printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild samtools 2>&1 The package 'samtools' will be built without being installed. Reading build dependency for samtools-0.1.19-2... Reading dependency for samtools-0.1.19-2... Reading dependency for libbam0-dev-0.1.19-2... Reading build conflict for samtools-0.1.19-2... The package 'fink-package-precedence' will be installed. Reading dependency for fink-package-precedence-0.18-1... Reading runtime dependency for fink-package-precedence-0.18-1... The package 'libncurses5' will be installed. Reading dependency for libncurses5-5.9-20110507-1... Reading runtime dependency for libncurses5-5.9-20110507-1... The following package will be rebuilt: samtools The following 2 additional packages will be installed: fink-package-precedence libncurses5 Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/samtools-0.1.19.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 0 502k 0 1205 0 0 5049 0 0:01:41 --:--:-- 0:01:41 5041 100 502k 100 502k 0 0 463k 0 0:00:01 0:00:01 --:--:-- 463k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/fink-package-precedence_0.18-1_darwin-x86_64.deb Selecting previously deselected package fink-package-precedence. (Reading database ... 4296 files and directories currently installed.) Unpacking fink-package-precedence (from .../fink-package-precedence_0.18-1_darwin-x86_64.deb) ... Setting up fink-package-precedence (0.18-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/libncurses5_5.9-20110507-1_darwin-x86_64.deb Selecting previously deselected package libncurses5. (Reading database ... 4297 files and directories currently installed.) Unpacking libncurses5 (from .../libncurses5_5.9-20110507-1_darwin-x86_64.deb) ... Setting up libncurses5 (5.9-20110507-1) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-samtools-0.1.19-2 /sw/build.build dpkg-deb: building package `fink-buildlock-samtools-0.1.19-2' in `/sw/build.build/fink-buildlock-samtools-0.1.19-2_2014.07.26-21.16.21_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-samtools-0.1.19-2_2014.07.26-21.16.21_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-samtools-0.1.19-2. (Reading database ... 4346 files and directories currently installed.) Unpacking fink-buildlock-samtools-0.1.19-2 (from .../fink-buildlock-samtools-0.1.19-2_2014.07.26-21.16.21_darwin-x86_64.deb) ... Setting up fink-buildlock-samtools-0.1.19-2 (2014.07.26-21.16.21) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.sWOvh env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/samtools-0.1.19.tar.bz2 samtools-0.1.19/ samtools-0.1.19/.gitignore samtools-0.1.19/AUTHORS samtools-0.1.19/COPYING samtools-0.1.19/ChangeLog.old samtools-0.1.19/INSTALL samtools-0.1.19/Makefile samtools-0.1.19/Makefile.mingw samtools-0.1.19/NEWS samtools-0.1.19/bam.c samtools-0.1.19/bam.h samtools-0.1.19/bam2bcf.c samtools-0.1.19/bam2bcf.h samtools-0.1.19/bam2bcf_indel.c samtools-0.1.19/bam2depth.c samtools-0.1.19/bam_aux.c samtools-0.1.19/bam_cat.c samtools-0.1.19/bam_color.c samtools-0.1.19/bam_endian.h samtools-0.1.19/bam_import.c samtools-0.1.19/bam_index.c samtools-0.1.19/bam_lpileup.c samtools-0.1.19/bam_mate.c samtools-0.1.19/bam_md.c samtools-0.1.19/bam_pileup.c samtools-0.1.19/bam_plcmd.c samtools-0.1.19/bam_reheader.c samtools-0.1.19/bam_rmdup.c samtools-0.1.19/bam_rmdupse.c samtools-0.1.19/bam_sort.c samtools-0.1.19/bam_stat.c samtools-0.1.19/bam_tview.c samtools-0.1.19/bam_tview.h samtools-0.1.19/bam_tview_curses.c samtools-0.1.19/bam_tview_html.c samtools-0.1.19/bamshuf.c samtools-0.1.19/bamtk.c samtools-0.1.19/bcftools/ samtools-0.1.19/bcftools/Makefile samtools-0.1.19/bcftools/README samtools-0.1.19/bcftools/bcf.c samtools-0.1.19/bcftools/bcf.h samtools-0.1.19/bcftools/bcf.tex samtools-0.1.19/bcftools/bcf2qcall.c samtools-0.1.19/bcftools/bcfutils.c samtools-0.1.19/bcftools/call1.c samtools-0.1.19/bcftools/em.c samtools-0.1.19/bcftools/fet.c samtools-0.1.19/bcftools/index.c samtools-0.1.19/bcftools/kfunc.c samtools-0.1.19/bcftools/kmin.c samtools-0.1.19/bcftools/kmin.h