jts / bri Goto Github PK

Folks
Followed instructions in README, I obtained the following..... (see below)
Any help gratefully received.
Mike

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make HTSDIR=/home/mike.harbour/nanopolish/htslibcc -o src/bri_index.o -c -O3 -std=c99 -fsigned-char -D_FILE_OFFSET_BITS=64 -g -I/home/mike.harbour/nanopolish/htslib/ -fPIC src/bri_index.c
cc -o src/bri_main.o -c -O3 -std=c99 -fsigned-char -D_FILE_OFFSET_BITS=64 -g -I/home/mike.harbour/nanopolish/htslib/ -fPIC src/bri_main.c
cc -o src/bri_test.o -c -O3 -std=c99 -fsigned-char -D_FILE_OFFSET_BITS=64 -g -I/home/mike.harbour/nanopolish/htslib/ -fPIC src/bri_test.c
cc -o src/bri_get.o -c -O3 -std=c99 -fsigned-char -D_FILE_OFFSET_BITS=64 -g -I/home/mike.harbour/nanopolish/htslib/ -fPIC src/bri_get.c
cc -o bri -O3 -std=c99 -fsigned-char -D_FILE_OFFSET_BITS=64 -g -I/home/mike.harbour/nanopolish/htslib/ -fPIC src/bri_index.o src/bri_main.o src/bri_test.o src/bri_get.o -lpthread -lz /home/mike.harbour/nanopolish/htslib/libhts.a
/home/mike.harbour/nanopolish/htslib/libhts.a(bgzf.o): In function mt_destroy': /home/mike.harbour/nanopolish/htslib/bgzf.c:1284: undefined reference to pthread_join'
/home/mike.harbour/nanopolish/htslib/libhts.a(bgzf.o): In function bgzf_write_init': /home/mike.harbour/nanopolish/htslib/bgzf.c:262: undefined reference to deflateInit2_'
/home/mike.harbour/nanopolish/htslib/libhts.a(bgzf.o): In function bgzf_uncompress': /home/mike.harbour/nanopolish/htslib/bgzf.c:456: undefined reference to inflateInit2_'
/home/mike.harbour/nanopolish/htslib/bgzf.c:464: undefined reference to inflate' /home/mike.harbour/nanopolish/htslib/bgzf.c:469: undefined reference to inflateEnd'
/home/mike.harbour/nanopolish/htslib/bgzf.c:477: undefined reference to inflateEnd' /home/mike.harbour/nanopolish/htslib/libhts.a(bgzf.o): In function bgzf_thread_pool':
/home/mike.harbour/nanopolish/htslib/bgzf.c:1247: undefined reference to pthread_create' /home/mike.harbour/nanopolish/htslib/libhts.a(bgzf.o): In function inflate_gzip_block':
/home/mike.harbour/nanopolish/htslib/bgzf.c:520: undefined reference to inflate' /home/mike.harbour/nanopolish/htslib/libhts.a(bgzf.o): In function bgzf_open':
/home/mike.harbour/nanopolish/htslib/bgzf.c:289: undefined reference to compressBound' /home/mike.harbour/nanopolish/htslib/libhts.a(bgzf.o): In function bgzf_dopen':
/home/mike.harbour/nanopolish/htslib/bgzf.c:312: undefined reference to compressBound' /home/mike.harbour/nanopolish/htslib/libhts.a(bgzf.o): In function bgzf_hopen':
/home/mike.harbour/nanopolish/htslib/bgzf.c:335: undefined reference to compressBound' /home/mike.harbour/nanopolish/htslib/libhts.a(bgzf.o): In function bgzf_compress':
/home/mike.harbour/nanopolish/htslib/bgzf.c:363: undefined reference to deflateInit2_' /home/mike.harbour/nanopolish/htslib/bgzf.c:371: undefined reference to deflate'
/home/mike.harbour/nanopolish/htslib/bgzf.c:378: undefined reference to deflateEnd' /home/mike.harbour/nanopolish/htslib/bgzf.c:390: undefined reference to crc32'
/home/mike.harbour/nanopolish/htslib/bgzf.c:390: undefined reference to crc32' /home/mike.harbour/nanopolish/htslib/libhts.a(bgzf.o): In function bgzf_gzip_compress':
/home/mike.harbour/nanopolish/htslib/bgzf.c:405: undefined reference to deflate' /home/mike.harbour/nanopolish/htslib/libhts.a(bgzf.o): In function bgzf_read_block':
/home/mike.harbour/nanopolish/htslib/bgzf.c:815: undefined reference to inflateInit2_' /home/mike.harbour/nanopolish/htslib/libhts.a(bgzf.o): In function bgzf_close':
/home/mike.harbour/nanopolish/htslib/bgzf.c:1495: undefined reference to deflateEnd' /home/mike.harbour/nanopolish/htslib/bgzf.c:1494: undefined reference to inflateEnd'
/home/mike.harbour/nanopolish/htslib/libhts.a(hts.o): In function decompress_peek': /home/mike.harbour/nanopolish/htslib/hts.c:139: undefined reference to inflateInit2_'
/home/mike.harbour/nanopolish/htslib/hts.c:142: undefined reference to inflate' /home/mike.harbour/nanopolish/htslib/hts.c:145: undefined reference to inflateEnd'
/home/mike.harbour/nanopolish/htslib/hts.c:145: undefined reference to inflateEnd' /home/mike.harbour/nanopolish/htslib/libhts.a(thread_pool.o): In function hts_tpool_init':
