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  • TopHat install errors

    hi there,

    I am trying to install TopHat and have completed the configure step successfully, but not when i run the 'make' command, I get the following error messages.

    (bowtie modules have been copied to the PATH already)

    Any ideas??

    natalie@natalie-desktop:~/software/tophat-1.0.10$ make

    make all-recursive

    make[1]: Entering directory `/home/natalie/software/tophat-1.0.10'

    Making all in src

    make[2]: Entering directory `/home/natalie/software/tophat-1.0.10/src'

    g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -m64 -O3 -DNDEBUG -I./SeqAn-1.1 -Wall -g -m64 -O3 -DNDEBUG -MT reads.o -MD -MP -MF .deps/reads.Tpo -c -o reads.o reads.cpp

    In file included from /usr/include/c++/4.3/bits/stl_algo.h:65,

    from /usr/include/c++/4.3/algorithm:67,

    from reads.cpp:16:

    /usr/include/c++/4.3/cstdlib:124: error: ‘::malloc’ has not been declared

    In file included from reads.cpp:19:

    bwt_map.h: In member function ‘bool HitStream::next_read_hits(HitsForRead&)’:

    bwt_map.h:547: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result

    make[2]: *** [reads.o] Error 1

    make[2]: Leaving directory `/home/natalie/software/tophat-1.0.10/src'

    make[1]: *** [all-recursive] Error 1

    make[1]: Leaving directory `/home/natalie/software/tophat-1.0.10'

    make: *** [all] Error 2

    natalie@natalie-desktop:~/software/tophat-1.0.10$ make install

    Making install in src

    make[1]: Entering directory `/home/natalie/software/tophat-1.0.10/src'

    g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -m64 -O3 -DNDEBUG -I./SeqAn-1.1 -Wall -g -m64 -O3 -DNDEBUG -MT reads.o -MD -MP -MF .deps/reads.Tpo -c -o reads.o reads.cpp

    In file included from /usr/include/c++/4.3/bits/stl_algo.h:65,

    from /usr/include/c++/4.3/algorithm:67,

    from reads.cpp:16:

    /usr/include/c++/4.3/cstdlib:124: error: ‘::malloc’ has not been declared

    In file included from reads.cpp:19:

    bwt_map.h: In member function ‘bool HitStream::next_read_hits(HitsForRead&)’:

    bwt_map.h:547: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result

    make[1]: *** [reads.o] Error 1

    make[1]: Leaving directory `/home/natalie/software/tophat-1.0.10/src'

    make: *** [install-recursive] Error 1

  • #2
    Re: Tophat install errors

    Hi Natalie,

    I am getting the exact same errors - were you able to find a solution?

    Thanks!

    Comment

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