samtools-0.1.19/bcftools/main.c samtools-0.1.19/bcftools/mut.c samtools-0.1.19/bcftools/prob1.c samtools-0.1.19/bcftools/prob1.h samtools-0.1.19/bcftools/vcf.c samtools-0.1.19/bcftools/vcfutils.pl samtools-0.1.19/bcftools/bcf.h~ samtools-0.1.19/bedcov.c samtools-0.1.19/bedidx.c samtools-0.1.19/bgzf.c samtools-0.1.19/bgzf.h samtools-0.1.19/bgzip.c samtools-0.1.19/cut_target.c samtools-0.1.19/errmod.c samtools-0.1.19/errmod.h samtools-0.1.19/examples/ samtools-0.1.19/examples/00README.txt samtools-0.1.19/examples/Makefile samtools-0.1.19/examples/bam2bed.c samtools-0.1.19/examples/calDepth.c samtools-0.1.19/examples/chk_indel.c samtools-0.1.19/examples/ex1.fa samtools-0.1.19/examples/ex1.sam.gz samtools-0.1.19/examples/toy.fa samtools-0.1.19/examples/toy.sam samtools-0.1.19/faidx.c samtools-0.1.19/faidx.h samtools-0.1.19/kaln.c samtools-0.1.19/kaln.h samtools-0.1.19/khash.h samtools-0.1.19/klist.h samtools-0.1.19/knetfile.c samtools-0.1.19/knetfile.h samtools-0.1.19/kprobaln.c samtools-0.1.19/kprobaln.h samtools-0.1.19/kseq.h samtools-0.1.19/ksort.h samtools-0.1.19/kstring.c samtools-0.1.19/kstring.h samtools-0.1.19/misc/ samtools-0.1.19/misc/HmmGlocal.java samtools-0.1.19/misc/Makefile samtools-0.1.19/misc/ace2sam.c samtools-0.1.19/misc/bamcheck.c samtools-0.1.19/misc/blast2sam.pl samtools-0.1.19/misc/bowtie2sam.pl samtools-0.1.19/misc/export2sam.pl samtools-0.1.19/misc/interpolate_sam.pl samtools-0.1.19/misc/maq2sam.c samtools-0.1.19/misc/md5.c samtools-0.1.19/misc/md5.h samtools-0.1.19/misc/md5fa.c samtools-0.1.19/misc/novo2sam.pl samtools-0.1.19/misc/plot-bamcheck samtools-0.1.19/misc/psl2sam.pl samtools-0.1.19/misc/r2plot.lua samtools-0.1.19/misc/sam2vcf.pl samtools-0.1.19/misc/samtools.pl samtools-0.1.19/misc/soap2sam.pl samtools-0.1.19/misc/varfilter.py samtools-0.1.19/misc/vcfutils.lua samtools-0.1.19/misc/wgsim.c samtools-0.1.19/misc/wgsim_eval.pl samtools-0.1.19/misc/zoom2sam.pl samtools-0.1.19/padding.c samtools-0.1.19/phase.c samtools-0.1.19/razf.c samtools-0.1.19/razf.h samtools-0.1.19/razip.c samtools-0.1.19/sam.c samtools-0.1.19/sam.h samtools-0.1.19/sam_header.c samtools-0.1.19/sam_header.h samtools-0.1.19/sam_view.c samtools-0.1.19/sample.c samtools-0.1.19/sample.h samtools-0.1.19/samtools.1 samtools-0.1.19/win32/ samtools-0.1.19/win32/libcurses.a samtools-0.1.19/win32/libz.a samtools-0.1.19/win32/xcurses.h samtools-0.1.19/win32/zconf.h samtools-0.1.19/win32/zlib.h samtools-0.1.19/bam.h~ sudo -u fink-bld [ENV] sh -c /tmp/fink.VzV52 [ -r /sw/fink/dists/stable/main/finkinfo/sci/samtools.patch ] sudo -u fink-bld [ENV] sh -c /tmp/fink.WKp34 patch -p1 < /sw/fink/dists/stable/main/finkinfo/sci/samtools.patch patching file bgzip.c perl -pi -e 's|O2|$& -MD|g' Makefile perl -pi -e 's|-I\.|$& -I/sw/include|g' Makefile rm win32/* sudo -u fink-bld [ENV] sh -c /tmp/fink.SKMNu make -w make: Entering directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19' make[1]: Entering directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19' gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_tview.c -o bam_tview.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_plcmd.c -o bam_plcmd.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include sam_view.c -o sam_view.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_rmdup.c -o bam_rmdup.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_mate.c -o bam_mate.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_stat.c -o bam_stat.o make[2]: Entering directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19' gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. -I/sw/include bgzf.c -o bgzf.