printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild bwa 2>&1 The package 'bwa' will be built without being installed. Reading build dependency for bwa-0.7.7-1... Reading dependency for bwa-0.7.7-1... Reading build conflict for bwa-0.7.7-1... The following package will be rebuilt: bwa curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/bwa-0.7.7.tar.bz2 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 148k 100 148k 0 0 242k 0 --:--:-- --:--:-- --:--:-- 242k Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-bwa-0.7.7-1 /sw/build.build dpkg-deb: building package `fink-buildlock-bwa-0.7.7-1' in `/sw/build.build/fink-buildlock-bwa-0.7.7-1_2014.07.30-05.42.53_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-bwa-0.7.7-1_2014.07.30-05.42.53_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-bwa-0.7.7-1. (Reading database ... 4296 files and directories currently installed.) Unpacking fink-buildlock-bwa-0.7.7-1 (from .../fink-buildlock-bwa-0.7.7-1_2014.07.30-05.42.53_darwin-x86_64.deb) ... Setting up fink-buildlock-bwa-0.7.7-1 (2014.07.30-05.42.53) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.PpCv9 env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/bwa-0.7.7.tar.bz2 bwa-0.7.7/ bwa-0.7.7/bamlite.c bwa-0.7.7/bamlite.h bwa-0.7.7/bntseq.c bwa-0.7.7/bntseq.h bwa-0.7.7/bwa.1 bwa-0.7.7/bwa.c bwa-0.7.7/bwa.h bwa-0.7.7/bwamem.c bwa-0.7.7/bwamem.h bwa-0.7.7/bwamem_pair.c bwa-0.7.7/bwape.c bwa-0.7.7/bwase.c bwa-0.7.7/bwase.h bwa-0.7.7/bwaseqio.c bwa-0.7.7/bwt.c bwa-0.7.7/bwt.h bwa-0.7.7/bwt_gen.c bwa-0.7.7/bwt_lite.c bwa-0.7.7/bwt_lite.h bwa-0.7.7/bwtaln.c bwa-0.7.7/bwtaln.h bwa-0.7.7/bwtgap.c bwa-0.7.7/bwtgap.h bwa-0.7.7/bwtindex.c bwa-0.7.7/bwtsw2.h bwa-0.7.7/bwtsw2_aux.c bwa-0.7.7/bwtsw2_chain.c bwa-0.7.7/bwtsw2_core.c bwa-0.7.7/bwtsw2_main.c bwa-0.7.7/bwtsw2_pair.c bwa-0.7.7/ChangeLog bwa-0.7.7/COPYING bwa-0.7.7/example.c bwa-0.7.7/fastmap.c bwa-0.7.7/is.c bwa-0.7.7/kbtree.h bwa-0.7.7/khash.h bwa-0.7.7/kopen.c bwa-0.7.7/kseq.h bwa-0.7.7/ksort.h bwa-0.7.7/kstring.c bwa-0.7.7/kstring.h bwa-0.7.7/ksw.c bwa-0.7.7/ksw.h bwa-0.7.7/kthread.c bwa-0.7.7/kvec.h bwa-0.7.7/main.c bwa-0.7.7/Makefile bwa-0.7.7/malloc_wrap.c bwa-0.7.7/malloc_wrap.h bwa-0.7.7/NEWS bwa-0.7.7/pemerge.c bwa-0.7.7/QSufSort.c bwa-0.7.7/QSufSort.h bwa-0.7.7/qualfa2fq.pl bwa-0.7.7/README.md bwa-0.7.7/utils.c bwa-0.7.7/utils.h bwa-0.7.7/xa2multi.pl sudo -u fink-bld [ENV] sh -c /tmp/fink.JiBsF make gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o bwamem.c:175:1: 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) \ ^ :64:1: note: expanded from here kb_get_chn ^ bwamem.c:175:1: 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) \ ^ :72:1: note: expanded from here kb_interval_chn ^ bwamem.c:175:1: 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) \ ^ :95:1: note: expanded from here kb_put_chn ^ bwamem.c:175:1: 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) \ ^ :111:1: note: expanded from here kb_del_chn ^ gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o In file included from bwtgap.c:4: In file included from ./bwtgap.h:4: ./bwt.h:106:14: warning: inline function 'bwt_2occ4' is not defined [-Wundefined-inline] inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]); ^ bwtgap.c:201:3: note: used here bwt_2occ4(bwt, k - 1, l, cnt_k, cnt_l); // retrieve Occ values ^ In file included from bwtaln.c:11: In file included from ./bwtaln.h:5: ./bwt.h:105:14: warning: inline function 'bwt_2occ' is not defined [-Wundefined-inline] inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol); ^ bwtaln.c:66:4: note: used here bwt_2occ(bwt, k - 1, l, c, &ok, &ol); ^ gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o 1 warning generated. gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o 1 warning generated. gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.