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Illumina / ExpansionHunter

A tool for estimating repeat sizes
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Install error "[stats/CMakeFiles/stats.dir/all] Error 2" #60

Closed YiweiNiu closed 5 years ago

YiweiNiu commented 5 years ago

Hi,

I got the following error message when typing make.

Scanning dependencies of target reads
[ 39%] Building CXX object reads/CMakeFiles/reads.dir/Read.cpp.o
[ 40%] Building CXX object reads/CMakeFiles/reads.dir/ReadPairs.cpp.o
[ 41%] Linking CXX static library libreads.a
[ 41%] Built target reads
Scanning dependencies of target stats
[ 41%] Building CXX object stats/CMakeFiles/stats.dir/LocusStats.cpp.o
In file included from /home/software/boost_1_64_0/boost/numeric/ublas/vector.hpp:21:0,
                 from /home/software/boost_1_64_0/boost/numeric/ublas/matrix.hpp:18,
                 from /home/software/boost_1_64_0/boost/accumulators/statistics/covariance.hpp:22,
                 from /home/software/boost_1_64_0/boost/accumulators/statistics.hpp:13,
                 from /home/niuyw/software/ExpansionHunter/stats/LocusStats.hh:29,
                 from /home/niuyw/software/ExpansionHunter/stats/LocusStats.cpp:22:
/home/software/boost_1_64_0/boost/numeric/ublas/storage.hpp: In member function ‘void boost::numeric::ublas::unbounded_array<T, ALLOC>::serialize(Archive&, unsigned int)’:
/home/software/boost_1_64_0/boost/numeric/ublas/storage.hpp:299:18: error: ‘make_array’ is not a member of ‘boost::serialization’
             ar & serialization::make_array(data_, s);
                  ^
/home/software/boost_1_64_0/boost/numeric/ublas/storage.hpp: In member function ‘void boost::numeric::ublas::bounded_array<T, N, ALLOC>::serialize(Archive&, unsigned int)’:
/home/software/boost_1_64_0/boost/numeric/ublas/storage.hpp:494:18: error: ‘make_array’ is not a member of ‘boost::serialization’
             ar & serialization::make_array(data_, s);
                  ^
In file included from /home/software/boost_1_64_0/boost/accumulators/statistics/covariance.hpp:22:0,
                 from /home/software/boost_1_64_0/boost/accumulators/statistics.hpp:13,
                 from /home/niuyw/software/ExpansionHunter/stats/LocusStats.hh:29,
                 from /home/niuyw/software/ExpansionHunter/stats/LocusStats.cpp:22:
/home/software/boost_1_64_0/boost/numeric/ublas/matrix.hpp: In member function ‘void boost::numeric::ublas::c_matrix<T, M, N>::serialize(Archive&, unsigned int)’:
/home/software/boost_1_64_0/boost/numeric/ublas/matrix.hpp:5977:18: error: ‘make_array’ is not a member of ‘boost::serialization’
             ar & serialization::make_array(data_, N);
                  ^
make[2]: *** [stats/CMakeFiles/stats.dir/LocusStats.cpp.o] Error 1
make[1]: *** [stats/CMakeFiles/stats.dir/all] Error 2
make: *** [all] Error 2

The boost version is 1.64.0. cmake version is 3.8.0-rc4. gcc version is 4.9.3.

Do you have any ideas?

Bests, Yiwei Niu

egor-dolzhenko commented 5 years ago

Hi Yiwei,

Thank you for reporting the issue. It might be caused by a Boost 1.64 bug (see https://svn.boost.org/trac10/ticket/12516). Could you please try a newer version of Boost?

Alternatively, if you are using a compatible version of Linux or MacOS, you could try running a pre-built binary included with the release:

Please let me know if any of this helps.

Best wishes, Egor

YiweiNiu commented 5 years ago

Thank you very much. I would use the binary version.