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) \ ^ :103:1: 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) \ ^ :106:1: 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) \ ^ :134:1: 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) \ ^ :148:1: note: expanded from here kh_del_lib ^ 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) \ ^ :232:1: 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) \ ^ :243:1: 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) \ ^ :260:1: 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) \ ^ :274:1: note: expanded from here kh_del_lib ^ 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) \ ^ :41:1: 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) \ ^ :55:1: note: expanded from here kh_del_rg ^ 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) \ ^ :98:1: note: expanded from here kh_clear_cache ^ gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_color.c -o bam_color.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bamtk.c -o bamtk.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include kaln.c -o kaln.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam2bcf.c -o bam2bcf.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam2bcf_indel.c -o bam2bcf_indel.o 2 warnings generated. gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include errmod.c -o errmod.o 4 warnings generated. gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include sample.c -o sample.o 4 warnings generated. gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include cut_target.c -o cut_target.o 1 warning generated. gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include kstring.c -o kstring.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 errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare] if (m > m) return -1; ^ 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) \ ^ :136:1: 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) \ ^ :150:1: note: expanded from here kh_del_sm ^ 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) \ ^ :200:1: 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) \ ^ :214:1: note: expanded from here kh_del_rg ^ gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include phase.c -o phase.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam2depth.c -o bam2depth.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_aux.c -o bam_aux.o 2 warnings generated. gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include padding.c -o padding.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) \ ^ :49:1: 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) \ ^ :63:1: 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) \ ^ :78:1: note: expanded from here kh_clear_64 ^ 1 warning generated. gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bedcov.c -o bedcov.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) \ ^ :200:1: 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) \ ^ :214:1: 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() { \ ^ :221:1: 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) \ ^ :226:1: 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) \ ^ :229:1: 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) \ ^ :232:1: 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) \ ^ :238:1: 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) \ ^ :243:1: note: expanded from here kh_del_r2l ^ gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bamshuf.c -o bamshuf.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_tview_curses.c -o bam_tview_curses.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_tview_html.c -o bam_tview_html.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) \ ^ 8 warnings generated. gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam.c -o bam.o 1 warning generated. gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_import.c -o bam_import.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include sam.c -o sam.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_index.c -o bam_index.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_pileup.c -o bam_pileup.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) \ ^ :200:1: 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) \ ^ :203:1: 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) \ ^ :214:1: note: expanded from here kh_del_ref ^ gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_lpileup.c -o bam_lpileup.