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  • Bcl2Fastq 1.8.3 install error on Ubuntu 12.04LTS: "No support for bzip2 compression"

    Hi,

    I was trying to install the CASAVA Bcl2Fastq 1.8.3 package on my Ubuntu Server 12.04LTS. First, I encountered the same "No support for gzip compression" discussed in the following thread:
    http://seqanswers.com/forums/showthread.php?t=11106
    Follow the solution in the thread, I solve the problem by:
    Code:
    sudo ln -s /usr/lib/x86_64-linux-gnu/libpthread* /usr/lib
    sudo ln -s /usr/lib/x86_64-linux-gnu/libz.so /usr/lib
    However, now I get another similar error: "No support for bzip2 compression".
    I am wondering if there is any way to solve this?

    Here is the detailed install log:

    Code:
    administrator@Epizyme2:/tmp/bcl2fastq-1.8.3-build$ sudo ${SOURCE}/src/configure --prefix=${INSTALL} --verbose
    [sudo] password for administrator: 
    cmake version "cmake version 2.8.4" is already installed at /tmp/bcl2fastq-1.8.3-build/bootstrap/bin/cmake
    nothing to be done
    Using installed /tmp/bcl2fastq-1.8.3-build/bootstrap/bin/cmake
    Source  directory: /tmp/bcl2fastq-1.8.3/src
    Prefix  directory: /usr/local/bcl2fastq-1.8.3
    Exec    directory: 
    Binary  directory: 
    Lib     directory: 
    Libexec directory: 
    Include directory: 
    Data    directory: 
    Doc     directory: 
    Man     directory: 
    Build   directory: /tmp/bcl2fastq-1.8.3-build
    Cmake  executable: /tmp/bcl2fastq-1.8.3-build/bootstrap/bin/cmake
    
    Running on: Linux Epizyme2 3.2.0-29-generic #46-Ubuntu SMP Fri Jul 27 17:03:23 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
    Configuring the build directory with:
        /tmp/bcl2fastq-1.8.3-build/bootstrap/bin/cmake -H"/tmp/bcl2fastq-1.8.3/src" -B"/tmp/bcl2fastq-1.8.3-build" -G"Unix Makefiles" -DCASAVA_PREFIX:PATH=/usr/local/bcl2fastq-1.8.3 -DCASAVA_EXEC_PREFIX:PATH= -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/bcl2fastq-1.8.3 -DCASAVA_BINDIR:PATH= -DCASAVA_LIBDIR:PATH= -DCASAVA_LIBEXECDIR:PATH= -DCASAVA_INCLUDEDIR:PATH= -DCASAVA_DATADIR:PATH= -DCASAVA_DOCDIR:PATH= -DCASAVA_MANDIR:PATH= -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DBoost_DEBUG:BOOL=ON
    
