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  • breakdancer compilation help

    I am a beginner for BreakDancer. When I downloaded the breakdancer (v1.3.5.1.zip) source file from https://github.com/genome/breakdancer/tags, I don't know how to compile properly these files to get the command 'breakdancer_max'. My working server is x86_64, Red Hat 4.4.5-6. Could any one help me? Thanks.

  • #2
    did you finally succeded to compile breakdancer? I really don't understand anything......

    Comment


    • #3
      Hi,
      I have problems in installing breakdancer.
      I downloaded the zip file from sourceforce and decompressed it.
      I found two suddirectories, perl and cpp.
      I try to make in cpp directory but I'm not able to compile breakdancer.
      Could anyone help me for this issue?
      Thanks

      Comment


      • #4
        Originally posted by simobioinfo View Post
        Hi,
        I have problems in installing breakdancer.
        I downloaded the zip file from sourceforce and decompressed it.
        I found two suddirectories, perl and cpp.
        I try to make in cpp directory but I'm not able to compile breakdancer.
        Could anyone help me for this issue?
        Thanks
        What OS are you using? Post the error(s) that are generated after "make".

        Comment


        • #5
          Originally posted by simobioinfo View Post
          Hi,
          I have problems in installing breakdancer.
          I downloaded the zip file from sourceforce and decompressed it.
          I found two suddirectories, perl and cpp.
          I try to make in cpp directory but I'm not able to compile breakdancer.
          Could anyone help me for this issue?
          Thanks
          Why don't you read the docs?
          INSTALL.md states:

          Code:
              $ cd breakdancer
              $ mkdir build
              $ cd build
          
              $ cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local
              ...
              -- Build files have been written to: .../breakdancer/build
          
              $ make
              ...
              Linking CXX executable ../../../../bin/breakdancer-max
              [100%] Built target breakdancer-max
          
              $ sudo make install
          Change CMAKE_INSTALL_PREFIX as needed.
          Last edited by sklages; 08-04-2015, 05:47 AM. Reason: reduced code to relevant section

          Comment


          • #6
            Hi,
            I read documentation and the message error was:
            [ 10%] Performing build step for 'boost-libs'
            [ 12%] No install step for 'boost-libs'
            [ 14%] Completed 'boost-libs'
            [ 14%] Built target boost-libs
            Scanning dependencies of target samtools-lib
            [ 15%] Creating directories for 'samtools-lib'
            [ 17%] Performing download step (verify and extract) for 'samtools-lib'
            -- verifying file...
            file='/root/breakdancer/vendor/samtools-0.1.19.tar.gz'
            -- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
            -- extracting...
            src='/root/breakdancer/vendor/samtools-0.1.19.tar.gz'
            dst='/root/breakdancer/build/vendor/samtools'
            -- extracting... [tar xfz]
            -- extracting... [analysis]
            -- extracting... [rename]
            -- extracting... [clean up]
            -- extracting... done
            [ 19%] No patch step for 'samtools-lib'
            [ 21%] No update step for 'samtools-lib'
            [ 22%] Performing configure step for 'samtools-lib'
            Building samtools, build log at /root/breakdancer/build/vendor/samtools/build.log
            [ 24%] Performing build step for 'samtools-lib'
            make[2]: *** [vendor/src/samtools-lib-stamp/samtools-lib-build] Error 2
            make[1]: *** [CMakeFiles/samtools-lib.dir/all] Error 2
            make: *** [all] Error 2

            Can anyone help me to understand?

            Comment


            • #7
              Is the samtools source included in breakdancer otherwise you will need to download it and then put the file in /root/breakdancer/build/vendor/ directory (http://sourceforge.net/projects/samt...r.bz2/download).

              Comment


              • #8
                So if understand you suggest me to:
                -download samtools
                -to put the tar.bz2 file into /root/breakdancer/build/vendor/ directory
                and then?
                Do I have to install it into that directory?
                If yes. These steps are correct?
                tar -jxvf samtools-0.1.19.tar.bz2
                - $ cd samtools-0.1.19
                - $ make
                - $ export SAMTOOLS_ROOT=$(pwd)
                - $ cd ..
                Then:
                cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local
                make
                sudo make install.