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) \ ^ :218:1: 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) \ ^ :232:1: note: expanded from here kh_del_i ^ gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_md.c -o bam_md.o 4 warnings generated. gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include razf.c -o razf.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include 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) \ ^ :154:1: 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) \ ^ :168:1: note: expanded from here kh_del_s ^ gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bedidx.c -o bedidx.o 3 warnings generated. gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include knetfile.c -o knetfile.o 3 warnings generated. gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_sort.c -o bam_sort.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include sam_header.c -o sam_header.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_reheader.c -o bam_reheader.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) \ ^ :214:1: 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) \ ^ :228:1: note: expanded from here kh_del_reg ^ gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include kprobaln.c -o kprobaln.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) \ ^ :154:1: 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) \ ^ :168:1: note: expanded from here kh_del_str ^ gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bam_cat.c -o bam_cat.o 2 warnings generated. 2 warnings generated. 2 warnings generated. 2 warnings generated. 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 make[2]: Leaving directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19' make[2]: Entering directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19/bcftools' gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. -I/sw/include bcf.c -o bcf.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. -I/sw/include vcf.c -o vcf.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. -I/sw/include bcfutils.c -o bcfutils.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. -I/sw/include prob1.c -o prob1.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. -I/sw/include em.c -o em.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. -I/sw/include kfunc.c -o kfunc.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. -I/sw/include kmin.c -o kmin.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. -I/sw/include index.c -o index.o vcf.c:243:15: warning: explicitly assigning a 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) \ ^ 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) \ ^ :51:1: 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) \ ^ :65:1: note: expanded from here kh_del_str2id ^ gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. -I/sw/include fet.c -o fet.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) \ ^ gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. -I/sw/include mut.c -o mut.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. -I/sw/include bcf2qcall.c -o bcf2qcall.o 2 warnings generated. 2 warnings generated. 1 warning generated. 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]: Leaving directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19/bcftools' make[2]: Entering directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19/misc' make[2]: Nothing to be done for `lib'. make[2]: Leaving directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19/misc' gcc -g -Wall -O2 -MD -o samtools 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 -L/sw/lib libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread make[1]: Leaving directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19' make[1]: Entering directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19/bcftools' gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. -I/sw/include call1.c -o call1.