Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

Latest Articles

Collapse

  • seqadmin
    Advancing Precision Medicine for Rare Diseases in Children
    by seqadmin




    Many organizations study rare diseases, but few have a mission as impactful as Rady Children’s Institute for Genomic Medicine (RCIGM). “We are all about changing outcomes for children,” explained Dr. Stephen Kingsmore, President and CEO of the group. The institute’s initial goal was to provide rapid diagnoses for critically ill children and shorten their diagnostic odyssey, a term used to describe the long and arduous process it takes patients to obtain an accurate...
    12-16-2024, 07:57 AM
  • seqadmin
    Recent Advances in Sequencing Technologies
    by seqadmin



    Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.

    Long-Read Sequencing
    Long-read sequencing has seen remarkable advancements,...
    12-02-2024, 01:49 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 12-17-2024, 10:28 AM
0 responses
22 views
0 likes
Last Post seqadmin  
Started by seqadmin, 12-13-2024, 08:24 AM
0 responses
42 views
0 likes
Last Post seqadmin  
Started by seqadmin, 12-12-2024, 07:41 AM
0 responses
28 views
0 likes
Last Post seqadmin  
Started by seqadmin, 12-11-2024, 07:45 AM
0 responses
42 views
0 likes
Last Post seqadmin  
Working...
X