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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SICtools
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘SICtools’ ...
** this is package ‘SICtools’ version ‘1.41.0’
** using staged installation
** libs
Makefile:24: warning: overriding commands for target `.c.o'
/Library/Frameworks/R.framework/Resources/etc/Makeconf:190: warning: ignoring old commands for target `.c.o'
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:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
392 | int i, tmp, stop = 0;
| ^
bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
572 | int ret, count, block_length;
| ^
bgzf.c:82:1: warning: unused function 'kh_clear_cache' [-Wunused-function]
82 | KHASH_MAP_INIT_INT64(cache, cache_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
510 | KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:53:1: note: expanded from here
53 | kh_clear_cache
| ^~~~~~~~~~~~~~
3 warnings 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]
5 | KHASH_MAP_INIT_STR(s, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:32:1: note: expanded from here
32 | kh_clear_s
| ^~~~~~~~~~
bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function]
5 | KHASH_MAP_INIT_STR(s, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:46:1: note: expanded from here
46 | kh_del_s
| ^~~~~~~~
bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function]
6 | KHASH_MAP_INIT_STR(r2l, str_p)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
168 | SCOPE kh_##name##_t *kh_init_##name() { \
| ^~~~~~~~~~~~~~
<scratch space>:53:1: note: expanded from here
53 | kh_init_r2l
| ^~~~~~~~~~~
bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function]
6 | KHASH_MAP_INIT_STR(r2l, str_p)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
171 | SCOPE void kh_destroy_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~~~
<scratch space>:58:1: note: expanded from here
58 | kh_destroy_r2l
| ^~~~~~~~~~~~~~
bam_aux.c:6:1: warning: unused function 'kh_clear_r2l' [-Wunused-function]
6 | KHASH_MAP_INIT_STR(r2l, str_p)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:61:1: note: expanded from here
61 | kh_clear_r2l
| ^~~~~~~~~~~~
bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function]
6 | KHASH_MAP_INIT_STR(r2l, str_p)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
186 | SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
| ^~~~~~~~~~~~~
<scratch space>:64:1: note: expanded from here
64 | kh_get_r2l
| ^~~~~~~~~~
bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function]
6 | KHASH_MAP_INIT_STR(r2l, str_p)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
260 | SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
| ^~~~~~~~~~~~~
<scratch space>:70:1: note: expanded from here
70 | kh_put_r2l
| ^~~~~~~~~~
bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function]
6 | KHASH_MAP_INIT_STR(r2l, str_p)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:75:1: note: expanded from here
75 | 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]
18 | KHASH_MAP_INIT_STR(ref, uint64_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:32:1: note: expanded from here
32 | kh_clear_ref
| ^~~~~~~~~~~~
bam_import.c:18:1: warning: unused function 'kh_get_ref' [-Wunused-function]
18 | KHASH_MAP_INIT_STR(ref, uint64_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
186 | SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
| ^~~~~~~~~~~~~
<scratch space>:35:1: note: expanded from here
35 | kh_get_ref
| ^~~~~~~~~~
bam_import.c:18:1: warning: unused function 'kh_del_ref' [-Wunused-function]
18 | KHASH_MAP_INIT_STR(ref, uint64_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:46:1: note: expanded from here
46 | 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]
64 | KHASH_MAP_INIT_INT(i, bam_binlist_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
495 | KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:52:1: note: expanded from here
52 | kh_clear_i
| ^~~~~~~~~~
bam_index.c:64:1: warning: unused function 'kh_del_i' [-Wunused-function]
64 | KHASH_MAP_INIT_INT(i, bam_binlist_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
495 | KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:66:1: note: expanded from here
66 | 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
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
75 | int k, is_head = 0;
| ^
1 warning generated.
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]
14 | KHASH_MAP_INIT_STR(s, faidx1_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:81:1: note: expanded from here
81 | kh_clear_s
| ^~~~~~~~~~
faidx.c:14:1: warning: unused function 'kh_del_s' [-Wunused-function]
14 | KHASH_MAP_INIT_STR(s, faidx1_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:95:1: note: expanded from here
95 | 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]
24 | KHASH_MAP_INIT_STR(reg, bed_reglist_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:46:1: note: expanded from here
46 | kh_clear_reg
| ^~~~~~~~~~~~
bedidx.c:24:1: warning: unused function 'kh_del_reg' [-Wunused-function]
24 | KHASH_MAP_INIT_STR(reg, bed_reglist_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:60:1: note: expanded from here
60 | 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]
9 | KHASH_MAP_INIT_STR(str, const char *)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:74:1: note: expanded from here
74 | kh_clear_str
| ^~~~~~~~~~~~
sam_header.c:9:1: warning: unused function 'kh_del_str' [-Wunused-function]
9 | KHASH_MAP_INIT_STR(str, const char *)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:88:1: note: expanded from here
88 | 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
bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
12 | bam_header_t *old;
| ^
1 warning generated.
