' (aka 'long long') and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare]
  cargo:warning=    if (end >= val->len) end = val->len;
  cargo:warning=        ~~~ ^  ~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/faidx.c:855:22: warning: comparison of integers of different signs: 'uint64_t' (aka 'unsigned long long') and 'hts_pos_t' (aka 'long long') [-Wsign-compare]
  cargo:warning=    else if(val->len <= *p_beg_i)
  cargo:warning=            ~~~~~~~~ ^  ~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/faidx.c:860:22: warning: comparison of integers of different signs: 'uint64_t' (aka 'unsigned long long') and 'hts_pos_t' (aka 'long long') [-Wsign-compare]
  cargo:warning=    else if(val->len <= *p_end_i)
  cargo:warning=            ~~~~~~~~ ^  ~~~~~~~~
  cargo:warning=4 warnings generated.
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c"
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:2391:22: warning: comparison of integers of different signs: 'off_t' (aka 'long long') and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare]
  cargo:warning=        if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1;
  cargo:warning=             ~~~~~~~ ^ ~~~~~~~~~~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/bgzf.c:2392:27: warning: comparison of integers of different signs: 'off_t' (aka 'long long') and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare]
  cargo:warning=        else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1;
  cargo:warning=                  ~~~~~~~ ^  ~~~~~~~~~~~~~~~~~~~~~~
  cargo:warning=6 warnings generated.
  cargo:warning=In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:44:
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=        if (fp->limit - fp->begin < nbytes){
  cargo:warning=            ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
  exit code: 0
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/header.c:59:19: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=    for (j = 0; j < len && line[j] != '\n'; j++)
  cargo:warning=                ~ ^ ~~~
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile_net.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile_net.c"
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:211:16: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'ptrdiff_t' (aka 'long') [-Wsign-compare]
  cargo:warning=    if (bufsiz < curr_used)
  cargo:warning=        ~~~~~~ ^ ~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:452:35: warning: comparison of integers of different signs: 'off_t' (aka 'long long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=        if (offset > 0 || -offset > length) {
  cargo:warning=                          ~~~~~~~ ^ ~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:570:28: warning: unused parameter 'fpv' [-Wunused-parameter]
  cargo:warning=static int fd_flush(hFILE *fpv)
  cargo:warning=                           ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:760:30: warning: unused parameter 'fpv' [-Wunused-parameter]
  cargo:warning=static off_t mem_seek(hFILE *fpv, off_t offset, int whence)
  cargo:warning=                             ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:760:41: warning: unused parameter 'offset' [-Wunused-parameter]
  cargo:warning=static off_t mem_seek(hFILE *fpv, off_t offset, int whence)
  cargo:warning=                                        ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:760:53: warning: unused parameter 'whence' [-Wunused-parameter]
  cargo:warning=static off_t mem_seek(hFILE *fpv, off_t offset, int whence)
  cargo:warning=                                                    ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:766:29: warning: unused parameter 'fpv' [-Wunused-parameter]
  cargo:warning=static int mem_close(hFILE *fpv)
  cargo:warning=                            ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:828:38: warning: unused parameter 'filename' [-Wunused-parameter]
  cargo:warning=static hFILE *hopenv_mem(const char *filename, const char *mode, va_list args)
  cargo:warning=                                     ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:946:51: warning: unused parameter 'scheme' [-Wunused-parameter]
  cargo:warning=static int try_exe_add_scheme_handler(const char *scheme,
  cargo:warning=                                                  ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:947:74: warning: unused parameter 'handler' [-Wunused-parameter]
  cargo:warning=                                      const struct hFILE_scheme_handler *handler)
  cargo:warning=                                                                         ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:998:64: warning: missing field 'vopen' initializer [-Wmissing-field-initializers]
  cargo:warning=        data = { hopen_mem, hfile_always_local, "built-in", 80 },
  cargo:warning=                                                               ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:999:71: warning: missing field 'vopen' initializer [-Wmissing-field-initializers]
  cargo:warning=        file = { hopen_fd_fileuri, hfile_always_local, "built-in", 80 },
  cargo:warning=                                                                      ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:1000:74: warning: missing field 'vopen' initializer [-Wmissing-field-initializers]
  cargo:warning=        preload = { hopen_preload, is_preload_url_remote, "built-in", 80 };