                Are these steps correct?

                Comment


                • #9
                  That sounds right (if you are following the install document). Give it a try and see what happens.

                  Comment


                  • #10
                    in the /root/breakdancer/build/vendor/ directory I found a directory named samtools.
                    Do I have to remove it before to install samtools?

                    Comment


                    • #11
                      What happens if you try to do the breakdancer install again?

                      BTW: What OS are you doing this on? When you cloned the source from github did you use the "--recursive" option since that is important as indicated in the INSTALL.md file.

                      Comment


                      • #12
                        I'm working with ubuntu.
                        I restart from the beginning.
                        I tried to install samtools but I failed.
                        I tried to put the tar.bz2 file into the vendor directory changing extension in tar.gz and launched the make command but I have had an error:
                        Scanning dependencies of target boost-libs
                        [ 1%] Creating directories for 'boost-libs'
                        [ 3%] Performing download step (verify and extract) for 'boost-libs'
                        -- verifying file...
                        file='/root/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
                        -- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
                        -- extracting...
                        src='/root/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
                        dst='/root/breakdancer/build/vendor/boost/boost-src'
                        -- extracting... [tar xfz]
                        -- extracting... [analysis]
                        -- extracting... [rename]
                        -- extracting... [clean up]
                        -- extracting... done
                        [ 5%] No patch step for 'boost-libs'
                        [ 7%] No update step for 'boost-libs'
                        [ 8%] Performing configure step for 'boost-libs'
                        Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86_64/b2
                        Detecting Python version... 2.7
                        Detecting Python root... /usr
                        Unicode/ICU support for Boost.Regex?... not found.
                        Generating Boost.Build configuration in project-config.jam...

                        Bootstrapping is done. To build, run:

                        ./b2

                        To adjust configuration, edit 'project-config.jam'.
                        Further information:

                        - Command line help:
                        ./b2 --help

                        - Getting started guide:


                        - Boost.Build documentation:


                        [ 10%] Performing build step for 'boost-libs'
                        [ 12%] No install step for 'boost-libs'
                        [ 14%] Completed 'boost-libs'
                        [ 14%] Built target boost-libs
                        Scanning dependencies of target samtools-lib
                        [ 15%] Creating directories for 'samtools-lib'
                        [ 17%] Performing download step (verify and extract) for 'samtools-lib'
                        -- verifying file...
                        file='/root/breakdancer/vendor/samtools-0.1.19.tar.gz'
                        -- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
                        -- extracting...
                        src='/root/breakdancer/vendor/samtools-0.1.19.tar.gz'
                        dst='/root/breakdancer/build/vendor/samtools'
                        -- extracting... [tar xfz]
                        -- extracting... [analysis]
                        -- extracting... [rename]
                        -- extracting... [clean up]
                        -- extracting... done
                        [ 19%] No patch step for 'samtools-lib'
                        [ 21%] No update step for 'samtools-lib'
                        [ 22%] Performing configure step for 'samtools-lib'
                        Building samtools, build log at /root/breakdancer/build/vendor/samtools/build.log
                        [ 24%] Performing build step for 'samtools-lib'
                        make[2]: *** [vendor/src/samtools-lib-stamp/samtools-lib-build] Error 2
                        make[1]: *** [CMakeFiles/samtools-lib.dir/all] Error 2
                        make: *** [all] Error 2


                        In the vendor directory now I have these subdirectories:
                        boost gtest160-build samtools samtools-0.1.1.19.tar.gz src tmp

                        the directory samtools it was created afte the command
                        cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local

                        samtools-0.1.1.19.tar.gz file was introduced by me.

                        I followed the install.md commands but I failed.

                        Could you help me step by step?