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
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
78 | int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
| ^
1 warning generated.
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
bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
233 | int iPL = -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.. -I. vcf.c -o vcf.o
vcf.c:243:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
243 | endblock: i = i;
| ~ ^ ~
vcf.c:8:1: warning: unused function 'ks_getc' [-Wunused-function]
8 | KSTREAM_INIT(gzFile, gzread, 4096)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
146 | __KS_GETC(__read, __bufsize) \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../kseq.h:67:20: note: expanded from macro '__KS_GETC'
67 | 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:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
119 | int ipl=-1, igt=-1;
| ^
bcfutils.c:7:1: warning: unused function 'kh_clear_str2id' [-Wunused-function]
7 | KHASH_MAP_INIT_STR(str2id, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:65:1: note: expanded from here
65 | kh_clear_str2id
| ^~~~~~~~~~~~~~~
bcfutils.c:7:1: warning: unused function 'kh_del_str2id' [-Wunused-function]
7 | KHASH_MAP_INIT_STR(str2id, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:79:1: note: expanded from here
79 | kh_del_str2id
| ^~~~~~~~~~~~~
3 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]
13 | KSTREAM_INIT(gzFile, gzread, 16384)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
146 | __KS_GETC(__read, __bufsize) \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../kseq.h:67:20: note: expanded from macro '__KS_GETC'
67 | 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
em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
174 | int i, n, n2;
| ^
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. 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
bam_plcmd.c:333:28: warning: variable 'ref16' set but not used [-Wunused-but-set-variable]
333 | int total_depth, _ref0, ref16;
| ^
1 warning generated.
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]
12 | KHASH_SET_INIT_STR(rg)
| ^~~~~~~~~~~~~~~~~~~~~~
./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
518 | KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:78:1: note: expanded from here
78 | kh_clear_rg
| ^~~~~~~~~~~
sam_view.c:12:1: warning: unused function 'kh_del_rg' [-Wunused-function]
12 | KHASH_SET_INIT_STR(rg)
| ^~~~~~~~~~~~~~~~~~~~~~
./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
518 | KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:92:1: note: expanded from here
92 | 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]
12 | KHASH_MAP_INIT_INT64(pos, bam1_p)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
510 | KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
186 | SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
| ^~~~~~~~~~~~~
<scratch space>:64:1: note: expanded from here
64 | kh_get_pos
| ^~~~~~~~~~
bam_rmdup.c:12:1: warning: unused function 'kh_del_pos' [-Wunused-function]
12 | KHASH_MAP_INIT_INT64(pos, bam1_p)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
510 | KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:75:1: note: expanded from here
75 | kh_del_pos
| ^~~~~~~~~~
bam_rmdup.c:20:1: warning: unused function 'kh_clear_lib' [-Wunused-function]
20 | KHASH_MAP_INIT_STR(lib, lib_aux_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:92:1: note: expanded from here
92 | kh_clear_lib
| ^~~~~~~~~~~~
bam_rmdup.c:20:1: warning: unused function 'kh_del_lib' [-Wunused-function]
20 | KHASH_MAP_INIT_STR(lib, lib_aux_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:106:1: note: expanded from here
106 | 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]
18 | KHASH_MAP_INIT_INT(best, elem_p)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
495 | KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:114:1: note: expanded from here
114 | kh_clear_best
| ^~~~~~~~~~~~~
bam_rmdupse.c:18:1: warning: unused function 'kh_get_best' [-Wunused-function]
18 | KHASH_MAP_INIT_INT(best, elem_p)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT'
495 | KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:186:16: note: expanded from macro 'KHASH_INIT2'
186 | SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \
| ^~~~~~~~~~~~~
<scratch space>:117:1: note: expanded from here
117 | kh_get_best
| ^~~~~~~~~~~
bam_rmdupse.c:25:1: warning: unused function 'kh_clear_lib' [-Wunused-function]
25 | KHASH_MAP_INIT_STR(lib, lib_aux_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:145:1: note: expanded from here
145 | kh_clear_lib
| ^~~~~~~~~~~~
bam_rmdupse.c:25:1: warning: unused function 'kh_del_lib' [-Wunused-function]
25 | KHASH_MAP_INIT_STR(lib, lib_aux_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:159:1: note: expanded from here
159 | 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]
32 | 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]
33 | 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:119:73: warning: variable 'score1' set but not used [-Wunused-but-set-variable]
119 | int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
| ^