  cargo:warning=                                                                         ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:1061:67: warning: missing field 'vopen' initializer [-Wmissing-field-initializers]
  cargo:warning=        { hopen_unknown_scheme, hfile_always_local, "built-in", 0 };
  cargo:warning=                                                                  ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:1066:19: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
  cargo:warning=    for (i = 0; i < sizeof scheme; i++)
  cargo:warning=                ~ ^ ~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:1073:21: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
  cargo:warning=    if (i <= 1 || i >= sizeof scheme) return NULL;
  cargo:warning=                  ~ ^  ~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:1107:37: warning: unused parameter 'fname' [-Wunused-parameter]
  cargo:warning=int hfile_always_local (const char *fname) { return 0; }
  cargo:warning=                                    ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile.c:1110:37: warning: unused parameter 'fname' [-Wunused-parameter]
  cargo:warning=int hfile_always_remote(const char *fname) { return 1; }
  cargo:warning=                                    ^
  cargo:warning=In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile_net.c:30:
  cargo:warning=In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile_internal.h:31:
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=        if (fp->limit - fp->begin < nbytes){
  cargo:warning=            ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile_net.c:106:57: warning: missing field 'vopen' initializer [-Wmissing-field-initializers]
  cargo:warning=        { hopen_net, hfile_always_remote, "knetfile", 0 };
  cargo:warning=                                                        ^
  cargo:warning=2 warnings generated.
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c"
  cargo:warning=19 warnings generated.
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts_os.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts_os.c"
  cargo:warning=10 warnings generated.
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/md5.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/md5.c"
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.c"
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/probaln.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/probaln.c"
  cargo:warning=In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:44:
  cargo:warning=In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/cram/cram.h:52:
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/cram/cram_codecs.h:164:20: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int32_t' (aka 'int') [-Wsign-compare]
  cargo:warning=        (blk->byte >= blk->uncomp_size && nbits > 0) ||
  cargo:warning=         ~~~~~~~~~ ^  ~~~~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/cram/cram_codecs.h:166:60: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
  cargo:warning=         (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
  cargo:warning=         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~
  cargo:warning=In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:45:
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=        if (fp->limit - fp->begin < nbytes){
  cargo:warning=            ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
  cargo:warning=In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.c:35:
  cargo:warning=In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hfile_internal.h:31:
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=        if (fp->limit - fp->begin < nbytes){
  cargo:warning=            ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.c:114:39: warning: unused parameter 'fpv' [-Wunused-parameter]
  cargo:warning=static ssize_t multipart_write(hFILE *fpv, const void *buffer, size_t nbytes)
  cargo:warning=                                      ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.c:114:56: warning: unused parameter 'buffer' [-Wunused-parameter]
  cargo:warning=static ssize_t multipart_write(hFILE *fpv, const void *buffer, size_t nbytes)
  cargo:warning=                                                       ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.c:114:71: warning: unused parameter 'nbytes' [-Wunused-parameter]
  cargo:warning=static ssize_t multipart_write(hFILE *fpv, const void *buffer, size_t nbytes)
  cargo:warning=                                                                      ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.c:120:36: warning: unused parameter 'fpv' [-Wunused-parameter]
  cargo:warning=static off_t multipart_seek(hFILE *fpv, off_t offset, int whence)
  cargo:warning=                                   ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.c:120:47: warning: unused parameter 'offset' [-Wunused-parameter]
  cargo:warning=static off_t multipart_seek(hFILE *fpv, off_t offset, int whence)
  cargo:warning=                                              ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/multipart.c:120:59: warning: unused parameter 'whence' [-Wunused-parameter]
  cargo:warning=static off_t multipart_seek(hFILE *fpv, off_t offset, int whence)
  cargo:warning=                                                          ^
  cargo:warning=1 warning generated.
