Created
October 17, 2012 19:00
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tmap-3.2.0 install log from OSX 10.8.2 with XCode-4.5.1+CLT showing missing symbols on link
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| $ brew install -vd --env=std tmap | |
| /usr/local/bin/brew: loading /usr/local/Library/Formula/tmap.rb | |
| /usr/local/bin/brew: loading /usr/local/Library/Formula/automake.rb | |
| /usr/local/bin/brew: loading /usr/local/Library/Formula/autoconf.rb | |
| /usr/local/bin/brew: loading /usr/local/Library/Formula/libtool.rb | |
| /usr/local/Library/Formula/tmap.rb: loading /usr/local/Library/Formula/automake.rb | |
| /usr/local/Library/Formula/tmap.rb: loading /usr/local/Library/Formula/autoconf.rb | |
| /usr/local/Library/Formula/tmap.rb: loading /usr/local/Library/Formula/libtool.rb | |
| ==> Cloning https://github.com/iontorrent/TMAP.git | |
| git status -s | |
| Updating /Library/Caches/Homebrew/tmap--git | |
| git config remote.origin.url https://github.com/iontorrent/TMAP.git | |
| git config remote.origin.fetch +refs/tags/tmap.3.2.0:refs/tags/tmap.3.2.0 | |
| git fetch origin | |
| ==> Checking out tag tmap.3.2.0 | |
| git checkout tmap.3.2.0 -- | |
| HEAD is now at 115c314... * moving master to 3.2.0 | |
| git checkout-index -a -f --prefix=/private/tmp/tmap-9XWR/ | |
| git submodule init | |
| git submodule update | |
| git submodule --quiet foreach --recursive git checkout-index -a -f "--prefix=/private/tmp/tmap-9XWR/$path/" | |
| ==> Patching | |
| /usr/bin/patch -f -p1 -i 000-homebrew.diff | |
| patching file configure.ac | |
| ==> sh autogen.sh | |
| sh autogen.sh | |
| running: aclocal | |
| running: autoheader | |
| running: automake -a | |
| running: autoconf | |
| ==> ./configure --disable-dependency-tracking --prefix=/usr/local/Cellar/tmap/3.2.0 | |
| ./configure --disable-dependency-tracking --prefix=/usr/local/Cellar/tmap/3.2.0 | |
| checking for a BSD-compatible install... /usr/bin/install -c | |
| checking whether build environment is sane... yes | |
| checking for a thread-safe mkdir -p... config/install-sh -c -d | |
| checking for gawk... no | |
| checking for mawk... no | |
| checking for nawk... no | |
| checking for awk... awk | |
| checking whether make sets $(MAKE)... yes | |
| checking build system type... x86_64-apple-darwin12.2.0 | |
| checking for gcc... /usr/bin/clang | |
| checking whether the C compiler works... yes | |
| checking for C compiler default output file name... a.out | |
| checking for suffix of executables... | |
| checking whether we are cross compiling... no | |
| checking for suffix of object files... o | |
| checking whether we are using the GNU C compiler... yes | |
| checking whether /usr/bin/clang accepts -g... yes | |
| checking for /usr/bin/clang option to accept ISO C89... none needed | |
| checking for style of include used by make... GNU | |
| checking dependency style of /usr/bin/clang... none | |
| checking whether /usr/bin/clang and cc understand -c and -o together... yes | |
| checking whether we are using the GNU C++ compiler... yes | |
| checking whether /usr/bin/clang++ accepts -g... yes | |
| checking dependency style of /usr/bin/clang++... none | |
| checking whether /usr/bin/clang++ understands -c and -o together... yes | |
| checking how to run the C preprocessor... /usr/bin/clang -E | |
| checking for grep that handles long lines and -e... /usr/bin/grep | |
| checking for egrep... /usr/bin/grep -E | |
| checking for ANSI C header files... yes | |
| checking for sys/types.h... yes | |
| checking for sys/stat.h... yes | |
| checking for stdlib.h... yes | |
| checking for string.h... yes | |
| checking for memory.h... yes | |
| checking for strings.h... yes | |
| checking for inttypes.h... yes | |
| checking for stdint.h... yes | |
| checking for unistd.h... yes | |
| checking minix/config.h usability... no | |
| checking minix/config.h presence... no | |
| checking for minix/config.h... no | |
| checking whether it is safe to define __EXTENSIONS__... yes | |
| checking whether the git revision is available... yes | |
| checking for BZ2_bzRead in -lbz2... yes | |
| checking for malloc in -ltcmalloc... no | |
| configure: WARNING: "Using 64-bit SA intervals; Genome sizes greater than 4Gb are supported" | |
| checking for an ANSI C-conforming const... yes | |
| checking for working volatile... yes | |
| checking for inline... inline | |
| checking for stdlib.h... (cached) yes | |
| checking for GNU libc compatible malloc... yes | |
| checking for stdlib.h... (cached) yes | |
| checking for GNU libc compatible realloc... yes | |
| checking for size_t... yes | |
| checking for working alloca.h... yes | |
| checking for alloca... yes | |
| checking for error_at_line... no | |