bam2bcf_indel.c:119:82: warning: variable 'score2' set but not used [-Wunused-but-set-variable]
119 | int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
| ^
bam2bcf_indel.c:120:9: warning: variable 'l_run' set but not used [-Wunused-but-set-variable]
120 | int N, l_run, ref_type;
| ^
bam2bcf_indel.c:120:16: warning: variable 'ref_type' set but not used [-Wunused-but-set-variable]
120 | int N, l_run, ref_type;
| ^
bam2bcf_indel.c:121:21: warning: variable 'ref2' set but not used [-Wunused-but-set-variable]
121 | char *inscns = 0, *ref2, *query, **ref_sample;
| ^
bam2bcf_indel.c:121:28: warning: variable 'query' set but not used [-Wunused-but-set-variable]
121 | char *inscns = 0, *ref2, *query, **ref_sample;
| ^
bam2bcf_indel.c:9:1: warning: unused function 'kh_clear_rg' [-Wunused-function]
9 | KHASH_SET_INIT_STR(rg)
| ^~~~~~~~~~~~~~~~~~~~~~
./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
518 | KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:31:1: note: expanded from here
31 | kh_clear_rg
| ^~~~~~~~~~~
bam2bcf_indel.c:9:1: warning: unused function 'kh_del_rg' [-Wunused-function]
9 | KHASH_SET_INIT_STR(rg)
| ^~~~~~~~~~~~~~~~~~~~~~
./khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR'
518 | KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:45:1: note: expanded from here
45 | kh_del_rg
| ^~~~~~~~~
bam2bcf_indel.c:92:19: warning: unused function 'est_seqQ' [-Wunused-function]
92 | static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run)
| ^~~~~~~~
11 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]
79 | 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]
5 | KHASH_MAP_INIT_STR(sm, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:60:1: note: expanded from here
60 | kh_clear_sm
| ^~~~~~~~~~~
sample.c:5:1: warning: unused function 'kh_del_sm' [-Wunused-function]
5 | KHASH_MAP_INIT_STR(sm, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:74:1: note: expanded from here
74 | 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
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
137 | int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l;
| ^
1 warning generated.
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]
45 | KHASH_SET_INIT_INT64(set64)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64'
502 | KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:70:1: note: expanded from here
70 | kh_clear_set64
| ^~~~~~~~~~~~~~
phase.c:45:1: warning: unused function 'kh_del_set64' [-Wunused-function]
45 | KHASH_SET_INIT_INT64(set64)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64'
502 | KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:84:1: note: expanded from here
84 | kh_del_set64
| ^~~~~~~~~~~~
phase.c:46:1: warning: unused function 'kh_clear_64' [-Wunused-function]
46 | KHASH_MAP_INIT_INT64(64, frag_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64'
510 | KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:99:1: note: expanded from here
99 | 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]
12 | KSTREAM_INIT(gzFile, gzread, 16384)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
146 | __KS_GETC(__read, __bufsize) \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
./kseq.h:67:20: note: expanded from macro '__KS_GETC'
67 | 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 samtools2SIC 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]
17 | KSTREAM_INIT(gzFile, gzread, 16384)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
146 | __KS_GETC(__read, __bufsize) \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../kseq.h:67:20: note: expanded from macro '__KS_GETC'
67 | 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:62:12: warning: variable 'lineno' set but not used [-Wunused-but-set-variable]
62 | int dret, lineno = 0;
| ^
main.c:9:1: warning: unused function 'ks_getc' [-Wunused-function]
9 | KSTREAM_INIT(gzFile, gzread, 0x10000)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
146 | __KS_GETC(__read, __bufsize) \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../kseq.h:67:20: note: expanded from macro '__KS_GETC'
67 | static inline int ks_getc(kstream_t *ks) \
| ^~~~~~~
2 warnings 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:51:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
51 | void MD5Init(ctx)
| ^
md5.c:67:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
67 | void MD5Update(ctx, buf, len)
| ^
md5.c:116:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
116 | void MD5Final(digest, ctx)
| ^
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]
155 | 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)?
155 | memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
| ^~~
md5.c:176:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
176 | void MD5Transform(buf, in)
| ^
5 warnings 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:51:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
51 | void MD5Init(ctx)
| ^
md5.c:67:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
67 | void MD5Update(ctx, buf, len)
| ^
md5.c:116:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
116 | void MD5Final(digest, ctx)
| ^
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]
155 | 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)?
