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Old 06-28-2019, 08:17 AM   #1
dfajar2
Junior Member
 
Location: Madison, WI

Join Date: Oct 2011
Posts: 2
Default 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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