| checking for _LARGEFILE_SOURCE value needed for large files... no | |
| checking for working memcmp... yes | |
| checking sys/select.h usability... yes | |
| checking sys/select.h presence... yes | |
| checking for sys/select.h... yes | |
| checking sys/socket.h usability... yes | |
| checking sys/socket.h presence... yes | |
| checking for sys/socket.h... yes | |
| checking types of arguments for select... int,fd_set *,struct timeval * | |
| checking whether lstat correctly handles trailing slash... no | |
| checking whether stat accepts an empty string... no | |
| checking for working strtod... yes | |
| checking for vprintf... yes | |
| checking for _doprnt... no | |
| checking for gzread in -lz... yes | |
| checking for pow in -lm... yes | |
| checking for pthread_create in -lpthread... yes | |
| checking for pow... yes | |
| checking for strdup... yes | |
| checking for memset... yes | |
| checking for strchr... yes | |
| checking for strdup... (cached) yes | |
| checking for strstr... yes | |
| checking for memmove... yes | |
| checking for getopt_long... yes | |
| checking for gettimeofday... yes | |
| checking for gethostbyaddr... yes | |
| checking for gethostbyname... yes | |
| checking for memchr... yes | |
| checking for select... yes | |
| checking for socket... yes | |
| checking for sqrt... yes | |
| checking for strerror... yes | |
| checking for strtol... yes | |
| checking for int8_t... yes | |
| checking for int16_t... yes | |
| checking for int32_t... yes | |
| checking for int64_t... yes | |
| checking for uint8_t... yes | |
| checking for uint16_t... yes | |
| checking for uint32_t... yes | |
| checking for uint64_t... yes | |
| checking for size_t... (cached) yes | |
| checking for off_t... yes | |
| checking return type of signal handlers... void | |
| checking for ssize_t... yes | |
| checking size of short int... 2 | |
| checking size of int... 4 | |
| checking size of long int... 8 | |
| checking for ANSI C header files... (cached) yes | |
| checking for stdbool.h that conforms to C99... yes | |
| checking for _Bool... yes | |
| checking whether time.h and sys/time.h may both be included... yes | |
| checking for stdlib.h... (cached) yes | |
| checking stdio.h usability... yes | |
| checking stdio.h presence... yes | |
| checking for stdio.h... yes | |
| checking for stdint.h... (cached) yes | |
| checking for string.h... (cached) yes | |
| checking sys/time.h usability... yes | |
| checking sys/time.h presence... yes | |
| checking for sys/time.h... yes | |
| checking for unistd.h... (cached) yes | |
| checking float.h usability... yes | |
| checking float.h presence... yes | |
| checking for float.h... yes | |
| checking zlib.h usability... yes | |
| checking zlib.h presence... yes | |
| checking for zlib.h... yes | |
| checking bzlib.h usability... yes | |
| checking bzlib.h presence... yes | |
| checking for bzlib.h... yes | |
| checking pthread.h usability... yes | |
| checking pthread.h presence... yes | |
| checking for pthread.h... yes | |
| checking limits.h usability... yes | |
| checking limits.h presence... yes | |
| checking for limits.h... yes | |
| checking netinet/in.h usability... yes | |
| checking netinet/in.h presence... yes | |
| checking for netinet/in.h... yes | |
| checking emmintrin.h usability... yes | |
| checking emmintrin.h presence... yes | |
| checking for emmintrin.h... yes | |
| checking getopt.h usability... yes | |
| checking getopt.h presence... yes | |
| checking for getopt.h... yes | |
| checking arpa/inet.h usability... yes | |
| checking arpa/inet.h presence... yes | |
| checking for arpa/inet.h... yes | |
| checking fcntl.h usability... yes | |
| checking fcntl.h presence... yes | |
| checking for fcntl.h... yes | |
| checking netdb.h usability... yes | |
| checking netdb.h presence... yes | |
| checking for netdb.h... yes | |
| checking stddef.h usability... yes | |
| checking stddef.h presence... yes | |
| checking for stddef.h... yes | |
| checking for sys/socket.h... (cached) yes | |
| checking wchar.h usability... yes | |
| checking wchar.h presence... yes | |
| checking for wchar.h... yes | |
| checking curses.h usability... yes | |
| checking curses.h presence... yes | |
| checking for curses.h... yes | |
| checking xcurses.h usability... no | |
| checking xcurses.h presence... no | |
| checking for xcurses.h... no | |
| checking that generated files are newer than configure... done | |
| configure: creating ./config.status | |
| config.status: creating Makefile | |
| config.status: creating config.h | |
| config.status: executing depfiles commands | |
| ==> make | |
| make | |
| make all-recursive | |