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/realn.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/realn.c"
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/probaln.c:179:28: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
  cargo:warning=            if (u < 3 || u >= i_dim - 3) continue;
  cargo:warning=                         ~ ^  ~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/probaln.c:203:24: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
  cargo:warning=        if (u < 3 || u >= i_dim - 3) continue;
  cargo:warning=                     ~ ^  ~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/probaln.c:241:28: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare]
  cargo:warning=            if (u < 3 || u >= i_dim - 3) continue;
  cargo:warning=                         ~ ^  ~~~~~~~~~
  cargo:warning=7 warnings generated.
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c"
  cargo:warning=3 warnings generated.
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/region.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/region.c"
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:1667:34: warning: comparison of integers of different signs: 'khint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
  cargo:warning=            if ( kh_key(bidx, k) < idx->n_bins )
  cargo:warning=                 ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:1694:55: warning: comparison of integers of different signs: 'khint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
  cargo:warning=            if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue;
  cargo:warning=                                      ~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:1724:51: warning: comparison of integers of different signs: 'khint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
  cargo:warning=        if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue;
  cargo:warning=                                  ~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:2121:60: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=            if (bgzf_read(fp, p->list, ((size_t) p->n)<<4) != ((size_t) p->n)<<4) return -1;
  cargo:warning=                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/realn.c:49:35: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=    for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
  cargo:warning=                                ~ ^ ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/realn.c:98:24: warning: comparison of integers of different signs: 'const int32_t' (aka 'const int') and 'unsigned long' [-Wsign-compare]
  cargo:warning=    if (b->core.l_qseq != strlen((const char *) tg + 1)) {
  cargo:warning=        ~~~~~~~~~~~~~~ ^  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/realn.c:161:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=    for (k = 0; k < c->n_cigar; ++k) {
  cargo:warning=                ~ ^ ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/realn.c:191:32: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int32_t' (aka 'int') [-Wsign-compare]
  cargo:warning=        if (extend_baq && lref < c->l_qseq)
  cargo:warning=                          ~~~~ ^ ~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/realn.c:224:46: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
  cargo:warning=                                           ~ ^ ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/realn.c:251:46: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
  cargo:warning=                                           ~ ^ ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:153:14: warning: comparison of integers of different signs: 'hts_pos_t' (aka 'long long') and 'unsigned long long' [-Wsign-compare]
  cargo:warning=    if ( beg > MAX_COOR_0 ) beg = MAX_COOR_0;
  cargo:warning=         ~~~ ^ ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:154:14: warning: comparison of integers of different signs: 'hts_pos_t' (aka 'long long') and 'unsigned long long' [-Wsign-compare]
  cargo:warning=    if ( end > MAX_COOR_0 ) end = MAX_COOR_0;
  cargo:warning=         ~~~ ^ ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:184:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=        if ( mreg != list->mreg ) {
  cargo:warning=             ~~~~ ^  ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:318:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            for (j=0; j<list->nreg; j++)
  cargo:warning=                      ~^~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:342:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            for (i=0; i<list->nreg; i++) ptr[i] = list->reg + i;
  cargo:warning=                      ~^~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:347:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            for (i=0; i<list->nreg; i++) {
  cargo:warning=                      ~^~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:358:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            for (i=0; i<list->nreg; i++) {
  cargo:warning=                      ~^~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:376:18: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
  cargo:warning=        if (midx <= iend) midx = iend;
  cargo:warning=            ~~~~ ^  ~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:391:27: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
  cargo:warning=            for (k=ibeg; k<=iend; k++)
