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bbuchfink / diamond

Accelerated BLAST compatible local sequence aligner.
GNU General Public License v3.0
1.04k stars 182 forks source link

Error while compiling from source diamond-0.8.5 #45

Closed VasilyTokarev closed 7 years ago

VasilyTokarev commented 8 years ago

Hello,

I have been trying to install diamond v 0.8.5 on account without root permission. This is what I have done:

$ wget http://github.com/bbuchfink/diamond/archive/v0.8.5.tar.gz
$ tar xzf v0.8.5.tar.gz
$ cd diamond-0.8.5
$ mkdir bin
$ cd bin
$ cmake .. -DCMAKE_INSTALL_PREFIX=/home/tokarev/programs/diamond
$ make install

This is what I get

[tokarev@hhmi bin]$ make install
[  3%] Building CXX object CMakeFiles/diamond.dir/src/run/main.cpp.o
In file included from /home/tokarev/tmp/install_files/diamond/src/run/../data/seed_histogram.h:26,
                 from /home/tokarev/tmp/install_files/diamond/src/run/../data/sorted_list.h:25,
                 from /home/tokarev/tmp/install_files/diamond/src/run/../data/reference.h:29,
                 from /home/tokarev/tmp/install_files/diamond/src/run/main.cpp:25:
/home/tokarev/tmp/install_files/diamond/src/run/../data/sequence_set.h: In constructor 'Sequence_set::Sequence_set(Input_stream&)':
/home/tokarev/tmp/install_files/diamond/src/run/../data/sequence_set.h:41: error: class 'Sequence_set' does not have any field named 'String_set'
make[2]: *** [CMakeFiles/diamond.dir/src/run/main.cpp.o] Error 1
make[1]: *** [CMakeFiles/diamond.dir/all] Error 2
make: *** [all] Error 2

I am trying to install humann2 using anaconda running on python 2.7, Humann2 requires diamond and I get this message while installing it.

Thank you! Vasily

bbuchfink commented 8 years ago

Hi, can you tell me what gcc version you use? (run g++ --version)

VasilyTokarev commented 8 years ago

I just updated gcc and successfully installed diamond! Thank you for your help!

nana-marinbio commented 8 years ago

Hi bbuchfink, I have gcc llvm-g++-4.2 and got the same error as Vasily make[2]: * [CMakeFiles/diamond.dir/src/run/main.cpp.o] Error 1 make[1]: * [CMakeFiles/diamond.dir/all] Error 2 make: *\ [all] Error 2 Is it possible to compile diamond with llvm-g++-4.2? Otherwise I think I have to update my OSX version (it is 10.7.5) Thank you AP

bbuchfink commented 8 years ago

Hi, I just uploaded a new release that should fix this problem.

nana-marinbio commented 8 years ago

Many thanks AP

Em terça-feira, 12 de julho de 2016, bbuchfink notifications@github.com escreveu:

Hi, I just uploaded a new release that should fix this problem.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/bbuchfink/diamond/issues/45#issuecomment-232045269, or mute the thread https://github.com/notifications/unsubscribe/ATL8fBXr9-4Xfag9lob9-HlYZ01tpRUzks5qU5UbgaJpZM4IwBOK .

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