| Making all in . | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/util/tmap_alloc.o src/util/tmap_alloc.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/util/tmap_definitions.o src/util/tmap_definitions.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/util/tmap_error.o src/util/tmap_error.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/util/tmap_rand.o src/util/tmap_rand.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/util/tmap_time.o src/util/tmap_time.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/util/tmap_fibheap.o src/util/tmap_fibheap.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/util/tmap_progress.o src/util/tmap_progress.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/util/tmap_string.o src/util/tmap_string.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/util/tmap_levenshtein.o src/util/tmap_levenshtein.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/util/tmap_sam_convert.o src/util/tmap_sam_convert.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/seq/tmap_fq.o src/seq/tmap_fq.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/seq/tmap_sff.o src/seq/tmap_sff.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/seq/tmap_sam.o src/seq/tmap_sam.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/seq/tmap_seq.o src/seq/tmap_seq.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/seq/tmap_seqs.o src/seq/tmap_seqs.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/io/tmap_file.o src/io/tmap_file.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/io/tmap_fq_io.o src/io/tmap_fq_io.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/io/tmap_sff_io.o src/io/tmap_sff_io.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/io/tmap_sam_io.o src/io/tmap_sam_io.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/io/tmap_seq_io.o src/io/tmap_seq_io.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/io/tmap_seqs_io.o src/io/tmap_seqs_io.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/index/tmap_bwt.o src/index/tmap_bwt.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/index/tmap_bwt_aux.o src/index/tmap_bwt_aux.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/index/tmap_bwtl.o src/index/tmap_bwtl.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/index/tmap_bwt_gen.o src/index/tmap_bwt_gen.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/index/tmap_bwt_match.o src/index/tmap_bwt_match.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/index/tmap_bwt_match_hash.o src/index/tmap_bwt_match_hash.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/index/tmap_bwt_smem.o src/index/tmap_bwt_smem.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/index/tmap_index.o src/index/tmap_index.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/index/tmap_refseq.o src/index/tmap_refseq.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/index/tmap_sa.o src/index/tmap_sa.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/index/tmap_sa_aux.o src/index/tmap_sa_aux.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/index/tmap_index_size.o src/index/tmap_index_size.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/sw/tmap_sw.o src/sw/tmap_sw.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/sw/tmap_fsw.o src/sw/tmap_fsw.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/sw/tmap_vsw_definitions.o src/sw/tmap_vsw_definitions.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/sw/tmap_vsw.o src/sw/tmap_vsw.c | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/vsw.o src/sw/lib/vsw.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/vsw16.o src/sw/lib/vsw16.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/sw-vector.o src/sw/lib/sw-vector.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution.o src/sw/lib/Solution.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution1.o src/sw/lib/Solution1.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution2.o src/sw/lib/Solution2.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution3.o src/sw/lib/Solution3.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution4.o src/sw/lib/Solution4.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution5.o src/sw/lib/Solution5.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution6.o src/sw/lib/Solution6.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution7.o src/sw/lib/Solution7.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution8.o src/sw/lib/Solution8.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution9.o src/sw/lib/Solution9.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/Solution10.o src/sw/lib/Solution10.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/AffineSWOptimization.o src/sw/lib/AffineSWOptimization.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/AffineSWOptimizationHash.o src/sw/lib/AffineSWOptimizationHash.cpp | |
