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  • #31
    What version of OS X and XCode are you running? You are issuing the make command inside the samtools-0.1.19 directory, correct?

    Comment


    • #32
      I'm using OS X ver 10.9.2 and Xcode 5.1 (5B130a) and yes I'm issuing the command into the samtools-0.1.19 directory.

      Comment


      • #33
        You have perhaps tried this already but if not can you start with a fresh download of the source and retry the compilation?

        I assume your samtools directory is right under /Users/Tiger. I am not sure why you are getting errors for that top level directory.

        Comment


        • #34
          That directory is "/Users/Tiger Mac"... and not just "/Users/Tiger". Now that you've pointed it out it must be that space that is giving me trouble.

          I created a new user with admin privileges and started from scratch there. Was able to successfully compile Samtools with the resulting executable! Thank you.

          I still get a long list of warnings as follows but not that last bit about there being "No such file or directory". I'm assuming the warnings are not serious.

          computer-3esktop unixuser$ cd samtools-0.1.19
          computer-3:samtools-0.1.19 unixuser$ make
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
          bgzf.c:82:1: warning: unused function 'kh_clear_cache' [-Wunused-function]
          KHASH_MAP_INIT_INT64(cache, cache_t)
          ^
          ./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
          KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_i...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:91:1: note: expanded from here
          kh_clear_cache
          ^
          1 warning generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
          bam_aux.c:5:1: warning: unused function 'kh_clear_s' [-Wunused-function]
          KHASH_MAP_INIT_STR(s, int)
          ^
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:193:1: note: expanded from here
          kh_clear_s
          ^
          bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function]
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:207:1: note: expanded from here
          kh_del_s
          ^
          bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function]
          KHASH_MAP_INIT_STR(r2l, str_p)
          ^
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
          SCOPE kh_##name##_t *kh_init_##name() ...
          ^
          <scratch space>:214:1: note: expanded from here
          kh_init_r2l
          ^
          bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function]
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_destroy_##name(kh_##name##_t *h...
          ^
          <scratch space>:219:1: note: expanded from here
          kh_destroy_r2l
          ^
          bam_aux.c:6:1: warning: unused function 'kh_clear_r2l' [-Wunused-function]
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:222:1: note: expanded from here
          kh_clear_r2l
          ^
          bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function]
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
          SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key...
          ^
          <scratch space>:225:1: note: expanded from here
          kh_get_r2l
          ^
          bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function]
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
          SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
          ^
          <scratch space>:231:1: note: expanded from here
          kh_put_r2l
          ^
          bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function]
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:236:1: note: expanded from here
          kh_del_r2l
          ^
          8 warnings generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
          bam_import.c:18:1: warning: unused function 'kh_clear_ref' [-Wunused-function]
          KHASH_MAP_INIT_STR(ref, uint64_t)
          ^
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:193:1: note: expanded from here
          kh_clear_ref
          ^
          bam_import.c:18:1: warning: unused function 'kh_get_ref' [-Wunused-function]
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
          SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key...
          ^
          <scratch space>:196:1: note: expanded from here
          kh_get_ref
          ^
          bam_import.c:18:1: warning: unused function 'kh_del_ref' [-Wunused-function]
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:207:1: note: expanded from here
          kh_del_ref
          ^
          3 warnings generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
          bam_index.c:64:1: warning: unused function 'kh_clear_i' [-Wunused-function]
          KHASH_MAP_INIT_INT(i, bam_binlist_t)
          ^
          ./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
          KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:211:1: note: expanded from here
          kh_clear_i
          ^
          bam_index.c:64:1: warning: unused function 'kh_del_i' [-Wunused-function]
          ./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
          KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:225:1: note: expanded from here
          kh_del_i
          ^
          2 warnings generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
          faidx.c:14:1: warning: unused function 'kh_clear_s' [-Wunused-function]
          KHASH_MAP_INIT_STR(s, faidx1_t)
          ^
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:154:1: note: expanded from here
          kh_clear_s
          ^
          faidx.c:14:1: warning: unused function 'kh_del_s' [-Wunused-function]
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:168:1: note: expanded from here
          kh_del_s
          ^
          2 warnings generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
          bedidx.c:24:1: warning: unused function 'kh_clear_reg' [-Wunused-function]
          KHASH_MAP_INIT_STR(reg, bed_reglist_t)
          ^
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:207:1: note: expanded from here
          kh_clear_reg
          ^
          bedidx.c:24:1: warning: unused function 'kh_del_reg' [-Wunused-function]
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:221:1: note: expanded from here
          kh_del_reg
          ^
          2 warnings generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
          sam_header.c:9:1: warning: unused function 'kh_clear_str' [-Wunused-function]
          KHASH_MAP_INIT_STR(str, const char *)
          ^
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:154:1: note: expanded from here
          kh_clear_str
          ^
          sam_header.c:9:1: warning: unused function 'kh_del_str' [-Wunused-function]
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:168:1: note: expanded from here
          kh_del_str
          ^
          2 warnings generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
          ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
          vcf.c:243:15: warning: explicitly assigning a variable of type 'int' to itself
          [-Wself-assign]
          endblock: i = i;
          ~ ^ ~
          vcf.c:8:1: warning: unused function 'ks_getc' [-Wunused-function]
          KSTREAM_INIT(gzFile, gzread, 4096)
          ^
          ../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
          __KS_GETC(__read, __bufsize) \
          ^
          ../kseq.h:67:20: note: expanded from macro '__KS_GETC'
          static inline int ks_getc(kstream_t *ks...
          ^
          2 warnings generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
          bcfutils.c:7:1: warning: unused function 'kh_clear_str2id' [-Wunused-function]
          KHASH_MAP_INIT_STR(str2id, int)