155 | memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */
| ^~~
md5.c:176:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype]
176 | void MD5Transform(buf, in)
| ^
5 warnings 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]
33 | KSTREAM_INIT(gzFile, gzread, 16384)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT'
146 | __KS_GETC(__read, __bufsize) \
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../kseq.h:67:20: note: expanded from macro '__KS_GETC'
67 | 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]
52 | KHASH_MAP_INIT_STR(kh_faidx, faidx1_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
168 | SCOPE kh_##name##_t *kh_init_##name() { \
| ^~~~~~~~~~~~~~
<scratch space>:51:1: note: expanded from here
51 | kh_init_kh_faidx
| ^~~~~~~~~~~~~~~~
bamcheck.c:52:1: warning: unused function 'kh_destroy_kh_faidx' [-Wunused-function]
52 | KHASH_MAP_INIT_STR(kh_faidx, faidx1_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
171 | SCOPE void kh_destroy_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~~~
<scratch space>:56:1: note: expanded from here
56 | kh_destroy_kh_faidx
| ^~~~~~~~~~~~~~~~~~~
bamcheck.c:52:1: warning: unused function 'kh_clear_kh_faidx' [-Wunused-function]
52 | KHASH_MAP_INIT_STR(kh_faidx, faidx1_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:59:1: note: expanded from here
59 | kh_clear_kh_faidx
| ^~~~~~~~~~~~~~~~~
bamcheck.c:52:1: warning: unused function 'kh_put_kh_faidx' [-Wunused-function]
52 | KHASH_MAP_INIT_STR(kh_faidx, faidx1_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
260 | SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
| ^~~~~~~~~~~~~
<scratch space>:68:1: note: expanded from here
68 | kh_put_kh_faidx
| ^~~~~~~~~~~~~~~
bamcheck.c:52:1: warning: unused function 'kh_del_kh_faidx' [-Wunused-function]
52 | KHASH_MAP_INIT_STR(kh_faidx, faidx1_t)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:73:1: note: expanded from here
73 | kh_del_kh_faidx
| ^~~~~~~~~~~~~~~
bamcheck.c:53:1: warning: unused function 'kh_init_kh_bam_tid' [-Wunused-function]
53 | KHASH_MAP_INIT_STR(kh_bam_tid, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:168:23: note: expanded from macro 'KHASH_INIT2'
168 | SCOPE kh_##name##_t *kh_init_##name() { \
| ^~~~~~~~~~~~~~
<scratch space>:80:1: note: expanded from here
80 | kh_init_kh_bam_tid
| ^~~~~~~~~~~~~~~~~~
bamcheck.c:53:1: warning: unused function 'kh_destroy_kh_bam_tid' [-Wunused-function]
53 | KHASH_MAP_INIT_STR(kh_bam_tid, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:171:13: note: expanded from macro 'KHASH_INIT2'
171 | SCOPE void kh_destroy_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~~~
<scratch space>:85:1: note: expanded from here
85 | kh_destroy_kh_bam_tid
| ^~~~~~~~~~~~~~~~~~~~~
bamcheck.c:53:1: warning: unused function 'kh_clear_kh_bam_tid' [-Wunused-function]
53 | KHASH_MAP_INIT_STR(kh_bam_tid, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:88:1: note: expanded from here
88 | kh_clear_kh_bam_tid
| ^~~~~~~~~~~~~~~~~~~
bamcheck.c:53:1: warning: unused function 'kh_put_kh_bam_tid' [-Wunused-function]
53 | KHASH_MAP_INIT_STR(kh_bam_tid, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:260:16: note: expanded from macro 'KHASH_INIT2'
260 | SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
| ^~~~~~~~~~~~~
<scratch space>:97:1: note: expanded from here
97 | kh_put_kh_bam_tid
| ^~~~~~~~~~~~~~~~~
bamcheck.c:53:1: warning: unused function 'kh_del_kh_bam_tid' [-Wunused-function]
53 | KHASH_MAP_INIT_STR(kh_bam_tid, int)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:102:1: note: expanded from here
102 | kh_del_kh_bam_tid
| ^~~~~~~~~~~~~~~~~
bamcheck.c:54:1: warning: unused function 'kh_clear_kh_rg' [-Wunused-function]
54 | KHASH_MAP_INIT_STR(kh_rg, const char *)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:179:13: note: expanded from macro 'KHASH_INIT2'
179 | SCOPE void kh_clear_##name(kh_##name##_t *h) \
| ^~~~~~~~~~~~~~~
<scratch space>:117:1: note: expanded from here
117 | kh_clear_kh_rg
| ^~~~~~~~~~~~~~
bamcheck.c:54:1: warning: unused function 'kh_del_kh_rg' [-Wunused-function]
54 | KHASH_MAP_INIT_STR(kh_rg, const char *)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR'
526 | KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:307:2: note: expanded from macro 'KHASH_INIT'
307 | KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../khash.h:298:13: note: expanded from macro 'KHASH_INIT2'
298 | SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \
| ^~~~~~~~~~~~~
<scratch space>:131:1: note: expanded from here
131 | kh_del_kh_rg
| ^~~~~~~~~~~~
12 warnings generated.
gcc -g -Wall -O2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
installing via 'install.libs.R' to /Library/Frameworks/R.framework/Versions/4.6/Resources/library/00LOCK-SICtools/00new/SICtools
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’
** testing if installed package keeps a record of temporary installation path
* DONE (SICtools)