  cargo:warning=                         ~^ ~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:2589:23: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            for(j=0; j<curr_reg->count; j++) {
  cargo:warning=                     ~^~~~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:422:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=        if ( ibeg >= list->nidx ) return 0;     // beg is too big
  cargo:warning=             ~~~~ ^  ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:429:23: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            if ( iend > list->nidx ) iend = list->nidx;
  cargo:warning=                 ~~~~ ^ ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:430:27: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
  cargo:warning=            for (i=ibeg; i<=iend; i++)
  cargo:warning=                         ~^ ~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:432:19: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
  cargo:warning=            if ( i>iend ) return 0;
  cargo:warning=                 ~^~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:435:28: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=        for (ireg=i-1; ireg<list->nreg; ireg++)
  cargo:warning=                       ~~~~^~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:441:19: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=        if ( ireg >= list->nreg ) return 0;   // no match
  cargo:warning=             ~~~~ ^  ~~~~~~~~~~
  cargo:warning=6 warnings generated.
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:464:110: warning: unused parameter 'payload' [-Wunused-parameter]
  cargo:warning=int regidx_parse_bed(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr)
  cargo:warning=                                                                                                             ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:464:125: warning: unused parameter 'usr' [-Wunused-parameter]
  cargo:warning=int regidx_parse_bed(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr)
  cargo:warning=                                                                                                                            ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:496:110: warning: unused parameter 'payload' [-Wunused-parameter]
  cargo:warning=int regidx_parse_tab(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr)
  cargo:warning=                                                                                                             ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:496:125: warning: unused parameter 'usr' [-Wunused-parameter]
  cargo:warning=int regidx_parse_tab(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr)
  cargo:warning=                                                                                                                            ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:543:110: warning: unused parameter 'payload' [-Wunused-parameter]
  cargo:warning=int regidx_parse_reg(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr)
  cargo:warning=                                                                                                             ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:543:125: warning: unused parameter 'usr' [-Wunused-parameter]
  cargo:warning=int regidx_parse_reg(const char *line, char **chr_beg, char **chr_end, hts_pos_t *beg, hts_pos_t *end, void *payload, void *usr)
  cargo:warning=                                                                                                                            ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:2701:25: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            for (j=0; j < curr_reg->count; j++) {
  cargo:warning=                      ~ ^ ~~~~~~~~~~~~~~~
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c"
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:626:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=    for (i=itr->ireg; i<list->nreg; i++)
  cargo:warning=                      ~^~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:632:12: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=    if ( i >= list->nreg ) return 0;   // no match
  cargo:warning=         ~ ^  ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:658:15: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
  cargo:warning=    if ( iseq >= regidx->nseq ) return 0;
  cargo:warning=         ~~~~ ^  ~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/regidx.c:663:19: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int' [-Wsign-compare]
  cargo:warning=        if ( iseq >= regidx->nseq ) return 0; // no more sequences, done
  cargo:warning=             ~~~~ ^  ~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:3340:17: warning: comparison of integers of different signs: 'hts_pos_t' (aka 'long long') and 'uint64_t' (aka 'unsigned long long') [-Wsign-compare]
  cargo:warning=        if (beg >  iter->off[iter->i].max) {
  cargo:warning=            ~~~ ^  ~~~~~~~~~~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:3347:24: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=        for (i = ci; i < iter->reg_list[cr].count; i++) {
  cargo:warning=                     ~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:3429:49: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
  cargo:warning=                if (fwrite(buf, 1, l, local_fp) != l) {
