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  • Error installing bcl2fastq 2.20 in make step - Ubuntu 18.04

    After spending unmerous hours trying to install bcl2fastq 2.20 in my server I decided to ask for help.

    I am trying to install bcl2fastq 2.20 in Ubuntu 18.04. I have followed multiple recommendations for fixing inconveniences while installing bcl2fastq with newer boost versions (as in these posts https://backwardincompatible.com/pos...on-ubuntu-with and https://gist.github.com/jblachly/f8d...e005548a5a2d2e).

    I don't get any errors after running configure from the build directory. My error appears after typing make afterwards.

    Code:
    $ make 
     
    Scanning dependencies of target BCL2FASTQ_OPT
    [  0%] Built target BCL2FASTQ_OPT
    Scanning dependencies of target bcl2fastq_common
    [  1%] Building CXX object cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/Logger.cpp.o
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp: In constructor ‘bcl2fastq::common::detail::LogStream::LogStream()’:
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:122:13: error: ‘clog’ is not a member of ‘std’
     , ias_(std::clog)
                 ^~~~
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:122:13: note: suggested alternative: ‘log’
     , ias_(std::clog)
                 ^~~~
                 log
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp: In constructor ‘bcl2fastq::common::detail::LogStream::LogStream(bcl2fastq::common::LogLevel::value_type)’:
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:130:13: error: ‘clog’ is not a member of ‘std’
     , ias_(std::clog)
                 ^~~~
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:130:13: note: suggested alternative: ‘log’
     , ias_(std::clog)
                 ^~~~
                 log
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp: In copy constructor ‘bcl2fastq::common::detail::LogStream::LogStream(const bcl2fastq::common::detail::LogStream&)’:
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:146:13: error: ‘clog’ is not a member of ‘std’
     , ias_(std::clog)
                 ^~~~
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:146:13: note: suggested alternative: ‘log’
     , ias_(std::clog)
                 ^~~~
                 log
    cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/build.make:57: recipe for target 'cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/Logger.cpp.o' failed
    make[2]: *** [cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/Logger.cpp.o] Error 1
    CMakeFiles/Makefile2:257: recipe for target 'cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/all' failed
    make[1]: *** [cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/all] Error 2
    Makefile:126: recipe for target 'all' failed
    make: *** [all] Error 2
    installing bcl2fastq
    [  0%] Built target BCL2FASTQ_OPT
    [  1%] Building CXX object cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/Logger.cpp.o
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp: In constructor ‘bcl2fastq::common::detail::LogStream::LogStream()’:
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:122:13: error: ‘clog’ is not a member of ‘std’
     , ias_(std::clog)
                 ^~~~
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:122:13: note: suggested alternative: ‘log’
     , ias_(std::clog)
                 ^~~~
                 log
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp: In constructor ‘bcl2fastq::common::detail::LogStream::LogStream(bcl2fastq::common::LogLevel::value_type)’:
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:130:13: error: ‘clog’ is not a member of ‘std’
     , ias_(std::clog)
                 ^~~~
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:130:13: note: suggested alternative: ‘log’
     , ias_(std::clog)
                 ^~~~
                 log
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp: In copy constructor ‘bcl2fastq::common::detail::LogStream::LogStream(const bcl2fastq::common::detail::LogStream&)’:
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:146:13: error: ‘clog’ is not a member of ‘std’
     , ias_(std::clog)
                 ^~~~
    /media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:146:13: note: suggested alternative: ‘log’
     , ias_(std::clog)
                 ^~~~
                 log
    cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/build.make:57: recipe for target 'cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/Logger.cpp.o' failed
    make[2]: *** [cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/Logger.cpp.o] Error 1
    CMakeFiles/Makefile2:257: recipe for target 'cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/all' failed
    make[1]: *** [cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/all] Error 2
    Makefile:126: recipe for target 'all' failed
    make: *** [all] Error 2
    Suggestions are highly appreciated.

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