| /usr/bin/clang++ -DHAVE_CONFIG_H -I. -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -c -o src/sw/lib/AffineSWOptimizationWrapper.o src/sw/lib/AffineSWOptimizationWrapper.cpp | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/sw/tmap_vsw_bm.o src/sw/tmap_vsw_bm.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam.o src/samtools/bam.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/sam.o src/samtools/sam.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/sam_header.o src/samtools/sam_header.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_import.o src/samtools/bam_import.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_aux.o src/samtools/bam_aux.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_pileup.o src/samtools/bam_pileup.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_lpileup.o src/samtools/bam_lpileup.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_md.o src/samtools/bam_md.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/faidx.o src/samtools/faidx.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bedidx.o src/samtools/bedidx.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/razf.o src/samtools/razf.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bgzf.o src/samtools/bgzf.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/kstring.o src/samtools/kstring.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/knetfile.o src/samtools/knetfile.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/kaln.o src/samtools/kaln.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/kprobaln.o src/samtools/kprobaln.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_index.o src/samtools/bam_index.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_sort.o src/samtools/bam_sort.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_reheader.o src/samtools/bam_reheader.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_cat.o src/samtools/bam_cat.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_tview.o src/samtools/bam_tview.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_plcmd.o src/samtools/bam_plcmd.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/sam_view.o src/samtools/sam_view.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_rmdup.o src/samtools/bam_rmdup.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_rmdupse.o src/samtools/bam_rmdupse.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_mate.o src/samtools/bam_mate.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_stat.o src/samtools/bam_stat.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam_color.o src/samtools/bam_color.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam2bcf.o src/samtools/bam2bcf.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam2bcf_indel.o src/samtools/bam2bcf_indel.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/errmod.o src/samtools/errmod.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/sample.o src/samtools/sample.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/cut_target.o src/samtools/cut_target.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/phase.o src/samtools/phase.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bam2depth.o src/samtools/bam2depth.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/padding.o src/samtools/padding.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bcftools/bcf.o src/samtools/bcftools/bcf.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bcftools/bcf2qcall.o src/samtools/bcftools/bcf2qcall.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bcftools/bcfutils.o src/samtools/bcftools/bcfutils.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bcftools/call1.o src/samtools/bcftools/call1.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bcftools/em.o src/samtools/bcftools/em.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bcftools/fet.o src/samtools/bcftools/fet.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bcftools/index.o src/samtools/bcftools/index.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bcftools/kfunc.o src/samtools/bcftools/kfunc.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bcftools/kmin.o src/samtools/bcftools/kmin.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bcftools/main.o src/samtools/bcftools/main.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bcftools/mut.o src/samtools/bcftools/mut.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bcftools/prob1.o src/samtools/bcftools/prob1.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bcftools/vcf.o src/samtools/bcftools/vcf.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/samtools/bamtk.o src/samtools/bamtk.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/server/tmap_server.o src/server/tmap_server.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/server/tmap_shm.o src/server/tmap_shm.