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gmarcais / Jellyfish

A fast multi-threaded k-mer counter
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Example compile error #33

Closed gonzalogacc closed 9 years ago

gonzalogacc commented 9 years ago

Hi, i'm trying to compile the examples, and i keep getting this error from the compiler

In file included from query_per_sequence.cc:22: include/jellyfish-2.2.0/jellyfish/stream_manager.hpp:98:12: error: calling a private constructor of class 'std::1::unique_ptrstd::__1::basic_istream<char, std::1::default_deletestd::__1::basic_istream >' return res; ^ Does anybody have any idea what i'm missing!?? Thanks Gonza.-

gmarcais commented 9 years ago

Can you give us some more information: what OS you are on, what compiler and version you are using?

Guillaume.

gonzalogacc commented 9 years ago

Sure, i' running MacOS yosemite v10.10.3 and this the compiler is:

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 6.1.0 (clang-602.0.49) (based on LLVM 3.6.0svn) Target: x86_64-apple-darwin14.3.0 Thread model: posix

Gonza.-

gmarcais commented 9 years ago

On some version of MacOS, the compiler is too old. We require at least version 4.4 of gcc (and the C++ standard library), and it ships with 4.2. You have to install a newer version of gcc, for example using macports. There is some information on the web page: http://www.genome.umd.edu/jellyfish.html

Another remark. This switch --prefix=/Applications/Xcode.app/Contents/Developer/usr tell where to install Jellyfish after compilation. I think you want to pass --prefix=$HOME (or some other place where you keep your manually compiled software) instead of installing in the Xcode app folder.

Guillaume.