                        Comment


                        • #13
                          Can you show us the commands you are using to do the install? It is difficult to understand exactly what is happening looking at the logs you posted above. It will also help if you can provide a recursive listing of the directory

                          Code:
                          $ ls -lhR /root/breakdancer/vendor/

                          Comment


                          • #14
                            Hi Genomax,
                            I restart the installation procedure and these are the command:
                            I also included a recursive listing of directory

                            root@ubuntulab:~# git clone --recursive https://github.com/genome/breakdancer.git
                            Cloning into 'breakdancer'...
                            remote: Counting objects: 4238, done.
                            remote: Total 4238 (delta 0), reused 0 (delta 0), pack-reused 4238
                            Receiving objects: 100% (4238/4238), 9.42 MiB | 2.93 MiB/s, done.
                            Resolving deltas: 100% (2004/2004), done.
                            root@ubuntulab:~# ls -lhR /root/breakdancer/vendor/
                            /root/breakdancer/vendor/:
                            total 5,8M
                            -rw-r--r-- 1 root root 5,2M ago 11 10:07 boost-1.54-breakdancer.tar.gz
                            -rw-r--r-- 1 root root 551K ago 11 10:07 samtools-0.1.19.tar.gz
                            root@ubuntulab:~# cd breakdancer/
                            root@ubuntulab:~/breakdancer# ls
                            build-common CMakeLists.txt gmt gmt.yml integration-test perl src test-data version
                            cmake debian gmt-web INSTALL.md PackageInfo.cmake README test vendor
                            root@ubuntulab:~/breakdancer# mkdir build
                            root@ubuntulab:~/breakdancer# cd build
                            root@ubuntulab:~/breakdancer/build# cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local
                            -- 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
                            Score floating point type: double
                            -- Looking for include files CMAKE_HAVE_PTHREAD_H
                            -- Looking for include files CMAKE_HAVE_PTHREAD_H - found
                            -- Looking for pthread_create in pthreads
                            -- Looking for pthread_create in pthreads - not found
                            -- Looking for pthread_create in pthread
                            -- Looking for pthread_create in pthread - found
                            -- Found Threads: TRUE
                            -- Performing Test CXX11_FLAG0
                            -- Performing Test CXX11_FLAG0 - Failed
                            -- Performing Test CXX11_FLAG1
                            -- Performing Test CXX11_FLAG1 - Success
                            -- C++11 support enabled via -std=c++0x
                            -- Performing Test CXX11_STDLIB_FLAG0
                            -- Performing Test CXX11_STDLIB_FLAG0 - Success
                            -- Sufficient C++11 library support found with flag ' '
                            -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.3.4")
                            -- Configuring done
                            -- Generating done
                            -- Build files have been written to: /root/breakdancer/build
                            root@ubuntulab:~/breakdancer/build# ls -lhR /root/breakdancer/build/
                            /root/breakdancer/build/:
                            total 92K
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 bin
                            drwxr-xr-x 4 root root 4,0K ago 11 10:09 build
                            -rw-r--r-- 1 root root 13K ago 11 10:09 CMakeCache.txt
                            drwxr-xr-x 9 root root 4,0K ago 11 10:09 CMakeFiles
                            -rw-r--r-- 1 root root 2,4K ago 11 10:09 cmake_install.cmake
                            -rw-r--r-- 1 root root 5,4K ago 11 10:09 CPackConfig.cmake
                            -rw-r--r-- 1 root root 5,8K ago 11 10:09 CPackSourceConfig.cmake
                            -rw-r--r-- 1 root root 517 ago 11 10:09 CTestTestfile.cmake
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 debian
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 integration-test
                            -rw-r--r-- 1 root root 11K ago 11 10:09 Makefile
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 perl
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 test-bin
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 test-data
                            drwxr-xr-x 7 root root 4,0K ago 11 10:09 vendor
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 version

                            /root/breakdancer/build/bin:
                            total 0

                            /root/breakdancer/build/build:
                            total 8,0K
                            drwxr-xr-x 4 root root 4,0K ago 11 10:09 src
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 test

                            /root/breakdancer/build/build/src:
                            total 8,0K
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 exe
                            drwxr-xr-x 5 root root 4,0K ago 11 10:09 lib

                            /root/breakdancer/build/build/src/exe:
                            total 4,0K
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 breakdancer-max

