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Old 01-20-2014, 11:24 AM   #1
Volklor
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Default MaSuRCA install error

I'm attempting to install the MaSuRCA assembly tool using the simple instructions on the quickstart guide. Basically, the instructions say to untar the package, cd into the resulting directory, and then run ./install.sh.

When I do this, the very end of the output gives a set of errors that apparently have to do with jellyfish. I'm not sure how to interpret this. Has anyone else seen this? I'm pasting just the part of the output that contains the errors and occurs at the very end of the process. There were not any obvious errors before this point:

# Output
In file included from sub_commands/count_main.cc:39:
./include/jellyfish/mer_qual_iterator.hpp: In member function ‚void jellyfish::mer_qual_iterator<SequencePool, MerType>::init_from_job()‚:
./include/jellyfish/mer_qual_iterator.hpp:108: error: ‚struct std::basic_string<char, std::char_traits<char>, std::allocator<char> >‚ has no member named ‚cbegin‚
./include/jellyfish/mer_qual_iterator.hpp:109: error: ‚struct std::basic_string<char, std::char_traits<char>, std::allocator<char> >‚ has no member named ‚cend‚
./include/jellyfish/mer_qual_iterator.hpp:111: error: ‚struct std::basic_string<char, std::char_traits<char>, std::allocator<char> >‚ has no member named ‚cbegin‚
./include/jellyfish/mer_qual_iterator.hpp:112: error: ‚struct std::basic_string<char, std::char_traits<char>, std::allocator<char> >‚ has no member named ‚cend‚
make[1]: *** [sub_commands/count_main.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: Leaving directory `/raid4/cgrb/MaSuRCA-2.2.0/jellyfish'
make: *** [install] Error 2
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Old 01-20-2014, 12:25 PM   #2
GenoMax
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Default

This particular excerpt does not raise any obvious flags. Can you post the earliest instances of "Error" from this output?

If it is easier, you can paste the whole output via pastebin (http://pastebin.com/). Remember to remove any identifying IP addresses/host names/account names etc.
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Old 01-21-2014, 07:35 AM   #3
Volklor
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Default Here's the entire output...

OK, I tried pasting the entire output in pastebin. How do I link the pastebin page back to this thread?

I titled the pastebin "MaSuRCA install error output".
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Old 01-21-2014, 07:46 AM   #4
GenoMax
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Here the pastebin link for your output: http://pastebin.com/zLDXsks7 Verify that it is right.
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Old 01-21-2014, 07:47 AM   #5
Volklor
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Yup, that's the one.
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Old 01-21-2014, 03:14 PM   #6
GenoMax
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Can you tell us what OS you are using and if it is 32- or 64-bit? This is a real server (and not a virtual machine).
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Old 01-22-2014, 07:10 AM   #7
Volklor
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Default OS

The OS is Linux - x86_64 GNU/Linux
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