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GATB / gatb-core

Core library of the Genome Analysis Toolbox with de-Bruijn graph
https://gatb.inria.fr/software/gatb-core/
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problem with <boost/graph/adjacency_list.hpp> #30

Closed MinzhuXie closed 4 years ago

MinzhuXie commented 5 years ago

I had only inserted "#include <boost/graph/adjacency_list.hpp>" at the head of the gatb-core example file debruijn1.cpp, and type the following commands:

cmake -DGATB_CORE_INCLUDE_EXAMPLES=True -DCMAKE_BUILD_TYPE=Debug ..
make -j4 debruijn1

there is a compile error: [100%] Building CXX object examples/CMakeFiles/debruijn1.dir/debruijn/debruijn1.cpp.o In file included from /usr/local/include/boost/pending/container_traits.hpp:15:0, from /usr/local/include/boost/graph/named_graph.hpp:23, from /usr/local/include/boost/graph/adjacency_list.hpp:37, from /home/xieminzhu/Downloads/GATB/gatb-core/gatb-core/examples/debruij/debruijn1.cpp:3: /usr/local/include/boost/next_prior.hpp:64:1: error: template argument 2 is invalid

^ The g++ version is : gcc version 7.4.0 (Ubuntu 7.4.0-1ubuntu1~18.04.1) The boost installed in the Ubuntu is boost_1_71_0

rchikhi commented 5 years ago

Indeed I get the same issue. It doesn't look like gatb-core plays well with an external Boost dependency. This could be because gatb-core already includes another version of Boost (in ../thirdparty). Do you really need to use boost::adjacency_list?

Best, Rayan

MinzhuXie commented 5 years ago

Yes. One of my student tried to use a gatb tool Bicolor but always got a compile error with the head file. Is there any solution to this issue? Best, Minzhu Xie

在 2019年10月25日，下午11:14，Rayan Chikhi notifications@github.com<mailto:notifications@github.com> 写道：

Indeed I get the same issue. It doesn't look like gatb-core plays well with an external Boost dependency. This could be because gatb-core already includes another version of Boost (in ../thirdparty). Do you really need to use boost::adjacency_list?

Best, Rayan

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rchikhi commented 4 years ago

Sorry for the delay, it should work now in the latest version of the master branch.