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) \ ^ :57:1: 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) \ ^ :60:1: 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) \ ^ :81:1: note: expanded from here kh_del_b128 ^ gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o 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) \ ^ :210:1: 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) \ ^ :231:1: 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) \ ^ :248:1: 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) \ ^ :272:1: 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) ^ In file included from bwtsw2_core.c:6: ./bwt_lite.h:22:14: warning: inline function 'bwtl_2occ4' is not defined [-Wundefined-inline] inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]); ^ bwtsw2_core.c:116:3: note: used here bwtl_2occ4(b, k-1, l, cntk, cntl); ^ In file included from bwtsw2_core.c:7: In file included from ./bwtsw2.h:7: ./bwt.h:106:14: warning: inline function 'bwt_2occ4' is not defined [-Wundefined-inline] inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]); ^ bwtsw2_core.c:551:7: note: used here bwt_2occ4(query, p->qk - 1, p->ql, qcntk, qcntl); ^ gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o 3 warnings generated. 7 warnings generated. 4 warnings generated. ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o malloc_wrap.o gcc -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.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 /bin/rm -rf /sw/build.build/root-bwa-0.7.7-1 /bin/mkdir -p /sw/build.build/root-bwa-0.7.7-1/sw /bin/mkdir -p /sw/build.build/root-bwa-0.7.7-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-bwa-0.7.7-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.RHmo0 mkdir /sw/build.build/root-bwa-0.7.7-1/sw/bin mkdir -p /sw/build.build/root-bwa-0.7.7-1/sw/share/man/man1 install -m 755 bwa qualfa2fq.pl xa2multi.pl /sw/build.build/root-bwa-0.7.7-1/sw/bin install -m 644 bwa.1 /sw/build.build/root-bwa-0.7.7-1/sw/share/man/man1 sudo -u fink-bld [ENV] sh -c /tmp/fink.kkWuZ /usr/bin/install -d -m 700 /sw/build.build/root-bwa-0.7.7-1/sw/share/doc/bwa /bin/cp -r COPYING /sw/build.build/root-bwa-0.7.7-1/sw/share/doc/bwa/ /bin/cp -r ChangeLog /sw/build.build/root-bwa-0.7.7-1/sw/share/doc/bwa/ /bin/cp -r NEWS /sw/build.build/root-bwa-0.7.7-1/sw/share/doc/bwa/ /bin/cp -r README.md /sw/build.build/root-bwa-0.7.7-1/sw/share/doc/bwa/ /bin/chmod -R go=u-w /sw/build.build/root-bwa-0.7.7-1/sw/share/doc/bwa /bin/rm -f /sw/build.build/root-bwa-0.7.7-1/sw/info/dir /sw/build.build/root-bwa-0.7.7-1/sw/info/dir.old /sw/build.build/root-bwa-0.7.7-1/sw/share/info/dir /sw/build.build/root-bwa-0.7.7-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-bwa-0.7.7-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `bwa' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/bwa_0.7.7-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-bwa-0.7.7-1 (Reading database ... 4297 files and directories currently installed.) Removing fink-buildlock-bwa-0.7.7-1 ...