  cargo:warning=                    ~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^  ~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:3740:62: warning: unused parameter 'func' [-Wunused-parameter]
  cargo:warning=                          int clear, void **ptr, const char *func) {
  cargo:warning=                                                             ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/hts.c:3891:18: warning: comparison of integers of different signs: 'enum htsLogLevel' and 'int' [-Wsign-compare]
  cargo:warning=    if (severity <= hts_verbose) {
  cargo:warning=        ~~~~~~~~ ^  ~~~~~~~~~~~
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/synced_bcf_reader.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/synced_bcf_reader.c"
  cargo:warning=25 warnings generated.
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/vcf_sweep.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/vcf_sweep.c"
  cargo:warning=In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:46:
  cargo:warning=In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/cram/cram.h:52:
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/cram/cram_codecs.h:164:20: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int32_t' (aka 'int') [-Wsign-compare]
  cargo:warning=        (blk->byte >= blk->uncomp_size && nbits > 0) ||
  cargo:warning=         ~~~~~~~~~ ^  ~~~~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/cram/cram_codecs.h:166:60: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
  cargo:warning=         (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
  cargo:warning=         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~
  cargo:warning=In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:49:
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=        if (fp->limit - fp->begin < nbytes){
  cargo:warning=            ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/vcf_sweep.c:169:53: warning: comparison of integers of different signs: 'unsigned long long' and 'int' [-Wsign-compare]
  cargo:warning=        if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size )
  cargo:warning=                          ~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:255:15: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=    if (bytes != h->l_text) goto read_err;
  cargo:warning=        ~~~~~ ^  ~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:425:34: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=                       b->l_data < b->m_data ? b->l_data : b->m_data);
  cargo:warning=                       ~~~~~~~~~ ^ ~~~~~~~~~
  cargo:warning=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/secure/_string.h:63:33: note: expanded from macro 'memcpy'
  cargo:warning=                __builtin___memcpy_chk (dest, __VA_ARGS__, __darwin_obsz0 (dest))
  cargo:warning=                                              ^~~~~~~~~~~
  cargo:warning=1 warning generated.
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:569:49: warning: unused parameter 'l_data' [-Wunused-parameter]
  cargo:warning=static void swap_data(const bam1_core_t *c, int l_data, uint8_t *data, int is_host)
  cargo:warning=                                                ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:569:76: warning: unused parameter 'is_host' [-Wunused-parameter]
  cargo:warning=static void swap_data(const bam1_core_t *c, int l_data, uint8_t *data, int is_host)
  cargo:warning=                                                                           ^
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/tbx.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/tbx.c"
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:947:30: warning: unused parameter 'ignored' [-Wunused-parameter]
  cargo:warning=static int sam_readrec(BGZF *ignored, void *fpv, void *bv, int *tid, hts_pos_t *beg, hts_pos_t *end)
  cargo:warning=                             ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:962:35: warning: unused parameter 'ignored' [-Wunused-parameter]
  cargo:warning=static int sam_readrec_rest(BGZF *ignored, void *fpv, void *bv, int *tid, hts_pos_t *beg, hts_pos_t *end)
  cargo:warning=                                  ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:962:70: warning: unused parameter 'tid' [-Wunused-parameter]
  cargo:warning=static int sam_readrec_rest(BGZF *ignored, void *fpv, void *bv, int *tid, hts_pos_t *beg, hts_pos_t *end)
  cargo:warning=                                                                     ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:962:86: warning: unused parameter 'beg' [-Wunused-parameter]
  cargo:warning=static int sam_readrec_rest(BGZF *ignored, void *fpv, void *bv, int *tid, hts_pos_t *beg, hts_pos_t *end)
  cargo:warning=                                                                                     ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:962:102: warning: unused parameter 'end' [-Wunused-parameter]
  cargo:warning=static int sam_readrec_rest(BGZF *ignored, void *fpv, void *bv, int *tid, hts_pos_t *beg, hts_pos_t *end)
  cargo:warning=                                                                                                     ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:971:31: warning: unused parameter 'ignored' [-Wunused-parameter]
  cargo:warning=static int cram_readrec(BGZF *ignored, void *fpv, void *bv, int *tid, hts_pos_t *beg, hts_pos_t *end)
