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  • blat error

    Hey, i download blat suite, now i am trying to install it.
    when i run make , i get this error:

    cd lib && make
    make[1]: Entering directory `/home/pa/Desktop/pa/blatSrc/lib'
    gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o common.o -c common.c
    cc1: warnings being treated as errors
    common.c: In function ‘firstWordInFile’:
    common.c:1695: error: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
    make[1]: *** [common.o] Error 1
    make[1]: Leaving directory `/home/dror/Desktop/Dror/blatSrc/lib'
    make: *** [all] Error 2

    what to do?

  • #2
    I have the same question, but you can see that https://lists.soe.ucsc.edu/pipermail...ch/018586.html

    good lucky!

    Comment


    • #3
      I have another question ,can you help?
      cd lib && make
      make[1]: Entering directory `/analysis/software_han/blatSrc/lib'
      gcc -O -g -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DCOLOR32 -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I/usr/lib/syslinux/com32/include -o aliType.o -c aliType.c
      In file included from ../inc/common.h:30:0,
      from aliType.c:5:
      /usr/lib/syslinux/com32/include/stdio.h: In function ‘fileno’:
      /usr/lib/syslinux/com32/include/stdio.h:39:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
      /usr/lib/syslinux/com32/include/stdio.h: In function ‘fdopen’:
      /usr/lib/syslinux/com32/include/stdio.h:56:12: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
      /usr/lib/syslinux/com32/include/stdio.h: At top level:
      /usr/lib/syslinux/com32/include/stdio.h:74:17: warning: conflicting types for built-in function ‘fwrite’ [enabled by default]
      /usr/lib/syslinux/com32/include/stdio.h:97:14: warning: conflicting types for built-in function ‘snprintf’ [enabled by default]
      /usr/lib/syslinux/com32/include/stdio.h:98:14: warning: conflicting types for built-in function ‘vsnprintf’ [enabled by default]
      In file included from ../inc/common.h:31:0,
      from aliType.c:5:
      /usr/lib/syslinux/com32/include/stdlib.h:39:29: warning: conflicting types for built-in function ‘malloc’ [enabled by default]
      /usr/lib/syslinux/com32/include/stdlib.h:41:29: warning: conflicting types for built-in function ‘calloc’ [enabled by default]
      /usr/lib/syslinux/com32/include/stdlib.h:42:29: warning: conflicting types for built-in function ‘realloc’ [enabled by default]
      In file included from ../inc/common.h:33:0,
      from aliType.c:5:
      /usr/lib/syslinux/com32/include/string.h:12:16: warning: conflicting types for built-in function ‘memchr’ [enabled by default]
      /usr/lib/syslinux/com32/include/string.h:13:14: warning: conflicting types for built-in function ‘memcmp’ [enabled by default]
      /usr/lib/syslinux/com32/include/string.h:14:16: warning: conflicting types for built-in function ‘memcpy’ [enabled by default]
      /usr/lib/syslinux/com32/include/string.h:15:16: warning: conflicting types for built-in function ‘mempcpy’ [enabled by default]
      /usr/lib/syslinux/com32/include/string.h:16:16: warning: conflicting types for built-in function ‘memmove’ [enabled by default]
      /usr/lib/syslinux/com32/include/string.h:17:16: warning: conflicting types for built-in function ‘memset’ [enabled by default]
      /usr/lib/syslinux/com32/include/string.h:21:14: warning: conflicting types for built-in function ‘strncasecmp’ [enabled by default]
      /usr/lib/syslinux/com32/include/string.h:26:17: warning: conflicting types for built-in function ‘strcspn’ [enabled by default]
      /usr/lib/syslinux/com32/include/string.h:28:16: warning: conflicting types for built-in function ‘strndup’ [enabled by default]
      /usr/lib/syslinux/com32/include/string.h:30:17: warning: conflicting types for built-in function ‘strlen’ [enabled by default]
      /usr/lib/syslinux/com32/include/string.h:32:16: warning: conflicting types for built-in function ‘strncat’ [enabled by default]
      /usr/lib/syslinux/com32/include/string.h:34:14: warning: conflicting types for built-in function ‘strncmp’ [enabled by default]
      /usr/lib/syslinux/com32/include/string.h:35:16: warning: conflicting types for built-in function ‘strncpy’ [enabled by default]
      /usr/lib/syslinux/com32/include/string.h:37:16: warning: conflicting types for built-in function ‘stpncpy’ [enabled by default]
      /usr/lib/syslinux/com32/include/string.h:42:17: warning: conflicting types for built-in function ‘strspn’ [enabled by default]
      In file included from /usr/lib/syslinux/com32/include/stdint.h:8:0,
      from /usr/lib/syslinux/com32/include/sys/types.h:10,
      from ../inc/common.h:35,
      from aliType.c:5:
      /usr/lib/syslinux/com32/include/bitsize/stdint.h:27:0: warning: "__INT64_C" redefined [enabled by default]
      <built-in>:0:0: note: this is the location of the previous definition
      /usr/lib/syslinux/com32/include/bitsize/stdint.h:28:0: warning: "__UINT64_C" redefined [enabled by default]
      <built-in>:0:0: note: this is the location of the previous definition
      In file included from aliType.c:5:0:
      ../inc/common.h:1460:1: error: unknown type name ‘time_t’
      ../inc/common.h:1460:30: warning: ‘struct tm’ declared inside parameter list [enabled by default]
      ../inc/common.h:1460:30: warning: its scope is only this definition or declaration, which is probably not what you want [enabled by default]
      ../inc/common.h:1467:1: error: unknown type name ‘time_t’
      ../inc/common.h:1473:59: error: unknown type name ‘time_t’
      make[1]: *** [aliType.o] Error 1
      make[1]: Leaving directory `/analysis/software_han/blatSrc/lib'
      make: *** [all] Error 2

      Comment


      • #4
        @myshu: This error probably refers to the program not finding time.h header file.

        What OS are you using? If you know where the time.h file is you could modify the #include line to point to this file.

        Comment

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