############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf SICtools.buildbin-libdir && mkdir SICtools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SICtools_1.36.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SICtools.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SICtools.buildbin-libdir SICtools_1.36.0.tar.gz' >>>>>>> * installing *source* package ‘SICtools’ ... ** using staged installation rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools2SIC *~ *.a *.so.* *.so *.dylib rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so* rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a ** libs Makefile:24: warning: overriding commands for target `.c.o' /Library/Frameworks/R.framework/Resources/etc/Makeconf:195: 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] int i, tmp, stop = 0; ^ bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable] int ret, count, block_length; ^ 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_int64_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :88:1: note: expanded from here 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] 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :85:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :99:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :106:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :111:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :114:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :117:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :123:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :128:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :93:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :96:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :107:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :105:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :119:1: 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 bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable] 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] 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :415:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :429:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :99:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :113:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :415:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :429:1: 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 bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable] 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] 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] 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] 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:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable] int ipl=-1, igt=-1; ^ 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_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :118:1: 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_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :132:1: note: expanded from here 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] 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 em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable] 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] 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] 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :121:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :135:1: 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_int64_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :117:1: 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_int64_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :128:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :145:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :159:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :179:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :182:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :210:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :224:1: 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:119:73: warning: variable 'score1' set but not used [-Wunused-but-set-variable] 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] 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] int N, l_run, ref_type; ^ bam2bcf_indel.c:120:16: warning: variable 'ref_type' set but not used [-Wunused-but-set-variable] int N, l_run, ref_type; ^ bam2bcf_indel.c:121:21: warning: variable 'ref2' set but not used [-Wunused-but-set-variable] char *inscns = 0, *ref2, *query, **ref_sample; ^ bam2bcf_indel.c:121:28: warning: variable 'query' set but not used [-Wunused-but-set-variable] char *inscns = 0, *ref2, *query, **ref_sample; ^ 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :85:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :99:1: note: expanded from here kh_del_rg ^ bam2bcf_indel.c:92:19: warning: unused function 'est_seqQ' [-Wunused-function] 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] 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :388:1: 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_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :402:1: 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 cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable] 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] 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_int64_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :120:1: 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_int64_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :134:1: 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_int64_hash_equal) ^ ./khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :149:1: 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 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] 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:62:12: warning: variable 'lineno' set but not used [-Wunused-but-set-variable] int dret, lineno = 0; ^ 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) \ ^ 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] 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] 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] 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] 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 */ ^~~ 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] 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] 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] 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] 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] 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 */ ^~~ 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] 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] 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_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :115:1: 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_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :120:1: 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_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :123:1: 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_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :132:1: 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_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :137:1: 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_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :144:1: 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_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :149:1: 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_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :152:1: 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_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :161:1: 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_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :166:1: 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_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :181:1: 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_hash_equal) ^ ../khash.h:307:2: note: expanded from macro 'KHASH_INIT' 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' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :195:1: note: expanded from here kh_del_kh_rg ^ 12 warnings generated. gcc -g -Wall -O2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz installing via 'install.libs.R' to /Users/biocbuild/bbs-3.20-bioc/meat/SICtools.buildbin-libdir/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)