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###
### Running command:
###
### rm -rf Rbwa.buildbin-libdir && mkdir Rbwa.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rbwa_1.4.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rbwa.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rbwa.buildbin-libdir Rbwa_1.4.0.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/x86_64/include -fPIC -g -Wall -O2 -c utils.c -o utils.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c kthread.c -o kthread.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c kstring.c -o kstring.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c ksw.c -o ksw.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwt.c -o bwt.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/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) \
^
<scratch space>:84:1: 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) \
^
<scratch space>:98:1: note: expanded from here
kh_del_str
^
2 warnings generated.
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwa.c -o bwa.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwamem.c -o bwamem.o
bwamem.c:213:1: warning: unused function 'kb_get_chn' [-Wunused-function]
KBTREE_INIT(chn, mem_chain_t, chain_cmp)
^
./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) \
^
<scratch space>:33:1: 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) \
^
<scratch space>:41:1: 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) \
^
<scratch space>:60:1: 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) \
^
<scratch space>:76:1: note: expanded from here
kb_del_chn
^
4 warnings generated.
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/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/x86_64/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/x86_64/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/x86_64/include -fPIC -g -Wall -O2 -c QSufSort.c -o QSufSort.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/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/x86_64/include -fPIC -g -Wall -O2 -c rope.c -o rope.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c rle.c -o rle.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c is.c -o is.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/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/x86_64/include -fPIC -g -Wall -O2 -c bwashm.c -o bwashm.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwase.c -o bwase.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwaseqio.c -o bwaseqio.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwtgap.c -o bwtgap.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bwtaln.c -o bwtaln.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c bamlite.c -o bamlite.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/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) \
^
<scratch space>:22:1: 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) \
^
<scratch space>:25:1: 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) \
^
<scratch space>:36:1: note: expanded from here
kh_del_b128
^
3 warnings generated.
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c kopen.c -o kopen.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c pemerge.c -o pemerge.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -g -Wall -O2 -c maxk.c -o maxk.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/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) \
^
<scratch space>:87:1: 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) \
^
<scratch space>:98:1: 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) \
^
<scratch space>:113:1: 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) \
^
<scratch space>:127:1: 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/x86_64/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/x86_64/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/x86_64/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/x86_64/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/x86_64/include -fPIC -g -Wall -O2 -c fastmap.c -o fastmap.o
gcc -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/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/x86_64/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)