/home/mike.harbour/nanopolish/htslib/thread_pool.c:681: undefined reference to pthread_mutexattr_init' /home/mike.harbour/nanopolish/htslib/thread_pool.c:682: undefined reference to pthread_mutexattr_settype'
/home/mike.harbour/nanopolish/htslib/thread_pool.c:684: undefined reference to pthread_mutexattr_destroy' /home/mike.harbour/nanopolish/htslib/thread_pool.c:698: undefined reference to pthread_create'
/home/mike.harbour/nanopolish/htslib/libhts.a(thread_pool.o): In function hts_tpool_destroy': /home/mike.harbour/nanopolish/htslib/thread_pool.c:948: undefined reference to pthread_join'
/home/mike.harbour/nanopolish/htslib/libhts.a(thread_pool.o): In function hts_tpool_kill': /home/mike.harbour/nanopolish/htslib/thread_pool.c:974: undefined reference to pthread_kill'
/home/mike.harbour/nanopolish/htslib/libhts.a(cram_io.o): In function zlib_mem_deflate': /home/mike.harbour/nanopolish/htslib/cram/cram_io.c:815: undefined reference to deflateInit2_'
/home/mike.harbour/nanopolish/htslib/cram/cram_io.c:829: undefined reference to deflate' /home/mike.harbour/nanopolish/htslib/cram/cram_io.c:836: undefined reference to deflate'
/home/mike.harbour/nanopolish/htslib/cram/cram_io.c:841: undefined reference to deflateEnd' /home/mike.harbour/nanopolish/htslib/libhts.a(cram_io.o): In function itf8_decode_crc':
/home/mike.harbour/nanopolish/htslib/cram/cram_io.c:222: undefined reference to crc32' /home/mike.harbour/nanopolish/htslib/cram/cram_io.c:233: undefined reference to crc32'
/home/mike.harbour/nanopolish/htslib/cram/cram_io.c:207: undefined reference to crc32' /home/mike.harbour/nanopolish/htslib/cram/cram_io.c:214: undefined reference to crc32'
/home/mike.harbour/nanopolish/htslib/cram/cram_io.c:201: undefined reference to crc32' /home/mike.harbour/nanopolish/htslib/libhts.a(cram_io.o):/home/mike.harbour/nanopolish/htslib/cram/cram_io.c:645: more undefined references to crc32' follow
/home/mike.harbour/nanopolish/htslib/libhts.a(cram_io.o): In function zlib_mem_inflate': /home/mike.harbour/nanopolish/htslib/cram/cram_io.c:751: undefined reference to inflateInit2_'
/home/mike.harbour/nanopolish/htslib/cram/cram_io.c:764: undefined reference to inflate' /home/mike.harbour/nanopolish/htslib/cram/cram_io.c:784: undefined reference to inflateEnd'
/home/mike.harbour/nanopolish/htslib/libhts.a(cram_io.o): In function cram_read_block': /home/mike.harbour/nanopolish/htslib/cram/cram_io.c:979: undefined reference to crc32'
/home/mike.harbour/nanopolish/htslib/cram/cram_io.c:981: undefined reference to crc32' /home/mike.harbour/nanopolish/htslib/cram/cram_io.c:1015: undefined reference to crc32'
/home/mike.harbour/nanopolish/htslib/libhts.a(cram_io.o): In function cram_write_block': /home/mike.harbour/nanopolish/htslib/cram/cram_io.c:1089: undefined reference to crc32'
/home/mike.harbour/nanopolish/htslib/cram/cram_io.c:1094: undefined reference to crc32' /home/mike.harbour/nanopolish/htslib/libhts.a(cram_io.o):/home/mike.harbour/nanopolish/htslib/cram/cram_io.c:3156: more undefined references to crc32' follow
/home/mike.harbour/nanopolish/htslib/libhts.a(zfio.o): In function zfputs': /home/mike.harbour/nanopolish/htslib/cram/zfio.c:81: undefined reference to gzputs'
/home/mike.harbour/nanopolish/htslib/libhts.a(zfio.o): In function zfpeek': /home/mike.harbour/nanopolish/htslib/cram/zfio.c:98: undefined reference to gzungetc'
/home/mike.harbour/nanopolish/htslib/cram/zfio.c:96: undefined reference to gzgetc' /home/mike.harbour/nanopolish/htslib/libhts.a(zfio.o): In function zfopen':
/home/mike.harbour/nanopolish/htslib/cram/zfio.c:137: undefined reference to gzopen' /home/mike.harbour/nanopolish/htslib/cram/zfio.c:142: undefined reference to gzopen'
/home/mike.harbour/nanopolish/htslib/libhts.a(zfio.o): In function zfclose': /home/mike.harbour/nanopolish/htslib/cram/zfio.c:151: undefined reference to gzclose'
/home/mike.harbour/nanopolish/htslib/libhts.a(zfio.o): In function zfgets': /home/mike.harbour/nanopolish/htslib/cram/zfio.c:70: undefined reference to gzgets'
/home/mike.harbour/nanopolish/htslib/libhts.a(zfio.o): In function zfeof': /home/mike.harbour/nanopolish/htslib/cram/zfio.c:106: undefined reference to gzeof'
collect2: error: ld returned 1 exit status
Makefile:46: recipe for target 'bri' failed
make: *** [bri] Error 1
mike.harbour@bioinf3:~/bri/bri$ ls