          ^
          ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:34:1: note: expanded from here
          kh_clear_str2id
          ^
          bcfutils.c:7:1: warning: unused function 'kh_del_str2id' [-Wunused-function]
          ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:48:1: note: expanded from here
          kh_del_str2id
          ^
          2 warnings generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
          prob1.c:13:1: warning: unused function 'ks_getc' [-Wunused-function]
          KSTREAM_INIT(gzFile, gzread, 16384)
          ^
          ../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
          __KS_GETC(__read, __bufsize) \
          ^
          ../kseq.h:67:20: note: expanded from macro '__KS_GETC'
          static inline int ks_getc(kstream_t *ks...
          ^
          1 warning generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
          ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
          make[2]: Nothing to be done for `lib'.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
          sam_view.c:12:1: warning: unused function 'kh_clear_rg' [-Wunused-function]
          KHASH_SET_INIT_STR(rg)
          ^
          ./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_ha...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:34:1: note: expanded from here
          kh_clear_rg
          ^
          sam_view.c:12:1: warning: unused function 'kh_del_rg' [-Wunused-function]
          ./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_ha...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:48:1: note: expanded from here
          kh_del_rg
          ^
          2 warnings generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
          bam_rmdup.c:12:1: warning: unused function 'kh_get_pos' [-Wunused-function]
          KHASH_MAP_INIT_INT64(pos, bam1_p)
          ^
          ./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
          KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_i...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
          SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key...
          ^
          <scratch space>:225:1: note: expanded from here
          kh_get_pos
          ^
          bam_rmdup.c:12:1: warning: unused function 'kh_del_pos' [-Wunused-function]
          ./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
          KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_i...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:236:1: note: expanded from here
          kh_del_pos
          ^
          bam_rmdup.c:20:1: warning: unused function 'kh_clear_lib' [-Wunused-function]
          KHASH_MAP_INIT_STR(lib, lib_aux_t)
          ^
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:253:1: note: expanded from here
          kh_clear_lib
          ^
          bam_rmdup.c:20:1: warning: unused function 'kh_del_lib' [-Wunused-function]
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:267:1: note: expanded from here
          kh_del_lib
          ^
          4 warnings generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
          bam_rmdupse.c:18:1: warning: unused function 'kh_clear_best' [-Wunused-function]
          KHASH_MAP_INIT_INT(best, elem_p)
          ^
          ./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
          KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:95:1: note: expanded from here
          kh_clear_best
          ^
          bam_rmdupse.c:18:1: warning: unused function 'kh_get_best' [-Wunused-function]
          ./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
          KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
          SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key...
          ^
          <scratch space>:98:1: note: expanded from here
          kh_get_best
          ^
          bam_rmdupse.c:25:1: warning: unused function 'kh_clear_lib' [-Wunused-function]
          KHASH_MAP_INIT_STR(lib, lib_aux_t)
          ^
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:126:1: note: expanded from here
          kh_clear_lib
          ^
          bam_rmdupse.c:25:1: warning: unused function 'kh_del_lib' [-Wunused-function]
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:140:1: note: expanded from here
          kh_del_lib
          ^
          4 warnings generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
          bam2bcf_indel.c:32:52: warning: for loop has empty body [-Wempty-body]
          ...for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
          ^
          bam2bcf_indel.c:32:52: note: put the semicolon on a separate line to silence
          this warning
          bam2bcf_indel.c:33:52: warning: for loop has empty body [-Wempty-body]
          ...for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q;
          ^
          bam2bcf_indel.c:33:52: note: put the semicolon on a separate line to silence
          this warning
          bam2bcf_indel.c:9:1: warning: unused function 'kh_clear_rg' [-Wunused-function]
          KHASH_SET_INIT_STR(rg)
          ^
          ./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_ha...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:193:1: note: expanded from here
          kh_clear_rg
          ^
          bam2bcf_indel.c:9:1: warning: unused function 'kh_del_rg' [-Wunused-function]
          ./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_ha...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:207:1: note: expanded from here
          kh_del_rg
          ^
          4 warnings generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
          errmod.c:79:8: warning: self-comparison always evaluates to false
          [-Wtautological-compare]
          if (m > m) return -1;
          ^
          1 warning generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
          sample.c:5:1: warning: unused function 'kh_clear_sm' [-Wunused-function]
          KHASH_MAP_INIT_STR(sm, int)
          ^
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:136:1: note: expanded from here
          kh_clear_sm
          ^
          sample.c:5:1: warning: unused function 'kh_del_sm' [-Wunused-function]
          ./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:150:1: note: expanded from here
          kh_del_sm
          ^
          2 warnings generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
          phase.c:45:1: warning: unused function 'kh_clear_set64' [-Wunused-function]
          KHASH_SET_INIT_INT64(set64)
          ^
          ./khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64'
          KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int6...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:40:1: note: expanded from here
          kh_clear_set64
          ^
          phase.c:45:1: warning: unused function 'kh_del_set64' [-Wunused-function]
          ./khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64'
          KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int6...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:54:1: note: expanded from here
          kh_del_set64
          ^
          phase.c:46:1: warning: unused function 'kh_clear_64' [-Wunused-function]
          KHASH_MAP_INIT_INT64(64, frag_t)
          ^
          ./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
          KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_i...
          ^
          ./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:69:1: note: expanded from here
          kh_clear_64
          ^
          3 warnings generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
          bedcov.c:12:1: warning: unused function 'ks_getc' [-Wunused-function]
          KSTREAM_INIT(gzFile, gzread, 16384)
          ^
          ./kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
          __KS_GETC(__read, __bufsize) \
