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Old 07-06-2011, 09:21 AM   #1
louis7781x
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Location: Hong Kong

Join Date: Oct 2010
Posts: 74
Default The problem of installing samtools on mac

Hi, I want to install samtools-0.1.16.tar.bz2 on mac

Afte runpacking the tarball ,I use "make" to install.

But it shows errors:
Quote:
bgzf.c:306: error: 'Z_DEFAULT_STRATEGY' undeclared (first use in this function)
bgzf.c:307: error: 'Z_OK' undeclared (first use in this function)
bgzf.c:308: warning: implicit declaration of function 'report_error'
bgzf.c:311: warning: implicit declaration of function 'deflate'
bgzf.c:311: error: 'Z_FINISH' undeclared (first use in this function)
bgzf.c:312: error: 'Z_STREAM_END' undeclared (first use in this function)
bgzf.c:313: warning: implicit declaration of function 'deflateEnd'
bgzf.c:336: error: 'MAX_BLOCK_SIZE' undeclared (first use in this function)
bgzf.c:344: warning: implicit declaration of function 'packInt16'
bgzf.c:344: error: 'uint8_t' undeclared (first use in this function)
bgzf.c:344: error: syntax error before ')' token
bgzf.c:345: error: 'uint32_t' undeclared (first use in this function)
bgzf.c:345: error: syntax error before 'crc'
bgzf.c:346: error: 'crc' undeclared (first use in this function)
bgzf.c:346: warning: implicit declaration of function 'crc32'
bgzf.c:346: error: invalid type argument of '->'
bgzf.c:347: warning: implicit declaration of function 'packInt32'
bgzf.c:347: error: syntax error before ')' token
bgzf.c:348: error: syntax error before ')' token
bgzf.c:357: error: invalid type argument of '->'
bgzf.c:358: error: invalid type argument of '->'
bgzf.c:361: error: invalid type argument of '->'
bgzf.c: At top level:
bgzf.c:367: error: syntax error before '*' token
bgzf.c: In function 'inflate_block':
bgzf.c:371: error: 'z_stream' undeclared (first use in this function)
bgzf.c:371: error: syntax error before 'zs'
bgzf.c:373: error: 'zs' undeclared (first use in this function)
bgzf.c:375: error: invalid type argument of '->'
bgzf.c:376: error: 'block_length' undeclared (first use in this function)
bgzf.c:377: error: invalid type argument of '->'
bgzf.c:378: error: invalid type argument of '->'
bgzf.c:380: warning: implicit declaration of function 'inflateInit2'
bgzf.c:380: error: 'GZIP_WINDOW_BITS' undeclared (first use in this function)
bgzf.c:381: error: 'Z_OK' undeclared (first use in this function)
bgzf.c:385: warning: implicit declaration of function 'inflate'
bgzf.c:385: error: 'Z_FINISH' undeclared (first use in this function)
bgzf.c:386: error: 'Z_STREAM_END' undeclared (first use in this function)
bgzf.c:387: warning: implicit declaration of function 'inflateEnd'
bgzf.c: At top level:
bgzf.c:401: warning: type defaults to 'int' in declaration of 'bgzf_byte_t'
bgzf.c:401: error: syntax error before '*' token
bgzf.c: In function 'check_header':
bgzf.c:403: error: 'header' undeclared (first use in this function)
bgzf.c:403: error: 'GZIP_ID1' undeclared (first use in this function)
bgzf.c:404: error: 'bgzf_byte_t' undeclared (first use in this function)
bgzf.c:404: error: syntax error before 'GZIP_ID2'
bgzf.c:407: warning: implicit declaration of function 'unpackInt16'
bgzf.c:407: error: 'uint8_t' undeclared (first use in this function)
bgzf.c:407: error: syntax error before ')' token
bgzf.c:407: error: 'BGZF_XLEN' undeclared (first use in this function)
bgzf.c:408: error: 'BGZF_ID1' undeclared (first use in this function)
bgzf.c:409: error: 'BGZF_ID2' undeclared (first use in this function)