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. -I/sw/include main.c -o main.o 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) \ ^ 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. 1 warning generated. gcc -g -Wall -O2 -MD -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread make[1]: Leaving directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19/bcftools' make[1]: Entering directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19/misc' gcc -c -g -Wall -O2 -MD -DMD5SUM_MAIN -o md5sum-lite.o md5.c gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include md5.c -o md5.o gcc -g -Wall -O2 -MD -c -I.. -o md5fa.o md5fa.c gcc -g -Wall -O2 -MD -o maq2sam-short maq2sam.c -lz gcc -g -Wall -O2 -MD -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz gcc -g -Wall -O2 -MD -c -I.. -o ace2sam.o ace2sam.c gcc -g -Wall -O2 -MD -c -I.. -o wgsim.o wgsim.c gcc -g -Wall -O2 -MD -c -I.. -o bamcheck.o bamcheck.c 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: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 */ ^~~ 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. 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() { \ ^ :42:1: 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) \ ^ :47:1: 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) \ ^ :50:1: 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) \ ^ :59:1: 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) \ ^ :64:1: 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() { \ ^ :71:1: 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) \ ^ :76:1: 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) \ ^ :79:1: 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) \ ^ :88:1: 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) \ ^ :93:1: 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) \ ^ :108:1: 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) \ ^ :122:1: note: expanded from here kh_del_kh_rg ^ 1 warning generated. gcc -g -Wall -O2 -MD -o md5sum-lite md5sum-lite.o gcc -g -Wall -O2 -MD -o md5fa md5.o md5fa.o -lz gcc -g -Wall -O2 -MD -o wgsim wgsim.o -lm -lz 1 warning generated. gcc -g -Wall -O2 -MD -o ace2sam ace2sam.o -lz 12 warnings generated. gcc -g -Wall -O2 -MD -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz make[1]: Leaving directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19/misc' make: Leaving directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19' make -w razip bgzip make: Entering directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19' gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include razip.c -o razip.o gcc -c -g -Wall -O2 -MD -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. -I/sw/include bgzip.c -o bgzip.o gcc -g -Wall -O2 -MD -o razip razip.o razf.o knetfile.o -lz gcc -g -Wall -O2 -MD -o bgzip bgzip.o bgzf.o knetfile.o -lz -lpthread make: Leaving directory `/sw/build.build/samtools-0.1.19-2/samtools-0.1.19' make -C bcftools bcftools gcc -g -Wall -O2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread fink-package-precedence --depfile-ext='\.d' . Scanning /\.d$/ dependency files... ./bam.d ./bam2bcf.d ./bam2bcf_indel.d ./bam2depth.d ./bam_aux.d ./bam_cat.d ./bam_color.d ./bam_import.d ./bam_index.d ./bam_lpileup.d ./bam_mate.d ./bam_md.d ./bam_pileup.d ./bam_plcmd.d ./bam_reheader.d ./bam_rmdup.d ./bam_rmdupse.d ./bam_sort.d ./bam_stat.d ./bam_tview.d ./bam_tview_curses.d ./bam_tview_html.d ./bamshuf.d ./bamtk.d ./bedcov.d ./bedidx.d ./bgzf.d ./bgzip.d ./cut_target.d ./errmod.d ./faidx.d ./kaln.d ./knetfile.d ./kprobaln.d ./kstring.d ./padding.d ./phase.d ./razf.d ./razip.d ./sam.d ./sam_header.d ./sam_view.d ./sample.d ./bcftools/bcf.d ./bcftools/bcf2qcall.d ./bcftools/bcfutils.d ./bcftools/call1.d ./bcftools/em.d ./bcftools/fet.d ./bcftools/index.d ./bcftools/kfunc.d ./bcftools/kmin.d ./bcftools/main.d ./bcftools/mut.d ./bcftools/prob1.d ./bcftools/vcf.d ./misc/ace2sam.d ./misc/bamcheck.d ./misc/maq2sam-long.d ./misc/maq2sam-short.d ./misc/md5.d ./misc/md5fa.d ./misc/md5sum-lite.d ./misc/wgsim.d Looking for incorrect headers in 64 dependency files... Determining fink providers of 3 headers... 