                            /root/breakdancer/build/build/src/exe/breakdancer-max:
                            total 20K
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles
                            -rw-r--r-- 1 root root 2,1K ago 11 10:09 cmake_install.cmake
                            -rw-r--r-- 1 root root 8,3K ago 11 10:09 Makefile

                            /root/breakdancer/build/build/src/exe/breakdancer-max/CMakeFiles:
                            total 12K
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 breakdancer-max.dir
                            -rw-r--r-- 1 root root 957 ago 11 10:09 CMakeDirectoryInformation.cmake
                            -rw-r--r-- 1 root root 3 ago 11 10:09 progress.marks

                            /root/breakdancer/build/build/src/exe/breakdancer-max/CMakeFiles/breakdancer-max.dir:
                            total 32K
                            -rw-r--r-- 1 root root 6,7K ago 11 10:09 build.make
                            -rw-r--r-- 1 root root 320 ago 11 10:09 cmake_clean.cmake
                            -rw-r--r-- 1 root root 858 ago 11 10:09 DependInfo.cmake
                            -rw-r--r-- 1 root root 99 ago 11 10:09 depend.make
                            -rw-r--r-- 1 root root 493 ago 11 10:09 flags.make
                            -rw-r--r-- 1 root root 747 ago 11 10:09 link.txt
                            -rw-r--r-- 1 root root 23 ago 11 10:09 progress.make

                            /root/breakdancer/build/build/src/lib:
                            total 12K
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 breakdancer
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 common
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 io

                            /root/breakdancer/build/build/src/lib/breakdancer:
                            total 20K
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles
                            -rw-r--r-- 1 root root 1,2K ago 11 10:09 cmake_install.cmake
                            -rw-r--r-- 1 root root 12K ago 11 10:09 Makefile

                            /root/breakdancer/build/build/src/lib/breakdancer/CMakeFiles:
                            total 12K
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 breakdancer.dir
                            -rw-r--r-- 1 root root 957 ago 11 10:09 CMakeDirectoryInformation.cmake
                            -rw-r--r-- 1 root root 2 ago 11 10:09 progress.marks

                            /root/breakdancer/build/build/src/lib/breakdancer/CMakeFiles/breakdancer.dir:
                            total 44K
                            -rw-r--r-- 1 root root 14K ago 11 10:09 build.make
                            -rw-r--r-- 1 root root 423 ago 11 10:09 cmake_clean.cmake
                            -rw-r--r-- 1 root root 43 ago 11 10:09 cmake_clean_target.cmake
                            -rw-r--r-- 1 root root 1,1K ago 11 10:09 DependInfo.cmake
                            -rw-r--r-- 1 root root 95 ago 11 10:09 depend.make
                            -rw-r--r-- 1 root root 493 ago 11 10:09 flags.make
                            -rw-r--r-- 1 root root 245 ago 11 10:09 link.txt
                            -rw-r--r-- 1 root root 89 ago 11 10:09 progress.make

                            /root/breakdancer/build/build/src/lib/common:
                            total 20K
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles
                            -rw-r--r-- 1 root root 1,2K ago 11 10:09 cmake_install.cmake
                            -rw-r--r-- 1 root root 8,8K ago 11 10:09 Makefile

                            /root/breakdancer/build/build/src/lib/common/CMakeFiles:
                            total 12K
                            -rw-r--r-- 1 root root 957 ago 11 10:09 CMakeDirectoryInformation.cmake
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 common.dir
                            -rw-r--r-- 1 root root 2 ago 11 10:09 progress.marks

                            /root/breakdancer/build/build/src/lib/common/CMakeFiles/common.dir:
                            total 36K
                            -rw-r--r-- 1 root root 7,4K ago 11 10:09 build.make
                            -rw-r--r-- 1 root root 295 ago 11 10:09 cmake_clean.cmake
                            -rw-r--r-- 1 root root 38 ago 11 10:09 cmake_clean_target.cmake
                            -rw-r--r-- 1 root root 687 ago 11 10:09 DependInfo.cmake
                            -rw-r--r-- 1 root root 90 ago 11 10:09 depend.make
                            -rw-r--r-- 1 root root 493 ago 11 10:09 flags.make
                            -rw-r--r-- 1 root root 130 ago 11 10:09 link.txt
                            -rw-r--r-- 1 root root 45 ago 11 10:09 progress.make