bgzf.c:410: error: syntax error before ')' token
bgzf.c:410: error: 'BGZF_LEN' undeclared (first use in this function)
bgzf.c:410: error: syntax error before ')' token
bgzf.c: At top level:
bgzf.c:413: error: syntax error before '*' token
bgzf.c: In function 'free_cache':
bgzf.c:415: error: 'khint_t' undeclared (first use in this function)
bgzf.c:415: error: syntax error before 'k'
bgzf.c:416: warning: implicit declaration of function 'khash_t'
bgzf.c:416: error: 'cache' undeclared (first use in this function)
bgzf.c:416: error: 'h' undeclared (first use in this function)
bgzf.c:416: error: syntax error before ')' token
bgzf.c:417: error: invalid type argument of '->'
bgzf.c:418: error: 'k' undeclared (first use in this function)
bgzf.c:418: warning: implicit declaration of function 'kh_begin'
bgzf.c:418: warning: implicit declaration of function 'kh_end'
bgzf.c:419: warning: implicit declaration of function 'kh_exist'
bgzf.c:419: warning: implicit declaration of function 'kh_val'
bgzf.c:419: error: request for member 'block' in something not a structure or union
bgzf.c:420: warning: implicit declaration of function 'kh_destroy'
bgzf.c: At top level:
bgzf.c:423: error: syntax error before '*' token
bgzf.c: In function 'load_block_from_cache':
bgzf.c:425: error: 'khint_t' undeclared (first use in this function)
bgzf.c:425: error: syntax error before 'k'
bgzf.c:426: error: 'p' undeclared (first use in this function)
bgzf.c:427: error: 'cache' undeclared (first use in this function)
bgzf.c:427: error: 'h' undeclared (first use in this function)
bgzf.c:427: error: syntax error before ')' token
bgzf.c:428: error: 'k' undeclared (first use in this function)
bgzf.c:428: warning: implicit declaration of function 'kh_get'
bgzf.c:428: error: 'block_address' undeclared (first use in this function)
bgzf.c:430: error: invalid lvalue in unary '&'
bgzf.c:431: error: invalid type argument of '->'
bgzf.c:431: error: invalid type argument of '->'
bgzf.c:432: error: invalid type argument of '->'
bgzf.c:433: error: invalid type argument of '->'
bgzf.c:434: error: invalid type argument of '->'
bgzf.c:434: error: 'MAX_BLOCK_SIZE' undeclared (first use in this function)
bgzf.c:436: warning: implicit declaration of function 'knet_seek'
bgzf.c:436: error: invalid type argument of '->'
bgzf.c: At top level:
bgzf.c:443: error: syntax error before '*' token
bgzf.c: In function 'cache_block':
bgzf.c:446: error: 'khint_t' undeclared (first use in this function)
bgzf.c:446: error: syntax error before 'k'
bgzf.c:447: error: 'p' undeclared (first use in this function)
bgzf.c:448: error: 'cache' undeclared (first use in this function)
bgzf.c:448: error: 'h' undeclared (first use in this function)
bgzf.c:448: error: syntax error before ')' token
bgzf.c:449: error: 'MAX_BLOCK_SIZE' undeclared (first use in this function)
bgzf.c:449: error: invalid type argument of '->'
bgzf.c:450: warning: implicit declaration of function 'kh_size'
bgzf.c:450: error: invalid type argument of '->'
bgzf.c:454: error: 'k' undeclared (first use in this function)
bgzf.c:457: error: request for member 'block' in something not a structure or union
bgzf.c:458: warning: implicit declaration of function 'kh_del'
bgzf.c:461: warning: implicit declaration of function 'kh_put'
bgzf.c:461: error: invalid type argument of '->'
bgzf.c:463: error: invalid lvalue in unary '&'
bgzf.c:464: error: invalid type argument of '->'
bgzf.c:465: error: invalid type argument of '->'
bgzf.c:465: error: 'size' undeclared (first use in this function)
bgzf.c:467: error: request for member 'block' in something not a structure or union