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/sam2fs/tmap_sam2fs_aux.o src/sam2fs/tmap_sam2fs_aux.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/sam2fs/tmap_sam2fs.o src/sam2fs/tmap_sam2fs.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/index/tmap_index_speed.o src/index/tmap_index_speed.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/index/tmap_bwt_check.o src/index/tmap_bwt_check.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/index/tmap_bwt_compare.o src/index/tmap_bwt_compare.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/util/tmap_map_opt.o src/map/util/tmap_map_opt.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/util/tmap_map_stats.o src/map/util/tmap_map_stats.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/util/tmap_map_util.o src/map/util/tmap_map_util.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/pairing/tmap_map_pairing.o src/map/pairing/tmap_map_pairing.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/map1/tmap_map1.o src/map/map1/tmap_map1.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/map1/tmap_map1_aux.o src/map/map1/tmap_map1_aux.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/map2/tmap_map2.o src/map/map2/tmap_map2.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/map2/tmap_map2_aux.o src/map/map2/tmap_map2_aux.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/map2/tmap_map2_chain.o src/map/map2/tmap_map2_chain.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/map2/tmap_map2_core.o src/map/map2/tmap_map2_core.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/map2/tmap_map2_mempool.o src/map/map2/tmap_map2_mempool.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/map3/tmap_map3.o src/map/map3/tmap_map3.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/map3/tmap_map3_aux.o src/map/map3/tmap_map3_aux.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/map4/tmap_map4.o src/map/map4/tmap_map4.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/map4/tmap_map4_aux.o src/map/map4/tmap_map4_aux.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/mapvsw/tmap_map_vsw.o src/map/mapvsw/tmap_map_vsw.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/mapall/tmap_map_all.o src/map/mapall/tmap_map_all.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/map/tmap_map_driver.o src/map/tmap_map_driver.c | |
| /usr/bin/clang -DHAVE_CONFIG_H -I. -w -pipe -pthread -D_TMAP_BWT_RUN_TYPE=0 -D_USE_KNETFILE -Isrc/samtools -DSAMTOOLS_MAIN -c -o src/tmap_main.o src/tmap_main.c | |
| /usr/bin/clang++ -w -pipe -pthread -D__STDC_LIMIT_MACROS -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -Isrc/samtools -L/usr/local/lib -o tmap src/util/tmap_alloc.o src/util/tmap_definitions.o src/util/tmap_error.o src/util/tmap_rand.o src/util/tmap_time.o src/util/tmap_fibheap.o src/util/tmap_progress.o src/util/tmap_string.o src/util/tmap_levenshtein.o src/util/tmap_sam_convert.o src/seq/tmap_fq.o src/seq/tmap_sff.o src/seq/tmap_sam.o src/seq/tmap_seq.o src/seq/tmap_seqs.o src/io/tmap_file.o src/io/tmap_fq_io.o src/io/tmap_sff_io.o src/io/tmap_sam_io.o src/io/tmap_seq_io.o src/io/tmap_seqs_io.o src/index/tmap_bwt.o src/index/tmap_bwt_aux.o src/index/tmap_bwtl.o src/index/tmap_bwt_gen.o src/index/tmap_bwt_match.o src/index/tmap_bwt_match_hash.o src/index/tmap_bwt_smem.o src/index/tmap_index.o src/index/tmap_refseq.o src/index/tmap_sa.o src/index/tmap_sa_aux.o src/index/tmap_index_size.o src/sw/tmap_sw.o src/sw/tmap_fsw.o src/sw/tmap_vsw_definitions.o src/sw/tmap_vsw.o src/sw/lib/vsw.o src/sw/lib/vsw16.o src/sw/lib/sw-vector.o src/sw/lib/Solution.o src/sw/lib/Solution1.o src/sw/lib/Solution2.o src/sw/lib/Solution3.o src/sw/lib/Solution4.o src/sw/lib/Solution5.o src/sw/lib/Solution6.o src/sw/lib/Solution7.o src/sw/lib/Solution8.o src/sw/lib/Solution9.o src/sw/lib/Solution10.o src/sw/lib/AffineSWOptimization.o src/sw/lib/AffineSWOptimizationHash.o src/sw/lib/AffineSWOptimizationWrapper.o src/sw/tmap_vsw_bm.o src/samtools/bam.o src/samtools/sam.o src/samtools/sam_header.o src/samtools/bam_import.o src/samtools/bam_aux.o src/samtools/bam_pileup.o src/samtools/bam_lpileup.o src/samtools/bam_md.o src/samtools/faidx.o src/samtools/bedidx.o src/samtools/razf.o src/samtools/bgzf.o src/samtools/kstring.o src/samtools/knetfile.o src/samtools/kaln.o src/samtools/kprobaln.o src/samtools/bam_index.o src/samtools/bam_sort.o src/samtools/bam_reheader.o src/samtools/bam_cat.o src/samtools/bam_tview.o src/samtools/bam_plcmd.o src/samtools/sam_view.o src/samtools/bam_rmdup.o src/samtools/bam_rmdupse.o src/samtools/bam_mate.o src/samtools/bam_stat.o src/samtools/bam_color.o src/samtools/bam2bcf.o src/samtools/bam2bcf_indel.o src/samtools/errmod.o src/samtools/sample.o src/samtools/cut_target.o