1 - 3 Found use of headers from 1 fink packages: libncurses5 Scanning binaries for incorrect dyld linking... /bin/rm -rf /sw/build.build/root-samtools-0.1.19-2 /bin/mkdir -p /sw/build.build/root-samtools-0.1.19-2/sw /bin/mkdir -p /sw/build.build/root-samtools-0.1.19-2/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-samtools-0.1.19-2 sudo -u fink-bld [ENV] sh -c /tmp/fink.Y9PmI /tmp/fink.IjOAX #!/bin/sh -ev mkdir -p /sw/build.build/root-samtools-0.1.19-2/sw/bin install -m 0755 bgzip razip samtools /sw/build.build/root-samtools-0.1.19-2/sw/bin install -m 0755 bcftools/{bcftools,vcfutils.pl} /sw/build.build/root-samtools-0.1.19-2/sw/bin install -m 0755 misc/{ace2sam,bamcheck,blast2sam.pl,bowtie2sam.pl,export2sam.pl,maq2sam-long,maq2sam-short,md5fa,md5sum-lite,novo2sam.pl,psl2sam.pl,sam2vcf.pl,samtools.pl,soap2sam.pl,varfilter.py,wgsim,wgsim_eval.pl,zoom2sam.pl} /sw/build.build/root-samtools-0.1.19-2/sw/bin mkdir -p /sw/build.build/root-samtools-0.1.19-2/sw/share/man/man1 install -m 0644 samtools.1 /sw/build.build/root-samtools-0.1.19-2/sw/share/man/man1 mkdir -p /sw/build.build/root-samtools-0.1.19-2/sw/include/bam install -m 0644 *.h /sw/build.build/root-samtools-0.1.19-2/sw/include/bam mkdir -p /sw/build.build/root-samtools-0.1.19-2/sw/lib install -m 0644 libbam.a /sw/build.build/root-samtools-0.1.19-2/sw/lib sudo -u fink-bld [ENV] sh -c /tmp/fink.2V7oO /usr/bin/install -d -m 700 /sw/build.build/root-samtools-0.1.19-2/sw/share/doc/samtools /bin/cp -r AUTHORS /sw/build.build/root-samtools-0.1.19-2/sw/share/doc/samtools/ /bin/cp -r COPYING /sw/build.build/root-samtools-0.1.19-2/sw/share/doc/samtools/ /bin/cp -r NEWS /sw/build.build/root-samtools-0.1.19-2/sw/share/doc/samtools/ /bin/cp -r bcftools/README /sw/build.build/root-samtools-0.1.19-2/sw/share/doc/samtools/README.bfctools /bin/chmod -R go=u-w /sw/build.build/root-samtools-0.1.19-2/sw/share/doc/samtools /bin/rm -f /sw/build.build/root-samtools-0.1.19-2/sw/info/dir /sw/build.build/root-samtools-0.1.19-2/sw/info/dir.old /sw/build.build/root-samtools-0.1.19-2/sw/share/info/dir /sw/build.build/root-samtools-0.1.19-2/sw/share/info/dir.old /bin/rm -rf /sw/build.build/root-libbam0-dev-0.1.19-2 /bin/mkdir -p /sw/build.build/root-libbam0-dev-0.1.19-2/sw /bin/mkdir -p /sw/build.build/root-libbam0-dev-0.1.19-2/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-libbam0-dev-0.1.19-2 sudo -u fink-bld [ENV] sh -c /tmp/fink.9zFR7 /usr/bin/install -d -m 755 /sw/build.build/root-libbam0-dev-0.1.19-2/sw /bin/mv /sw/build.build/root-samtools-0.1.19-2/sw/include /sw/build.build/root-libbam0-dev-0.1.19-2/sw/ /bin/mv /sw/build.build/root-samtools-0.1.19-2/sw/lib /sw/build.build/root-libbam0-dev-0.1.19-2/sw/ /usr/bin/install -d -m 700 /sw/build.build/root-libbam0-dev-0.1.19-2/sw/share/doc/libbam0-dev /bin/cp -r AUTHORS /sw/build.build/root-libbam0-dev-0.1.19-2/sw/share/doc/libbam0-dev/ /bin/cp -r COPYING /sw/build.build/root-libbam0-dev-0.1.19-2/sw/share/doc/libbam0-dev/ /bin/cp -r NEWS /sw/build.build/root-libbam0-dev-0.1.19-2/sw/share/doc/libbam0-dev/ /bin/chmod -R go=u-w /sw/build.build/root-libbam0-dev-0.1.19-2/sw/share/doc/libbam0-dev /bin/rm -f /sw/build.build/root-libbam0-dev-0.1.19-2/sw/info/dir /sw/build.build/root-libbam0-dev-0.1.19-2/sw/info/dir.old /sw/build.build/root-libbam0-dev-0.1.19-2/sw/share/info/dir /sw/build.build/root-libbam0-dev-0.1.19-2/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-samtools-0.1.19-2 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `samtools' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/samtools_0.1.19-2_darwin-x86_64.deb'. Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-libbam0-dev-0.1.19-2 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `libbam0-dev' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/libbam0-dev_0.1.19-2_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-samtools-0.1.19-2 (Reading database ... 4347 files and directories currently installed.) Removing fink-buildlock-samtools-0.1.19-2 ...