Question: Tophat Install Error During Make Step
0
gravatar for Nirvana
8.0 years ago by
Nirvana0
Nirvana0 wrote:

I am trying to install TopHat 1.2.0 and have completed the configure step successfully, but not when i run the 'make' command, I get the following error messages.

reads.cpp:327:   instantiated from here
SeqAn-1.1/seqan/basic/basic_alphabet_interface.h:353: no match for `*
   seqan::Iter<const std::basic_string<char, std::char_traits<char>,
   std::allocator<char> >, seqan::StdIteratorAdaptor>&' operator
make[2]: *** [reads.o] Error 1
make[2]: Leaving directory `/usr/local/tophat-1.2.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/usr/local/tophat-1.2.0'
make: *** [all] Error 2

Anybody could help me? Thanks for your time and attention.

installation tophat • 2.6k views
ADD COMMENTlink modified 8.0 years ago by Gww2.6k • written 8.0 years ago by Nirvana0

Please try to format these long log messages for better readability (4 leading spaces per line usually does the trick; I added them to your question.) Also, consider including only the relevant parts.

ADD REPLYlink written 8.0 years ago by Neilfws48k

Fixed formatting.

ADD REPLYlink written 8.0 years ago by Lars Juhl Jensen11k

Only relevant parts are included. Thanks a lot to both of you.

ADD REPLYlink written 8.0 years ago by Nirvana0

Which C++ compiler and version are you using?

ADD REPLYlink written 8.0 years ago by Lars Juhl Jensen11k

gcc (GCC) 3.2.2 20030222

ADD REPLYlink written 8.0 years ago by Nirvana0

Is it possible to upgrade your compiler to something more recent?

ADD REPLYlink written 8.0 years ago by Gww2.6k

Is it possible to upgrade your compiler to something more recent? GCC 3.2.2 is over 8 years old.

ADD REPLYlink written 8.0 years ago by Gww2.6k
2
gravatar for Joachim
8.0 years ago by
Joachim2.8k
San Francisco, California
Joachim2.8k wrote:

Well, this does not answer your question directly, but there are also ready-made binary versions available (from http://tophat.cbcb.umd.edu/):

Unless you are specifically trying to compile it as 32bit, you could have a go with those files.

ADD COMMENTlink written 8.0 years ago by Joachim2.8k

However,the 64 bit version dosen't match my machine. Thank you all the same.

ADD REPLYlink written 8.0 years ago by Nirvana0
1
gravatar for Gww
8.0 years ago by
Gww2.6k
Canada
Gww2.6k wrote:

Usually the errors related to the SeqAn library can be resolved by replacing the source files included with the TopHat installation with the SeqAn 1.2 source files (ie. copy the files into the folder tophat/src/SeqAn-1.1/).

ADD COMMENTlink written 8.0 years ago by Gww2.6k

I have tried this. However, it doesn't work. Thank you all the same.

ADD REPLYlink written 8.0 years ago by Nirvana0

Did it give you the same error message? OR something different?

ADD REPLYlink written 8.0 years ago by Gww2.6k

The same error message.

ADD REPLYlink written 8.0 years ago by Nirvana0
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