src/samtools/phase.o src/samtools/bam2depth.o src/samtools/padding.o src/samtools/bcftools/bcf.o src/samtools/bcftools/bcf2qcall.o src/samtools/bcftools/bcfutils.o src/samtools/bcftools/call1.o src/samtools/bcftools/em.o src/samtools/bcftools/fet.o src/samtools/bcftools/index.o src/samtools/bcftools/kfunc.o src/samtools/bcftools/kmin.o src/samtools/bcftools/main.o src/samtools/bcftools/mut.o src/samtools/bcftools/prob1.o src/samtools/bcftools/vcf.o src/samtools/bamtk.o src/server/tmap_server.o src/server/tmap_shm.o src/sam2fs/tmap_sam2fs_aux.o src/sam2fs/tmap_sam2fs.o src/index/tmap_index_speed.o src/index/tmap_bwt_check.o src/index/tmap_bwt_compare.o src/map/util/tmap_map_opt.o src/map/util/tmap_map_stats.o src/map/util/tmap_map_util.o src/map/pairing/tmap_map_pairing.o src/map/map1/tmap_map1.o src/map/map1/tmap_map1_aux.o src/map/map2/tmap_map2.o src/map/map2/tmap_map2_aux.o src/map/map2/tmap_map2_chain.o src/map/map2/tmap_map2_core.o src/map/map2/tmap_map2_mempool.o src/map/map3/tmap_map3.o src/map/map3/tmap_map3_aux.o src/map/map4/tmap_map4.o src/map/map4/tmap_map4_aux.o src/map/mapvsw/tmap_map_vsw.o src/map/mapall/tmap_map_all.o src/map/tmap_map_driver.o src/tmap_main.o -lpthread -lm -lz -lbz2 | |
| Undefined symbols for architecture x86_64: | |
| "___ks_insertsort_heap", referenced from: | |
| _ks_combsort_heap in bam_sort.o | |
| _ks_introsort_heap in bam_sort.o | |
| "___ks_insertsort_node", referenced from: | |
| _ks_combsort_node in bam_lpileup.o | |
| _ks_introsort_node in bam_lpileup.o | |
| "___ks_insertsort_off", referenced from: | |
| _ks_combsort_off in bam_index.o | |
| _ks_introsort_off in bam_index.o | |
| "___ks_insertsort_rseq", referenced from: | |
| _ks_combsort_rseq in phase.o | |
| _ks_introsort_rseq in phase.o | |
| "___ks_insertsort_sort", referenced from: | |
| _ks_combsort_sort in bam_sort.o | |
| _ks_introsort_sort in bam_sort.o | |
| "___ks_insertsort_uint16_t", referenced from: | |
| _ks_combsort_uint16_t in errmod.o | |
| _ks_introsort_uint16_t in errmod.o | |
| "___ks_insertsort_uint32_t", referenced from: | |
| _ks_combsort_uint32_t in bam2bcf_indel.o | |
| _ks_introsort_uint32_t in bam2bcf_indel.o | |
| "___ks_insertsort_uint64_t", referenced from: | |
| _ks_combsort_uint64_t in bedidx.o | |
| _ks_introsort_uint64_t in bedidx.o | |
| "___tmap_sort_insertsort_hit", referenced from: | |
| _tmap_sort_combsort_hit in tmap_map2_aux.o | |
| _tmap_sort_introsort_hit in tmap_map2_aux.o | |
| "___tmap_sort_insertsort_hitG", referenced from: | |
| _tmap_sort_combsort_hitG in tmap_map2_aux.o | |
| _tmap_sort_introsort_hitG in tmap_map2_aux.o | |
| "___tmap_sort_insertsort_int32_t", referenced from: | |
| _tmap_sort_combsort_int32_t in tmap_map2_core.o | |
| _tmap_sort_introsort_int32_t in tmap_map2_core.o | |
| "___tmap_sort_insertsort_tmap_map1_sam_sort_score", referenced from: | |
| _tmap_sort_combsort_tmap_map1_sam_sort_score in tmap_map1.o | |
| _tmap_sort_introsort_tmap_map1_sam_sort_score in tmap_map1.o | |
| "___tmap_sort_insertsort_tmap_map2_chain", referenced from: | |
| _tmap_sort_combsort_tmap_map2_chain in tmap_map2_chain.o | |
| _tmap_sort_introsort_tmap_map2_chain in tmap_map2_chain.o | |
| "___tmap_sort_insertsort_tmap_map2_sam_sort_score", referenced from: | |
| _tmap_sort_combsort_tmap_map2_sam_sort_score in tmap_map2.o | |
| _tmap_sort_introsort_tmap_map2_sam_sort_score in tmap_map2.o | |
| "___tmap_sort_insertsort_tmap_map_all_stages_used", referenced from: | |
| _tmap_sort_combsort_tmap_map_all_stages_used in tmap_map_all.o | |
| _tmap_sort_introsort_tmap_map_all_stages_used in tmap_map_all.o | |
| "___tmap_sort_insertsort_tmap_map_driver_sort_isize", referenced from: | |
| _tmap_sort_combsort_tmap_map_driver_sort_isize in tmap_map_driver.o | |
| _tmap_sort_introsort_tmap_map_driver_sort_isize in tmap_map_driver.o | |
| "___tmap_sort_insertsort_tmap_map_opt_sort_rg", referenced from: | |
| _tmap_sort_combsort_tmap_map_opt_sort_rg in tmap_map_opt.o | |
| _tmap_sort_introsort_tmap_map_opt_sort_rg in tmap_map_opt.o | |
| "___tmap_sort_insertsort_tmap_map_sam_sort_coord", referenced from: | |
| _tmap_sort_combsort_tmap_map_sam_sort_coord in tmap_map_util.o | |
| _tmap_sort_introsort_tmap_map_sam_sort_coord in tmap_map_util.o | |
| "___tmap_sort_insertsort_tmap_map_sam_sort_coord_end", referenced from: | |
| _tmap_sort_combsort_tmap_map_sam_sort_coord_end in tmap_map_util.o | |
| _tmap_sort_introsort_tmap_map_sam_sort_coord_end in tmap_map_util.o | |
| "___tmap_sort_insertsort_tmap_map_sam_sort_coord_score", referenced from: | |
| _tmap_sort_combsort_tmap_map_sam_sort_coord_score in tmap_map_util.o | |
| _tmap_sort_introsort_tmap_map_sam_sort_coord_score in tmap_map_util.o | |
| "___tmap_sort_insertsort_tmap_map_sam_sort_score", referenced from: | |
