Tophat Install Error During Make Step

Question

[Nirvana]

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.

[Neilfws]

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.

[Lars Juhl Jensen]

Fixed formatting.

[Nirvana]

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

[Lars Juhl Jensen]

Which C++ compiler and version are you using?

[Nirvana]

gcc (GCC) 3.2.2 20030222

[Gww]

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

[Gww]

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

Answer 1

[Joachim]

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

• http://tophat.cbcb.umd.edu/downloads/tophat-1.2.0.Linux_x86_64.tar.gz
• http://tophat.cbcb.umd.edu/downloads/tophat-1.2.0.OSX_x86_64.tar.gz

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

[Nirvana]

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

Answer 2

[Gww]

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/).

[Nirvana]

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

[Gww]

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

[Nirvana]

The same error message.