bgzf.c:467: error: invalid type argument of '->'
bgzf.c: At top level:
bgzf.c:471: error: syntax error before '*' token
bgzf.c: In function 'bgzf_read_block':
bgzf.c:473: error: 'bgzf_byte_t' undeclared (first use in this function)
bgzf.c:473: error: syntax error before 'header'
bgzf.c:476: warning: implicit declaration of function 'knet_tell'
bgzf.c:476: error: invalid type argument of '->'
bgzf.c:478: warning: implicit declaration of function 'knet_read'
bgzf.c:478: error: invalid type argument of '->'
bgzf.c:478: error: 'header' undeclared (first use in this function)
bgzf.c:485: error: invalid type argument of '->'
bgzf.c:497: error: 'uint8_t' undeclared (first use in this function)
bgzf.c:497: error: syntax error before ')' token
bgzf.c:498: error: 'compressed_block' undeclared (first use in this function)
bgzf.c:498: error: syntax error before ')' token
bgzf.c:499: error: 'BLOCK_HEADER_LENGTH' undeclared (first use in this function)
bgzf.c:502: error: invalid type argument of '->'
bgzf.c:513: error: invalid type argument of '->'
bgzf.c:515: error: invalid type argument of '->'
bgzf.c:517: error: invalid type argument of '->'
bgzf.c:518: error: invalid type argument of '->'
bgzf.c: At top level:
bgzf.c:524: error: syntax error before '*' token
bgzf.c: In function 'bgzf_read':
bgzf.c:526: error: 'length' undeclared (first use in this function)
bgzf.c:529: error: invalid type argument of '->'
bgzf.c:535: error: 'bgzf_byte_t' undeclared (first use in this function)
bgzf.c:535: error: 'output' undeclared (first use in this function)
bgzf.c:535: error: 'data' undeclared (first use in this function)
bgzf.c:537: error: invalid type argument of '->'
bgzf.c:537: error: invalid type argument of '->'
bgzf.c:538: error: 'buffer' undeclared (first use in this function)
bgzf.c:543: error: invalid type argument of '->'
bgzf.c:543: error: invalid type argument of '->'
bgzf.c:548: warning: implicit declaration of function 'bgzf_min'
bgzf.c:549: error: invalid type argument of '->'
bgzf.c:550: error: invalid type argument of '->'
bgzf.c:551: error: invalid type argument of '->'
bgzf.c:555: error: invalid type argument of '->'
bgzf.c:555: error: invalid type argument of '->'
bgzf.c:557: error: invalid type argument of '->'
bgzf.c:557: error: invalid type argument of '->'
bgzf.c:561: error: invalid type argument of '->'
bgzf.c:562: error: invalid type argument of '->'
bgzf.c: At top level:
bgzf.c:567: error: syntax error before '*' token
bgzf.c: In function 'bgzf_flush':
bgzf.c:569: error: invalid type argument of '->'
bgzf.c:571: error: invalid type argument of '->'
bgzf.c:574: error: invalid type argument of '->'
bgzf.c:574: error: invalid type argument of '->'
bgzf.c:582: error: invalid type argument of '->'
bgzf.c: At top level:
bgzf.c:587: error: syntax error before '*' token
bgzf.c: In function 'bgzf_flush_try':
bgzf.c:589: error: invalid type argument of '->'
bgzf.c:589: error: 'size' undeclared (first use in this function)
bgzf.c:589: error: invalid type argument of '->'
bgzf.c: At top level:
bgzf.c:594: error: syntax error before '*' token
bgzf.c: In function 'bgzf_write':
bgzf.c:596: error: nested functions are disabled, use -fnested-functions to re-enable
bgzf.c:596: error: syntax error before '*' token
bgzf.c:598: error: invalid type argument of '->'
bgzf.c:603: error: invalid type argument of '->'
bgzf.c:604: error: invalid type argument of '->'
bgzf.c:604: error: invalid type argument of '->'
bgzf.c:606: error: 'input' undeclared (first use in this function)
bgzf.c:606: error: 'data' undeclared (first use in this function)
