############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Rbwa.buildbin-libdir && mkdir Rbwa.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rbwa_1.11.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rbwa.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rbwa.buildbin-libdir Rbwa_1.11.0.tar.gz' >>>>>>> * installing *source* package ‘Rbwa’ ... ** using staged installation rm -f gmon.out *.o a.out bwa *~ *.a rm -f bwa ** libs gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c utils.c -o utils.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c kthread.c -o kthread.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c kstring.c -o kstring.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c ksw.c -o ksw.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwt.c -o bwt.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bntseq.c -o bntseq.o bntseq.c:40:1: warning: unused function 'kh_clear_str' [-Wunused-function] KHASH_MAP_INIT_STR(str, int) ^ ./khash.h:612:2: 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:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:210:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :85:1: note: expanded from here kh_clear_str ^ bntseq.c:40:1: warning: unused function 'kh_del_str' [-Wunused-function] ./khash.h:612:2: 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:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:337:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :99:1: note: expanded from here kh_del_str ^ 2 warnings generated. gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwa.c -o bwa.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwamem.c -o bwamem.o bwamem.c:213:1: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] KBTREE_INIT(chn, mem_chain_t, chain_cmp) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./kbtree.h:366:2: note: expanded from macro 'KBTREE_INIT' __KB_PUT(name, key_t, __cmp) \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./kbtree.h:218:32: note: expanded from macro '__KB_PUT' b->root = s; s->is_internal = 1; s->n = 0; \ ^ ~ bwamem.c:213:1: warning: unused function 'kb_get_chn' [-Wunused-function] ./kbtree.h:364:2: note: expanded from macro 'KBTREE_INIT' __KB_GET(name, key_t) \ ^ ./kbtree.h:146:23: note: expanded from macro '__KB_GET' static inline key_t *kb_get_##name(kbtree_##name##_t *b, const key_t k) \ ^ :139:1: note: expanded from here kb_get_chn ^ bwamem.c:213:1: warning: unused function 'kb_interval_chn' [-Wunused-function] ./kbtree.h:365:2: note: expanded from macro 'KBTREE_INIT' __KB_INTERVAL(name, key_t) \ ^ ./kbtree.h:169:21: note: expanded from macro '__KB_INTERVAL' static inline void kb_interval_##name(kbtree_##name##_t *b, const key_t k, key_t **lower, key_t **upper) \ ^ :147:1: note: expanded from here kb_interval_chn ^ bwamem.c:213:1: warning: unused function 'kb_put_chn' [-Wunused-function] ./kbtree.h:366:2: note: expanded from macro 'KBTREE_INIT' __KB_PUT(name, key_t, __cmp) \ ^ ./kbtree.h:225:21: note: expanded from macro '__KB_PUT' static inline void kb_put_##name(kbtree_##name##_t *b, const key_t k) \ ^ :166:1: note: expanded from here kb_put_chn ^ bwamem.c:213:1: warning: unused function 'kb_del_chn' [-Wunused-function] ./kbtree.h:367:2: note: expanded from macro 'KBTREE_INIT' __KB_DEL(name, key_t) ^ ./kbtree.h:326:22: note: expanded from macro '__KB_DEL' static inline key_t kb_del_##name(kbtree_##name##_t *b, const key_t k) \ ^ :182:1: note: expanded from here kb_del_chn ^ 5 warnings generated. gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwamem_pair.c -o bwamem_pair.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwamem_extra.c -o bwamem_extra.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c malloc_wrap.c -o malloc_wrap.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c QSufSort.c -o QSufSort.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwt_gen.c -o bwt_gen.o bwt_gen.c:879:10: warning: variable 'oldInverseSa0RelativeRank' set but not used [-Wunused-but-set-variable] bgint_t oldInverseSa0RelativeRank = 0; ^ bwt_gen.c:953:15: warning: variable 'bitsInWordMinusBitPerChar' set but not used [-Wunused-but-set-variable] unsigned int bitsInWordMinusBitPerChar; ^ 2 warnings generated. gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c rope.c -o rope.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c rle.c -o rle.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c is.c -o is.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwtindex.c -o bwtindex.o ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwashm.c -o bwashm.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwase.c -o bwase.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwaseqio.c -o bwaseqio.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwtgap.c -o bwtgap.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwtaln.c -o bwtaln.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bamlite.c -o bamlite.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwape.c -o bwape.o bwape.c:33:1: warning: unused function 'kh_clear_b128' [-Wunused-function] KHASH_INIT(b128, pair64_t, poslist_t, 1, b128_hash, b128_eq) ^ ./khash.h:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:210:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :136:1: note: expanded from here kh_clear_b128 ^ bwape.c:33:1: warning: unused function 'kh_get_b128' [-Wunused-function] ./khash.h:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:217:16: note: expanded from macro '__KHASH_IMPL' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :139:1: note: expanded from here kh_get_b128 ^ bwape.c:33:1: warning: unused function 'kh_del_b128' [-Wunused-function] ./khash.h:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:337:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :150:1: note: expanded from here kh_del_b128 ^ 3 warnings generated. gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c kopen.c -o kopen.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c pemerge.c -o pemerge.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c maxk.c -o maxk.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwtsw2_core.c -o bwtsw2_core.o bwtsw2_core.c:453:45: warning: variable 'n_tot' set but not used [-Wunused-but-set-variable] int i, j, score_mat[16], *heap, heap_size, n_tot = 0; ^ bwtsw2_core.c:23:1: warning: unused function 'kh_get_qintv' [-Wunused-function] KHASH_INIT(qintv, qintv_t, uint64_t, 1, qintv_hash, qintv_eq) ^ ./khash.h:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:217:16: note: expanded from macro '__KHASH_IMPL' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :88:1: note: expanded from here kh_get_qintv ^ bwtsw2_core.c:23:1: warning: unused function 'kh_del_qintv' [-Wunused-function] ./khash.h:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:337:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :99:1: note: expanded from here kh_del_qintv ^ bwtsw2_core.c:24:1: warning: unused function 'kh_clear_64' [-Wunused-function] KHASH_MAP_INIT_INT64(64, uint64_t) ^ ./khash.h:596:2: 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:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:210:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :114:1: note: expanded from here kh_clear_64 ^ bwtsw2_core.c:24:1: warning: unused function 'kh_del_64' [-Wunused-function] ./khash.h:596:2: 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:354:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:351:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ ./khash.h:337:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :128:1: note: expanded from here kh_del_64 ^ bwtsw2_core.c:214:22: warning: unused function 'time_elapse' [-Wunused-function] static inline double time_elapse(const struct rusage *curr, const struct rusage *last) ^ 6 warnings generated. gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwtsw2_main.c -o bwtsw2_main.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwtsw2_aux.c -o bwtsw2_aux.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwt_lite.c -o bwt_lite.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwtsw2_chain.c -o bwtsw2_chain.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c fastmap.c -o fastmap.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c bwtsw2_pair.c -o bwtsw2_pair.o gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -g -Wall -O2 -c main.c -o main.o gcc -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread mkdir -p ../inst cp bwa ../inst/bwa rm -f gmon.out *.o a.out bwa *~ *.a rm -f bwa ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rbwa)