  cargo:warning=                              ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:989:53: warning: unused parameter 'whence' [-Wunused-parameter]
  cargo:warning=static int cram_pseek(void *fp, int64_t offset, int whence)
  cargo:warning=                                                    ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:1622:19: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=        if (bytes != l_text)
  cargo:warning=            ~~~~~ ^  ~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:1642:27: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=                if (bytes != fp->line.l)
  cargo:warning=                    ~~~~~ ^  ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:1684:36: warning: comparison of integers of different signs: 'unsigned long' and 'long' [-Wsign-compare]
  cargo:warning=                    && strlen(val) == end - beg - 4)
  cargo:warning=                       ~~~~~~~~~~~ ^  ~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:2015:23: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=        for (i = 0; i < c->n_cigar; ++i) {
  cargo:warning=                    ~ ^ ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:2067:18: warning: comparison of integers of different signs: 'unsigned int' and 'int32_t' (aka 'int') [-Wsign-compare]
  cargo:warning=        for (; i < c->l_qseq; ++i)
  cargo:warning=               ~ ^ ~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:2077:38: warning: comparison of integers of different signs: 'unsigned long' and 'int32_t' (aka 'int') [-Wsign-compare]
  cargo:warning=        _parse_err(s->l - (p - s->s) < c->l_qseq
  cargo:warning=                   ~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:1950:40: note: expanded from macro '_parse_err'
  cargo:warning=#define _parse_err(cond, msg) do { if (cond) { hts_log_error(msg); goto err_ret; } } while (0)
  cargo:warning=                                       ^~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:2080:9: warning: comparison of integers of different signs: 'size_t' (aka 'unsigned long') and 'int32_t' (aka 'int') [-Wsign-compare]
  cargo:warning=        COPY_MINUS_N(t, p, 33, c->l_qseq, failed);
  cargo:warning=        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:1928:23: note: expanded from macro 'COPY_MINUS_N'
  cargo:warning=        for (i<<=3; i < (l); ++i) {                             \
  cargo:warning=                    ~ ^  ~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:2331:21: error: implicit declaration of function 'usleep' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
  cargo:warning=                    usleep(10000);
  cargo:warning=                    ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:2477:34: warning: unused parameter 'arg' [-Wunused-parameter]
  cargo:warning=static void *sam_parse_eof(void *arg) {
  cargo:warning=                                 ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3010:23: warning: comparison of integers of different signs: 'int' and 'const uint32_t' (aka 'const unsigned int') [-Wsign-compare]
  cargo:warning=        for (i = 0; i < c->n_cigar; ++i) {
  cargo:warning=                    ~ ^ ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3125:31: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=                for (i = 0; i < n; ++i) {r |= kputc_(',', str); r |= kputw(*(int8_t*)s, str); ++s;}
  cargo:warning=                            ~ ^ ~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3129:31: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=                for (i = 0; i < n; ++i) {r |= kputc_(',', str); r |= kputw(*(uint8_t*)s, str); ++s;}
  cargo:warning=                            ~ ^ ~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3133:31: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=                for (i = 0; i < n; ++i) {r |= kputc_(',', str); r |= kputw(le_to_i16(s), str); s += 2; }
  cargo:warning=                            ~ ^ ~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3137:31: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=                for (i = 0; i < n; ++i) {r |= kputc_(',', str); r |= kputw(le_to_u16(s), str); s += 2; }
  cargo:warning=                            ~ ^ ~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3141:31: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=                for (i = 0; i < n; ++i) {r |= kputc_(',', str); r |= kputw(le_to_i32(s), str); s += 4; }
  cargo:warning=                            ~ ^ ~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3145:31: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=                for (i = 0; i < n; ++i) {r |= kputc_(',', str); r |= kputuw(le_to_u32(s), str); s += 4; }
  cargo:warning=                            ~ ^ ~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3149:31: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=                for (i = 0; i < n; ++i) {r |= kputc_(',', str); r |= kputd(le_to_float(s), str); s += 4; }
  cargo:warning=                            ~ ^ ~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3281:70: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=                if ( bgzf_write(fp->fp.bgzf, fp->line.s, fp->line.l) != fp->line.l ) return -1;
  cargo:warning=                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3283:67: warning: comparison of integers of different signs: 'ssize_t' (aka 'long') and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=                if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1;