bgzf.c:607: error: invalid type argument of '->'
bgzf.c:609: error: 'length' undeclared (first use in this function)
bgzf.c:610: error: invalid type argument of '->'
bgzf.c:611: error: 'bgzf_byte_t' undeclared (first use in this function)
bgzf.c:611: error: 'buffer' undeclared (first use in this function)
bgzf.c:611: error: invalid type argument of '->'
bgzf.c:612: error: invalid type argument of '->'
bgzf.c:613: error: invalid type argument of '->'
bgzf.c:616: error: invalid type argument of '->'
bgzf.c: At top level:
bgzf.c:625: error: syntax error before '*' token
bgzf.c: In function 'bgzf_close':
bgzf.c:627: error: invalid type argument of '->'
bgzf.c:632: error: invalid type argument of '->'
bgzf.c:632: error: invalid type argument of '->'
bgzf.c:638: error: invalid type argument of '->'
bgzf.c:646: error: invalid type argument of '->'
bgzf.c:649: error: invalid type argument of '->'
bgzf.c:649: error: invalid type argument of '->'
bgzf.c:650: warning: implicit declaration of function 'knet_close'
bgzf.c:650: error: invalid type argument of '->'
bgzf.c:656: error: invalid type argument of '->'
bgzf.c:657: error: invalid type argument of '->'
bgzf.c:659: warning: passing argument 1 of 'free' makes pointer from integer without a cast
bgzf.c: At top level:
bgzf.c:663: error: syntax error before '*' token
bgzf.c: In function 'bgzf_set_cache_size':
bgzf.c:665: error: invalid type argument of '->'
bgzf.c:665: error: 'cache_size' undeclared (first use in this function)
bgzf.c: At top level:
bgzf.c:668: error: syntax error before '*' token
bgzf.c: In function 'bgzf_check_EOF':
bgzf.c:670: error: nested functions are disabled, use -fnested-functions to re-enable
bgzf.c:670: error: syntax error before 'magic'
bgzf.c:671: error: 'uint8_t' undeclared (first use in this function)
bgzf.c:674: error: invalid type argument of '->'
bgzf.c:675: error: invalid type argument of '->'
bgzf.c:676: error: invalid type argument of '->'
bgzf.c:676: error: 'buf' undeclared (first use in this function)
bgzf.c:677: error: invalid type argument of '->'
bgzf.c:684: error: 'magic' undeclared (first use in this function)
bgzf.c: At top level:
bgzf.c:687: error: syntax error before '*' token
bgzf.c: In function 'bgzf_seek':
bgzf.c:692: error: invalid type argument of '->'
bgzf.c:696: error: 'where' undeclared (first use in this function)
bgzf.c:700: error: 'pos' undeclared (first use in this function)
bgzf.c:703: error: invalid type argument of '->'
bgzf.c:710: error: invalid type argument of '->'
bgzf.c:711: error: invalid type argument of '->'
bgzf.c:712: error: invalid type argument of '->'
make[2]: *** [bgzf.o] Error 1
make[1]: *** [lib-recur] Error 1
make: *** [all-recur] Error 1

Does anyone know how to solve?

Thanks!
louis7781x is offline   Reply With Quote
Old 07-06-2011, 09:54 AM   #2
BENM
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Location: PRC

Join Date: May 2009
Posts: 33
Default

it looks like it can't find zlib on your system, and did you install c/c++ compiler and SDK at your Mac, like xcode?
BENM is offline   Reply With Quote
Old 07-06-2011, 09:57 AM   #3
BAMseek
Senior Member
 
Location: St. Louis, MO, USA

Join Date: Apr 2011
Posts: 124
Default

It looks like it is not finding the zlib library. Variables such as "Z_DEFAULT_STRATEGY" are defined in the zlib.h file, which should already be on your Mac. The -lz flag in the Makefile will link to that library. Which version of Mac are you on? I was able to download 0.1.16 just now on my Snow Leopard and compile it by typing "make" just as you tried.
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