| _tmap_sort_combsort_tmap_map_sam_sort_score in tmap_map_driver.o | |
| _tmap_sort_introsort_tmap_map_sam_sort_score in tmap_map_driver.o | |
| "___tmap_sort_insertsort_tmap_map_sam_sort_score_coord", referenced from: | |
| _tmap_sort_combsort_tmap_map_sam_sort_score_coord in tmap_map_util.o | |
| _tmap_sort_introsort_tmap_map_sam_sort_score_coord in tmap_map_util.o | |
| "_tmap_bwt_2occ", referenced from: | |
| _tmap_index_speed_test in tmap_index_speed.o | |
| "_tmap_bwt_2occ4", referenced from: | |
| _tmap_bwt_smem_extend in tmap_bwt_smem.o | |
| _tmap_index_speed_test in tmap_index_speed.o | |
| "_tmap_bwt_match_cal_width_reverse", referenced from: | |
| _tmap_map1_thread_map_core in tmap_map1.o | |
| "_tmap_bwt_match_hash_2occ", referenced from: | |
| _tmap_bwt_match_hash_cal_width_forward in tmap_bwt_match_hash.o | |
| _tmap_bwt_match_hash_cal_width_reverse in tmap_bwt_match_hash.o | |
| _tmap_bwt_match_hash_exact in tmap_bwt_match_hash.o | |
| _tmap_bwt_match_hash_exact_reverse in tmap_bwt_match_hash.o | |
| _tmap_bwt_match_hash_exact_alt in tmap_bwt_match_hash.o | |
| _tmap_bwt_match_hash_exact_alt_reverse in tmap_bwt_match_hash.o | |
| _tmap_map3_aux_core_seed in tmap_map3_aux.o | |
| ... | |
| "_tmap_bwt_match_hash_2occ4", referenced from: | |
| _tmap_map1_aux_core in tmap_map1_aux.o | |
| _tmap_map2_core_aln in tmap_map2_core.o | |
| "_tmap_bwt_match_hash_occ", referenced from: | |
| _tmap_bwt_match_hash_invPsi in tmap_bwt_match_hash.o | |
| "_tmap_bwt_occ", referenced from: | |
| _tmap_sa_bwt2sa in tmap_sa.o | |
| _tmap_index_speed_test in tmap_index_speed.o | |
| "_tmap_bwt_occ4", referenced from: | |
| _tmap_index_speed_test in tmap_index_speed.o | |
| "_tmap_bwtl_2occ4", referenced from: | |
| _tmap_map2_core_aln in tmap_map2_core.o | |
| _tmap_map2_core_connectivity in tmap_map2_core.o | |
| "_tmap_compliment", referenced from: | |
| _tmap_string_compliment in tmap_string.o | |
| "_tmap_fq_clone", referenced from: | |
| _tmap_seq_clone in tmap_seq.o | |
| "_tmap_fq_destroy", referenced from: | |
| _tmap_seq_destroy in tmap_seq.o | |
| "_tmap_fq_init", referenced from: | |
| _tmap_seq_init in tmap_seq.o | |
| "_tmap_fsw_sub_core", referenced from: | |
| _tmap_fsw_clipping_core in tmap_fsw.o | |
| _tmap_fsw_get_path in tmap_fsw.o | |
| "_tmap_get_file_name", referenced from: | |
| _tmap_bwt_read in tmap_bwt.o | |
| _tmap_bwt_write in tmap_bwt.o | |
| _tmap_bwt_shm_read_num_bytes in tmap_bwt.o | |
| _tmap_bwt_pac2bwt in tmap_bwt_gen.o | |
| _tmap_refseq_fasta2pac in tmap_refseq.o | |
| _tmap_refseq_read in tmap_refseq.o | |
| _tmap_refseq_write in tmap_refseq.o | |
| ... | |
| "_tmap_interval_overlap", referenced from: | |
| _tmap_refseq_pac2fasta_main in tmap_refseq.o | |
| "_tmap_log2", referenced from: | |
| _tmap_bwt_update_optimizations in tmap_bwt.o | |
| _tmap_sa_read in tmap_sa.o | |
| _tmap_sa_shm_unpack in tmap_sa.o | |
| "_tmap_map2_mempool_pop", referenced from: | |
| _tmap_map2_core_aln in tmap_map2_core.o | |
| _tmap_map2_core_init in tmap_map2_core.o | |
| "_tmap_map2_stack_pop", referenced from: | |
| _tmap_map2_core_aln in tmap_map2_core.o | |
| "_tmap_map2_stack_push0", referenced from: | |
| _tmap_map2_core_aln in tmap_map2_core.o | |
| _tmap_map2_core_init in tmap_map2_core.o | |
| "_tmap_map_sam_copy", referenced from: | |
| _tmap_map_sams_clone in tmap_map_util.o | |
| _tmap_map_sams_merge in tmap_map_util.o | |
| _tmap_map_pairing_read_rescue_helper in tmap_map_pairing.o | |
| (maybe you meant: _tmap_map_sam_copy_and_nullify) | |
| "_tmap_map_sam_destroy_aux", referenced from: | |
| _tmap_map_sam_destroy in tmap_map_util.o | |
| "_tmap_refseq_pac2real", referenced from: | |
| _tmap_map1_sam_to_real in tmap_map1_aux.o | |
| _tmap_map2_aux_store_hits in tmap_map2_aux.o | |
| _tmap_map3_aux_core in tmap_map3_aux.o | |
| _tmap_map4_aux_core in tmap_map4_aux.o | |
| "_tmap_refseq_subseq", referenced from: | |
| _tmap_index_speed_test in tmap_index_speed.o | |
| _tmap_map_util_fsw in tmap_map_util.o | |
| "_tmap_refseq_subseq2", referenced from: | |
| _tmap_map_util_sw_gen_score_helper in tmap_map_util.o | |
| _tmap_map_util_sw_gen_cigar in tmap_map_util.o | |
| _tmap_map_util_end_repair in tmap_map_util.o | |
| "_tmap_reverse_compliment", referenced from: | |
| _tmap_string_reverse_compliment in tmap_string.o | |
| _tmap_sam2fs_aux in tmap_sam2fs.o | |
| "_tmap_reverse_compliment_int", referenced from: | |
| _tmap_map_util_sw_gen_score_helper in tmap_map_util.o | |
| _tmap_map_util_sw_gen_cigar in tmap_map_util.o | |
| _tmap_map_util_fsw in tmap_map_util.o | |
| "_tmap_reverse_int", referenced from: | |
| _tmap_sw_clipping_core2 in tmap_sw.o | |
| "_tmap_sam_clone", referenced from: | |
| _tmap_seq_clone in tmap_seq.o | |