  cargo:warning=                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^  ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3367:40: warning: comparison of integers of different signs: 'uint32_t' (aka 'unsigned int') and 'int' [-Wsign-compare]
  cargo:warning=    if (new_len > INT32_MAX || new_len < b->l_data) goto nomem;
  cargo:warning=                               ~~~~~~~ ^ ~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3980:52: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) {
  cargo:warning=                                                 ~ ^ ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3987:22: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            assert(k < c->n_cigar);
  cargo:warning=                   ~ ^ ~~~~~~~~~~
  cargo:warning=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/assert.h:93:25: note: expanded from macro 'assert'
  cargo:warning=    (__builtin_expect(!(e), 0) ? __assert_rtn(__func__, __FILE__, __LINE__, #e) : (void)0)
  cargo:warning=                        ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:3993:25: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            assert(s->k < c->n_cigar); // otherwise a bug: this function should not be called in this case
  cargo:warning=                   ~~~~ ^ ~~~~~~~~~~
  cargo:warning=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/assert.h:93:25: note: expanded from macro 'assert'
  cargo:warning=    (__builtin_expect(!(e), 0) ? __assert_rtn(__func__, __FILE__, __LINE__, #e) : (void)0)
  cargo:warning=                        ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4002:38: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=                for (k = s->k + 1; k < c->n_cigar; ++k) {
  cargo:warning=                                   ~ ^ ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4009:25: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            assert(s->k < c->n_cigar); // otherwise a bug
  cargo:warning=                   ~~~~ ^ ~~~~~~~~~~
  cargo:warning=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/assert.h:93:25: note: expanded from macro 'assert'
  cargo:warning=    (__builtin_expect(!(e), 0) ? __assert_rtn(__func__, __FILE__, __LINE__, #e) : (void)0)
  cargo:warning=                        ^
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4016:45: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=        if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation
  cargo:warning=                                   ~~~~~~~~ ^ ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4021:50: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding
  cargo:warning=                                        ~~~~~~~~ ^ ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4023:38: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=                for (k = s->k + 2; k < c->n_cigar; ++k) {
  cargo:warning=                                   ~ ^ ~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4073:14: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=    while (k < p->b->core.n_cigar) {
  cargo:warning=           ~ ^ ~~~~~~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4093:14: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=    while (k < p->b->core.n_cigar) {
  cargo:warning=           ~ ^ ~~~~~~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4097:27: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            for (l = 0; l < (cigar[k]>>BAM_CIGAR_SHIFT); l++)
  cargo:warning=                        ~ ^  ~~~~~~~~~~~~~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4101:27: warning: comparison of integers of different signs: 'int' and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            for (l = 0; l < (cigar[k]>>BAM_CIGAR_SHIFT); l++, j++) {
  cargo:warning=                        ~ ^  ~~~~~~~~~~~~~~~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4672:30: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            if (iter->tid[i] < new_min_tid) {
  cargo:warning=                ~~~~~~~~~~~~ ^ ~~~~~~~~~~~
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:4675:37: warning: comparison of integers of different signs: 'int32_t' (aka 'int') and 'uint32_t' (aka 'unsigned int') [-Wsign-compare]
  cargo:warning=            } else if (iter->tid[i] == new_min_tid && iter->pos[i] < new_min_pos) {
  cargo:warning=                       ~~~~~~~~~~~~ ^  ~~~~~~~~~~~
  exit code: 0
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/textutils.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/textutils.c"
  cargo:warning=47 warnings and 1 error generated.
  exit code: 1
  running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/thread_pool.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/thread_pool.c"
  exit code: 0
  cargo:warning=In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/textutils.c:31:
  cargo:warning=/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/htslib/hfile.h:271:35: warning: comparison of integers of different signs: 'long' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
  cargo:warning=        if (fp->limit - fp->begin < nbytes){
  cargo:warning=            ~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~
  cargo:warning=14 warnings generated.
  exit code: 0
  cargo:warning=1 warning generated.
  exit code: 0
  exit code: 0