          ^
          ./kseq.h:67:20: note: expanded from macro '__KS_GETC'
          static inline int ks_getc(kstream_t *ks...
          ^
          1 warning generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
          gcc -g -Wall -O2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
          call1.c:17:1: warning: unused function 'ks_getc' [-Wunused-function]
          KSTREAM_INIT(gzFile, gzread, 16384)
          ^
          ../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
          __KS_GETC(__read, __bufsize) \
          ^
          ../kseq.h:67:20: note: expanded from macro '__KS_GETC'
          static inline int ks_getc(kstream_t *ks...
          ^
          1 warning generated.
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
          main.c:9:1: warning: unused function 'ks_getc' [-Wunused-function]
          KSTREAM_INIT(gzFile, gzread, 0x10000)
          ^
          ../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
          __KS_GETC(__read, __bufsize) \
          ^
          ../kseq.h:67:20: note: expanded from macro '__KS_GETC'
          static inline int ks_getc(kstream_t *ks...
          ^
          1 warning generated.
          gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
          gcc -c -g -Wall -O2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
          md5.c:155:27: warning: 'memset' call operates on objects of type
          'struct MD5Context' while the size is based on a different type
          'struct MD5Context *' [-Wsizeof-pointer-memaccess]
          memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
          ~~~ ^~~
          md5.c:155:27: note: did you mean to dereference the argument to 'sizeof' (and
          multiply it by the number of elements)?
          memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
          ^~~
          1 warning generated.
          gcc -g -Wall -O2 -o md5sum-lite md5sum-lite.o
          gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
          md5.c:155:27: warning: 'memset' call operates on objects of type
          'struct MD5Context' while the size is based on a different type
          'struct MD5Context *' [-Wsizeof-pointer-memaccess]
          memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
          ~~~ ^~~
          md5.c:155:27: note: did you mean to dereference the argument to 'sizeof' (and
          multiply it by the number of elements)?
          memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
          ^~~
          1 warning generated.
          gcc -g -Wall -O2 -c -I.. -o md5fa.o md5fa.c
          gcc -g -Wall -O2 -o md5fa md5.o md5fa.o -lz
          gcc -g -Wall -O2 -o maq2sam-short maq2sam.c -lz
          gcc -g -Wall -O2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
          gcc -g -Wall -O2 -c -I.. -o ace2sam.o ace2sam.c
          ace2sam.c:33:1: warning: unused function 'ks_getc' [-Wunused-function]
          KSTREAM_INIT(gzFile, gzread, 16384)
          ^
          ../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
          __KS_GETC(__read, __bufsize) \
          ^
          ../kseq.h:67:20: note: expanded from macro '__KS_GETC'
          static inline int ks_getc(kstream_t *ks...
          ^
          1 warning generated.
          gcc -g -Wall -O2 -o ace2sam ace2sam.o -lz
          gcc -g -Wall -O2 -c -I.. -o wgsim.o wgsim.c
          gcc -g -Wall -O2 -o wgsim wgsim.o -lm -lz
          gcc -g -Wall -O2 -c -I.. -o bamcheck.o bamcheck.c
          bamcheck.c:52:1: warning: unused function 'kh_init_kh_faidx' [-Wunused-function]
          KHASH_MAP_INIT_STR(kh_faidx, faidx1_t)
          ^
          ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ../khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
          SCOPE kh_##name##_t *kh_init_##name() ...
          ^
          <scratch space>:35:1: note: expanded from here
          kh_init_kh_faidx
          ^
          bamcheck.c:52:1: warning: unused function 'kh_destroy_kh_faidx'
          [-Wunused-function]
          ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ../khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_destroy_##name(kh_##name##_t *h...
          ^
          <scratch space>:40:1: note: expanded from here
          kh_destroy_kh_faidx
          ^
          bamcheck.c:52:1: warning: unused function 'kh_clear_kh_faidx'
          [-Wunused-function]
          ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:43:1: note: expanded from here
          kh_clear_kh_faidx
          ^
          bamcheck.c:52:1: warning: unused function 'kh_put_kh_faidx' [-Wunused-function]
          ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ../khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
          SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
          ^
          <scratch space>:52:1: note: expanded from here
          kh_put_kh_faidx
          ^
          bamcheck.c:52:1: warning: unused function 'kh_del_kh_faidx' [-Wunused-function]
          ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:57:1: note: expanded from here
          kh_del_kh_faidx
          ^
          bamcheck.c:53:1: warning: unused function 'kh_init_kh_bam_tid'
          [-Wunused-function]
          KHASH_MAP_INIT_STR(kh_bam_tid, int)
          ^
          ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ../khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
          SCOPE kh_##name##_t *kh_init_##name() ...
          ^
          <scratch space>:64:1: note: expanded from here
          kh_init_kh_bam_tid
          ^
          bamcheck.c:53:1: warning: unused function 'kh_destroy_kh_bam_tid'
          [-Wunused-function]
          ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ../khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_destroy_##name(kh_##name##_t *h...
          ^
          <scratch space>:69:1: note: expanded from here
          kh_destroy_kh_bam_tid
          ^
          bamcheck.c:53:1: warning: unused function 'kh_clear_kh_bam_tid'
          [-Wunused-function]
          ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:72:1: note: expanded from here
          kh_clear_kh_bam_tid
          ^
          bamcheck.c:53:1: warning: unused function 'kh_put_kh_bam_tid'
          [-Wunused-function]
          ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ../khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
          SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
          ^
          <scratch space>:81:1: note: expanded from here
          kh_put_kh_bam_tid
          ^
          bamcheck.c:53:1: warning: unused function 'kh_del_kh_bam_tid'
          [-Wunused-function]
          ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:86:1: note: expanded from here
          kh_del_kh_bam_tid
          ^
          bamcheck.c:54:1: warning: unused function 'kh_clear_kh_rg' [-Wunused-function]
          KHASH_MAP_INIT_STR(kh_rg, const char *)
          ^
          ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_clear_##name(kh_##name##_t *h...
          ^
          <scratch space>:101:1: note: expanded from here
          kh_clear_kh_rg
          ^
          bamcheck.c:54:1: warning: unused function 'kh_del_kh_rg' [-Wunused-function]
          ../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
          KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str...
          ^
          ../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
          KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __...
          ^
          ../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
          SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x...
          ^
          <scratch space>:115:1: note: expanded from here
          kh_del_kh_rg
          ^
          12 warnings generated.
          gcc -g -Wall -O2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz

