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Old 08-10-2009, 07:24 PM   #1
nat
Junior Member
 
Location: Sydney

Join Date: Jul 2009
Posts: 8
Default 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
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Old 01-17-2010, 03:55 PM   #2
ac13
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Location: california

Join Date: Jan 2010
Posts: 1
Default Re: Tophat install errors

Hi Natalie,

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

Thanks!
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