  --- stderr


  error occurred: Command "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c" with args "cc" did not execute successfully (status code exit code: 1).

[edmundlth]

(Sorry for the spam)
Running the failed cc command manually in verbose mode generate the following (warnings removed):

cc -v "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-arch" "x86_64" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include" "-I" "/Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api" "-I" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include" "-Wall" "-Wextra" "-o" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.o" "-c" "/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c"
Apple clang version 12.0.0 (clang-1200.0.31.1)
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
 "/Library/Developer/CommandLineTools/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.15.0 -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -Werror=implicit-function-declaration -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -discard-value-names -main-file-name sam.c -mrelocation-model pic -pic-level 2 -mthread-model posix -mframe-pointer=all -fno-strict-return -masm-verbose -munwind-tables -target-sdk-version=10.15.6 -fcompatibility-qualified-id-block-type-checking -target-cpu penryn -dwarf-column-info -debug-info-kind=standalone -dwarf-version=4 -debugger-tuning=lldb -target-linker-version 609 -v -ffunction-sections -fdata-sections -resource-dir /Library/Developer/CommandLineTools/usr/lib/clang/12.0.0 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk -I /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib -I /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include -I /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include -I /Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api -I /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include -I/usr/local/include -internal-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/local/include -internal-isystem /Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include -internal-externc-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include -internal-externc-isystem /Library/Developer/CommandLineTools/usr/include -O0 -Wall -Wextra -Wno-reorder-init-list -Wno-implicit-int-float-conversion -Wno-c99-designator -Wno-final-dtor-non-final-class -Wno-extra-semi-stmt -Wno-misleading-indentation -Wno-quoted-include-in-framework-header -Wno-implicit-fallthrough -Wno-enum-enum-conversion -Wno-enum-float-conversion -fdebug-compilation-dir /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib -ferror-limit 19 -fmessage-length 318 -stack-protector 1 -fstack-check -mdarwin-stkchk-strong-link -fblocks -fencode-extended-block-signature -fregister-global-dtors-with-atexit -fgnuc-version=4.2.1 -fobjc-runtime=macosx-10.15.0 -fmax-type-align=16 -fdiagnostics-show-option -fcolor-diagnostics -o /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.o -x c /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c
clang -cc1 version 12.0.0 (clang-1200.0.31.1) default target x86_64-apple-darwin19.6.0
ignoring nonexistent directory "/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/local/include"
ignoring nonexistent directory "/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/Library/Frameworks"
#include "..." search starts here:
#include <...> search starts here:
 /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib
 /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/libz-sys-7c94d09687ec3ebf/out/include
 /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/bzip2-sys-1b34115e67e42ca9/out/include
 /Users/admin/.cargo/registry/src/github.com-1ecc6299db9ec823/lzma-sys-0.1.16/xz-5.2/src/liblzma/api
 /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/curl-sys-6886d1c85d5521de/out/include
 /usr/local/include
 /Library/Developer/CommandLineTools/usr/lib/clang/12.0.0/include
 /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include
 /Library/Developer/CommandLineTools/usr/include
 /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Frameworks (framework directory)
End of search list.
In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:46:
In file included from /Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/cram/cram.h:52:
/Users/admin/Desktop/MGHA_bioinformatics/PROJECT_rust_bio/rust-htslib/target/debug/build/hts-sys-bf3eaa6abc104e1b/out/htslib/sam.c:2331:21: error: implicit declaration of function 'usleep' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
                    usleep(10000);
                    ^
47 warnings and 1 error generated.

[andrewpatto]

On a similar Mac, but with Xcode 11 it builds fine. So maybe an Xcode 12/clang 12 being especially finicky about the C99 spec?

[brainstorm]

Yeah, I was suspecting something along those lines... @edmundlth can you take a look at this:

https://github.com/samtools/htslib/blob/develop/Makefile#L36

And try to modify the build.rs accordingly so that it (hopefully) builds with your compiler? build.rs files work like this:

https://doc.rust-lang.org/cargo/reference/build-scripts.html

[edmundlth]

By the way,
cross build succeeded when I added
#include <unistd.h> here https://github.com/samtools/htslib/blob/9279d76e1186d7155ceea9db9db8c9298f6139bd/sam.c#L37
which is where usleep() is defined I think.

[brainstorm]

Aha, interesting... could you compare with upstream htslib and see if that header is present there in more recent versions? We are pinning htslib to 1.0.2 via submodule IIRC, maybe it's just time to track newer commits from upstream and not lose version wagon :)

[brainstorm]

Or even just submodule update --remote --init to a newer version and retry cross build?

[edmundlth]

This fails with the same error on sam.c:

$ git submodule update --remote --init 
$ cargo clean
$ cross build

and

cd rust-htslib/hts-sys/htslib
git diff origin sam.c

doesn't reveal any changes in preprocessing part of sam.c source code.

[brainstorm]

@edmundlth Since you managed to pull off #263, I guess you got this issue sorted? Please let us know how if so :)

[brainstorm]

@edmundlth Actually, sorry, my bad, I recall you switched to cargo doc because you couldn't compile w/ XCode 12.

With the newest htslib merged in #270 , could you give it a try now? The changelog lists some .h's included and some build system improvements, perhaps your compiler will not be as angry now? Thanks a ton in advance!

[pjedge]

I get this same error, even after switching to #270

[pjedge]

Solved by downgrading to Xcode 11.5