    -- The C compiler identification is GNU
    -- The CXX compiler identification is GNU
    -- Check for working C compiler: /usr/bin/gcc
    -- Check for working C compiler: /usr/bin/gcc -- works
    -- Detecting C compiler ABI info
    -- Detecting C compiler ABI info - done
    -- Check for working CXX compiler: /usr/bin/c++
    -- Check for working CXX compiler: /usr/bin/c++ -- works
    -- Detecting CXX compiler ABI info
    -- Detecting CXX compiler ABI info - done
    -- install      prefix: /usr/local/bcl2fastq-1.8.3
    -- install exec prefix: .
    -- install     bin dir: ./bin
    -- install     lib dir: ./lib/bcl2fastq-1.8.3
    -- install libexec dir: ./libexec/bcl2fastq-1.8.3
    -- install include dir: include/bcl2fastq-1.8.3
    -- install    data dir: share/bcl2fastq-1.8.3
    -- install     doc dir: doc/bcl2fastq-1.8.3
    -- install     man dir: man
    -- Verifying target directories access
    -- Creating external tools in subdirectory opt
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:461 ] Boost not in cache
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:464 ] _boost_TEST_VERSIONS = 1.46.0;1.46;1.45.0;1.45;1.44.0;1.44
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:466 ] Boost_USE_MULTITHREADED = TRUE
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:468 ] Boost_USE_STATIC_LIBS = 
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:470 ] Boost_USE_STATIC_RUNTIME = 
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:472 ] Boost_ADDITIONAL_VERSIONS = 
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:474 ] Boost_NO_SYSTEM_PATHS = 
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:537 ] Declared as CMake or Environmental Variables:
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:539 ]   BOOST_ROOT = 
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:541 ]   BOOST_INCLUDEDIR = 
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:543 ]   BOOST_LIBRARYDIR = 
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:545 ] _boost_TEST_VERSIONS = 1.46.0;1.46;1.45.0;1.45;1.44.0;1.44
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:598 ] Include debugging info:
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:600 ]   _boost_INCLUDE_SEARCH_DIRS = C:/boost/include;C:/boost;/boost/include;/boost;/sw/local/include
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:602 ]   _boost_PATH_SUFFIXES = boost-1_46_0;boost_1_46_0;boost-1_46;boost_1_46;boost-1_45_0;boost_1_45_0;boost-1_45;boost_1_45;boost-1_44_0;boost_1_44_0;boost-1_44;boost_1_44
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:737 ] guessed _boost_COMPILER = -gcc
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:747 ] _boost_MULTITHREADED = -mt
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:790 ] _boost_RELEASE_ABI_TAG = -
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:792 ] _boost_DEBUG_ABI_TAG = -d
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:835 ] _boost_LIBRARY_SEARCH_DIRS = Boost_INCLUDE_DIR-NOTFOUND/lib;Boost_INCLUDE_DIR-NOTFOUND/../lib;Boost_INCLUDE_DIR-NOTFOUND/stage/lib;C:/boost/lib;C:/boost;/boost/boost___/lib;/boost/boost__/lib;/boost/lib;/boost;/sw/local/lib
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for DATE_TIME_LIBRARY_RELEASE: boost_date_time-gcc-mt-;boost_date_time-gcc-mt;boost_date_time-mt-;boost_date_time-mt;boost_date_time
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for DATE_TIME_LIBRARY_DEBUG: boost_date_time-gcc-mt-d-;boost_date_time-gcc-mt-d;boost_date_time-mt-d-;boost_date_time-mt-d;boost_date_time-mt;boost_date_time
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for FILESYSTEM_LIBRARY_RELEASE: boost_filesystem-gcc-mt-;boost_filesystem-gcc-mt;boost_filesystem-mt-;boost_filesystem-mt;boost_filesystem
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for FILESYSTEM_LIBRARY_DEBUG: boost_filesystem-gcc-mt-d-;boost_filesystem-gcc-mt-d;boost_filesystem-mt-d-;boost_filesystem-mt-d;boost_filesystem-mt;boost_filesystem
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for IOSTREAMS_LIBRARY_RELEASE: boost_iostreams-gcc-mt-;boost_iostreams-gcc-mt;boost_iostreams-mt-;boost_iostreams-mt;boost_iostreams
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for IOSTREAMS_LIBRARY_DEBUG: boost_iostreams-gcc-mt-d-;boost_iostreams-gcc-mt-d;boost_iostreams-mt-d-;boost_iostreams-mt-d;boost_iostreams-mt;boost_iostreams
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for PROGRAM_OPTIONS_LIBRARY_RELEASE: boost_program_options-gcc-mt-;boost_program_options-gcc-mt;boost_program_options-mt-;boost_program_options-mt;boost_program_options
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for PROGRAM_OPTIONS_LIBRARY_DEBUG: boost_program_options-gcc-mt-d-;boost_program_options-gcc-mt-d;boost_program_options-mt-d-;boost_program_options-mt-d;boost_program_options-mt;boost_program_options
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for REGEX_LIBRARY_RELEASE: boost_regex-gcc-mt-;boost_regex-gcc-mt;boost_regex-mt-;boost_regex-mt;boost_regex
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for REGEX_LIBRARY_DEBUG: boost_regex-gcc-mt-d-;boost_regex-gcc-mt-d;boost_regex-mt-d-;boost_regex-mt-d;boost_regex-mt;boost_regex
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for SERIALIZATION_LIBRARY_RELEASE: boost_serialization-gcc-mt-;boost_serialization-gcc-mt;boost_serialization-mt-;boost_serialization-mt;boost_serialization
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for SERIALIZATION_LIBRARY_DEBUG: boost_serialization-gcc-mt-d-;boost_serialization-gcc-mt-d;boost_serialization-mt-d-;boost_serialization-mt-d;boost_serialization-mt;boost_serialization
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for SYSTEM_LIBRARY_RELEASE: boost_system-gcc-mt-;boost_system-gcc-mt;boost_system-mt-;boost_system-mt;boost_system
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for SYSTEM_LIBRARY_DEBUG: boost_system-gcc-mt-d-;boost_system-gcc-mt-d;boost_system-mt-d-;boost_system-mt-d;boost_system-mt;boost_system
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:906 ] Searching for THREAD_LIBRARY_RELEASE: boost_thread-gcc-mt-;boost_thread-gcc-mt;boost_thread-mt-;boost_thread-mt;boost_thread
    -- [ /tmp/bcl2fastq-1.8.3-build/bootstrap/share/cmake-2.8/Modules/FindBoost.cmake:938 ] Searching for THREAD_LIBRARY_DEBUG: boost_thread-gcc-mt-d-;boost_thread-gcc-mt-d;boost_thread-mt-d-;boost_thread-mt-d;boost_thread-mt;boost_thread
    -- Could NOT find Boost
    Unable to find the Boost header files. Please set BOOST_ROOT to the root directory containing Boost or BOOST_INCLUDEDIR to the directory containing Boost's headers.
    -- Boost 1.44.0 not found. Boost will be built from the distribution...
    Decompressing /tmp/bcl2fastq-1.8.3/src/../redist/boost_1_44_0.tar.gz
    Building Boost.Jam with toolset gcc... tools/jam/src/bin.linuxx86_64/bjam
    Unicode/ICU support for Boost.Regex?... not found.
    Backing up existing Boost.Build configuration in project-config.jam.5
    Generating Boost.Build configuration in project-config.jam...
    