          Comment


          • #35
            Spaces in file/directory names will result in unforeseen consequences. If you are coming to Unix from PC/Mac it is a good idea to get into the habit of putting "_" in names when you feel like using a space.

            I am little surprised that you are seeing so many warnings but as long as the executable was made and you are able to run it I think it should be fine to go forward.

            Comment


            • #36
              I had basically the same problem as many on this thread. I have a mac and recently "upgraded" to Mavericks. What ended up working was deleting every version of samtools I have from my laptop. Then following the post I'm quoting here exactly. I didn't even move samtools after I downloaded it, I left it in the Downloads folder just to be safe and now it works. Thank you to all of those that contributed to this thread. I then used another post to place samtools in my PATH and that worked too.



              Originally posted by GenoMax View Post
              1. Download and install Xcode 5.1 from app store if you have not done so already.
              2. Download samtools source from: http://sourceforge.net/projects/samt...d?source=files
              3. Change to the directory where you downloaded the source file.

              Code:
              $ bunzip2 samtools*.bz2
              $ tar -xvf samtools-0.1.19.tar
              $ cd samtools-0.1.19
              $ make
              If all goes well there should be an executable produced that you can test run

              Code:
              $ ./samtools
              You strictly do not have to "install", but if you want you could copy the executable to a directory that is in your $PATH in case you do not want to provide full path to the samtools executable when you run it.

              Comment

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