| "_tmap_sam_convert_mapped", referenced from: | |
| _tmap_map_sam_print in tmap_map_util.o | |
| "_tmap_sam_convert_unmapped", referenced from: | |
| _tmap_seqs_io_sff2sam_main in tmap_seqs_io.o | |
| _tmap_map_sam_print in tmap_map_util.o | |
| "_tmap_sam_io_init2", referenced from: | |
| _tmap_seqs_io_sff2sam_main in tmap_seqs_io.o | |
| _tmap_map_driver_core in tmap_map_driver.o | |
| "_tmap_seq_get_bases", referenced from: | |
| _tmap_fsw_flowseq_from_seq in tmap_fsw.o | |
| _tmap_map_util_sw_gen_score in tmap_map_util.o | |
| _tmap_map_util_sw_gen_score_helper in tmap_map_util.o | |
| _tmap_map_util_sw_gen_cigar in tmap_map_util.o | |
| _tmap_map1_thread_map_core in tmap_map1.o | |
| _tmap_map1_aux_core in tmap_map1_aux.o | |
| _tmap_map2_aux_core in tmap_map2_aux.o | |
| ... | |
| "_tmap_seq_get_bases_length", referenced from: | |
| _tmap_map_util_sw_gen_score in tmap_map_util.o | |
| _tmap_map_util_sw_gen_score_helper in tmap_map_util.o | |
| _tmap_map_util_sw_gen_cigar in tmap_map_util.o | |
| _tmap_map_pairing_pick_pairs in tmap_map_pairing.o | |
| _tmap_map_pairing_read_rescue_helper in tmap_map_pairing.o | |
| _tmap_map1_thread_map in tmap_map1.o | |
| _tmap_map2_thread_map in tmap_map2.o | |
| ... | |
| "_tmap_seq_io_destroy", referenced from: | |
| _tmap_seq_io_sff2fq_main in tmap_seq_io.o | |
| _tmap_refseq_fasta2pac in tmap_refseq.o | |
| "_tmap_seq_io_init", referenced from: | |
| _tmap_seq_io_sff2fq_main in tmap_seq_io.o | |
| _tmap_refseq_fasta2pac in tmap_refseq.o | |
| "_tmap_seq_io_read", referenced from: | |
| _tmap_seq_io_read_buffer in tmap_seq_io.o | |
| _tmap_seq_io_sff2fq_main in tmap_seq_io.o | |
| _tmap_refseq_fasta2pac in tmap_refseq.o | |
| (maybe you meant: _tmap_seq_io_read_buffer) | |
| "_tmap_seqs_io_destroy", referenced from: | |
| _tmap_seqs_io_sff2sam_main in tmap_seqs_io.o | |
| _tmap_map_driver_core in tmap_map_driver.o | |
| "_tmap_seqs_io_init", referenced from: | |
| _tmap_seqs_io_sff2sam_main in tmap_seqs_io.o | |
| _tmap_map_driver_core in tmap_map_driver.o | |
| "_tmap_seqs_io_read", referenced from: | |
| _tmap_seqs_io_read_buffer in tmap_seqs_io.o | |
| _tmap_seqs_io_sff2sam_main in tmap_seqs_io.o | |
| (maybe you meant: _tmap_seqs_io_read_buffer) | |
| "_tmap_sff_get_bases", referenced from: | |
| _tmap_sff_to_int in tmap_sff.o | |
| "_tmap_shm_add_listing", referenced from: | |
| _tmap_server_start in tmap_server.o | |
| "_tmap_shm_get_buffer", referenced from: | |
| _tmap_index_init in tmap_index.o | |
| "_tmap_shm_get_state", referenced from: | |
| _tmap_server_start in tmap_server.o | |
| _tmap_shm_init in tmap_shm.o | |
| "_tmap_shm_set_dead", referenced from: | |
| _tmap_server_sigint in tmap_server.o | |
| _tmap_server_stop in tmap_server.o | |
| _tmap_server_kill in tmap_server.o | |
| "_tmap_shm_set_not_ready", referenced from: | |
| _tmap_shm_init in tmap_shm.o | |
| "_tmap_shm_set_ready", referenced from: | |
| _tmap_server_start in tmap_server.o | |
| "_tmap_string_clone", referenced from: | |
| _tmap_sff_read_header_clone in tmap_sff.o | |
| _tmap_sff_read_clone in tmap_sff.o | |
| _tmap_refseq_fasta2pac in tmap_refseq.o | |
| _tmap_refseq_anno_clone in tmap_refseq.o | |
| "_tmap_string_clone2", referenced from: | |
| _tmap_refseq_fasta2pac in tmap_refseq.o | |
| "_tmap_string_copy", referenced from: | |
| _tmap_seq_sff2fq in tmap_seq.o | |
| "_tmap_string_destroy", referenced from: | |
| _tmap_sff_header_destroy in tmap_sff.o | |
| _tmap_sff_read_header_destroy in tmap_sff.o | |
| _tmap_sff_read_destroy in tmap_sff.o | |
| _tmap_sam_destroy in tmap_sam.o | |
| _tmap_sam_io_update_string in tmap_sam_io.o | |
| _tmap_refseq_destroy in tmap_refseq.o | |
| "_tmap_string_init", referenced from: | |
| _tmap_sff_header_read in tmap_sff.o | |
| _tmap_sff_read_header_read in tmap_sff.o | |
| _tmap_sff_read_read in tmap_sff.o | |
| _tmap_sam_io_update_string in tmap_sam_io.o | |
| _tmap_refseq_shm_unpack in tmap_refseq.o | |
| _tmap_refseq_read_header in tmap_refseq.o | |
| _tmap_refseq_read_annos in tmap_refseq.o | |
| ... | |
| "_tmap_string_reverse", referenced from: | |
| _tmap_fq_reverse in tmap_fq.o | |
| _tmap_fq_reverse_compliment in tmap_fq.o | |
| _tmap_sff_reverse in tmap_sff.o | |
| _tmap_sff_reverse_compliment in tmap_sff.o | |
| _tmap_sam_reverse in tmap_sam.o | |
| _tmap_sam_reverse_compliment in tmap_sam.o | |
| (maybe you meant: _tmap_string_reverse_compliment) | |
| "_tmap_to_int", referenced from: | |
| _tmap_map_util_fsw in tmap_map_util.o | |
| ld: symbol(s) not found for architecture x86_64 | |
| clang: error: linker command failed with exit code 1 (use -v to see invocation) | |
| make[2]: *** [tmap] Error 1 | |
| make[1]: *** [all-recursive] Error 1 | |
| make: *** [all] Error 2 |
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