    Bootstrapping is done. To build, run:
    
        ./bjam
        
    To adjust configuration, edit 'project-config.jam'.
    Further information:
    
       - Command line help:
         ./bjam --help
         
       - Getting started guide: 
         http://www.boost.org/more/getting_started/unix-variants.html
         
       - Boost.Build documentation:
         http://www.boost.org/boost-build2/doc/html/index.html
    
    Performing configuration checks
    
        - has_icu builds           : no
    
    Component configuration:
    
        - date_time                : building
        - filesystem               : building
        - graph                    : not building
        - graph_parallel           : not building
        - iostreams                : building
        - math                     : not building
        - mpi                      : not building
        - program_options          : building
        - python                   : not building
        - random                   : not building
        - regex                    : building
        - serialization            : building
        - signals                  : not building
        - system                   : building
        - test                     : not building
        - thread                   : building
        - wave                     : not building
    
    ...patience...
    ...patience...
    ...found 17154 targets...
    boost-1_44_0 installed successfully
    -- Successfuly built boost 1.44.0 from the distribution package...
    -- Check if the system is big endian
    -- Searching 16 bit integer
    -- Looking for sys/types.h
    -- Looking for sys/types.h - found
    -- Looking for stdint.h
    -- Looking for stdint.h - found
    -- Looking for stddef.h
    -- Looking for stddef.h - found
    -- Check size of unsigned short
    -- Check size of unsigned short - done
    -- Using unsigned short
    -- Check if the system is big endian - little endian
    -- Looking for floorf
    -- Looking for floorf - found
    -- Looking for round
    -- Looking for round - found
    -- Looking for roundf
    -- Looking for roundf - found
    -- Looking for powf
    -- Looking for powf - found
    -- Looking for erf
    -- Looking for erf - found
    -- Looking for erf
    -- Looking for erf - found
    -- Looking for erfc
    -- Looking for erfc - found
    -- Looking for erfc
    -- Looking for erfc - found
    -- Found ZLIB  header: /usr/include/zlib.h
    -- Found ZLIB library: /usr/lib/libz.so
    -- gzip compression supported
    CMake Error at cmake/cxxConfigure.cmake:84 (message):
      No support for bzip2 compression
    Call Stack (most recent call first):
      c++/CMakeLists.txt:33 (include)
    
    
    -- Configuring incomplete, errors occurred!
    Couldn't configure the project:
    
    /tmp/bcl2fastq-1.8.3-build/bootstrap/bin/cmake -H"/tmp/bcl2fastq-1.8.3/src" -B"/tmp/bcl2fastq-1.8.3-build" -G"Unix Makefiles"  -DCASAVA_PREFIX:PATH=/usr/local/bcl2fastq-1.8.3 -DCASAVA_EXEC_PREFIX:PATH= -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/bcl2fastq-1.8.3 -DCASAVA_BINDIR:PATH= -DCASAVA_LIBDIR:PATH= -DCASAVA_LIBEXECDIR:PATH= -DCASAVA_INCLUDEDIR:PATH= -DCASAVA_DATADIR:PATH= -DCASAVA_DOCDIR:PATH= -DCASAVA_MANDIR:PATH= -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DBoost_DEBUG:BOOL=ON
    
    Moving CMakeCache.txt to CMakeCache.txt.removed

  • #2
    ln -s /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/libbz2.so

    However I wasn't able to compile BclToFastq on Ubuntu 12.10 because of an incompatibility between the gcc version 4.7.2 and the lib boost supplied in BclToFastq.

    I got around this by running alien on the BclToFastq supplied rpm and installing the new deb using dpkg - only as a one off hack though, I've got a CentOS cluster here now where it's properly compiled/installed.

    Comment


    • #3
      worked

      Thank you frozenlyse!

      "ln -s /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/libbz2.so" solved this problem!

      However, some more errors appeared after this. After installing some Perl Modules and "xsltproc" package, I finally made Bcl2Fastq 1.8.3 work on Ubuntu 12.04

      I think I should also have CentOS installed on one of our servers in the future
      Last edited by slees; 01-29-2013, 07:40 PM.

      Comment


      • #4
        The system is centOS 6.4

        Comment

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