                            /root/breakdancer/build/build/src/lib/io:
                            total 28K
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles
                            -rw-r--r-- 1 root root 1,2K ago 11 10:09 cmake_install.cmake
                            -rw-r--r-- 1 root root 18K ago 11 10:09 Makefile

                            /root/breakdancer/build/build/src/lib/io/CMakeFiles:
                            total 12K
                            -rw-r--r-- 1 root root 957 ago 11 10:09 CMakeDirectoryInformation.cmake
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 io.dir
                            -rw-r--r-- 1 root root 3 ago 11 10:09 progress.marks

                            /root/breakdancer/build/build/src/lib/io/CMakeFiles/io.dir:
                            total 56K
                            -rw-r--r-- 1 root root 27K ago 11 10:09 build.make
                            -rw-r--r-- 1 root root 655 ago 11 10:09 cmake_clean.cmake
                            -rw-r--r-- 1 root root 34 ago 11 10:09 cmake_clean_target.cmake
                            -rw-r--r-- 1 root root 1,9K ago 11 10:09 DependInfo.cmake
                            -rw-r--r-- 1 root root 86 ago 11 10:09 depend.make
                            -rw-r--r-- 1 root root 493 ago 11 10:09 flags.make
                            -rw-r--r-- 1 root root 458 ago 11 10:09 link.txt
                            -rw-r--r-- 1 root root 245 ago 11 10:09 progress.make

                            /root/breakdancer/build/build/test:
                            total 4,0K
                            drwxr-xr-x 5 root root 4,0K ago 11 10:09 lib

                            /root/breakdancer/build/build/test/lib:
                            total 12K
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 breakdancer
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 common
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 io

                            /root/breakdancer/build/build/test/lib/breakdancer:
                            total 24K
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles
                            -rw-r--r-- 1 root root 1,2K ago 11 10:09 cmake_install.cmake
                            -rw-r--r-- 1 root root 424 ago 11 10:09 CTestTestfile.cmake
                            -rw-r--r-- 1 root root 9,4K ago 11 10:09 Makefile

                            /root/breakdancer/build/build/test/lib/breakdancer/CMakeFiles:
                            total 12K
                            -rw-r--r-- 1 root root 971 ago 11 10:09 CMakeDirectoryInformation.cmake
                            -rw-r--r-- 1 root root 3 ago 11 10:09 progress.marks
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 TestBdLib.dir

                            /root/breakdancer/build/build/test/lib/breakdancer/CMakeFiles/TestBdLib.dir:
                            total 36K
                            -rw-r--r-- 1 root root 9,0K ago 11 10:09 build.make
                            -rw-r--r-- 1 root root 362 ago 11 10:09 cmake_clean.cmake
                            -rw-r--r-- 1 root root 851 ago 11 10:09 DependInfo.cmake
                            -rw-r--r-- 1 root root 93 ago 11 10:09 depend.make
                            -rw-r--r-- 1 root root 529 ago 11 10:09 flags.make
                            -rw-r--r-- 1 root root 815 ago 11 10:09 link.txt
                            -rw-r--r-- 1 root root 43 ago 11 10:09 progress.make

                            /root/breakdancer/build/build/test/lib/common:
                            total 24K
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles
                            -rw-r--r-- 1 root root 1,2K ago 11 10:09 cmake_install.cmake
                            -rw-r--r-- 1 root root 426 ago 11 10:09 CTestTestfile.cmake
                            -rw-r--r-- 1 root root 11K ago 11 10:09 Makefile

                            /root/breakdancer/build/build/test/lib/common/CMakeFiles:
                            total 12K
                            -rw-r--r-- 1 root root 971 ago 11 10:09 CMakeDirectoryInformation.cmake
                            -rw-r--r-- 1 root root 3 ago 11 10:09 progress.marks
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 TestCommonLib.dir

                            /root/breakdancer/build/build/test/lib/common/CMakeFiles/TestCommonLib.dir:
                            total 36K
                            -rw-r--r-- 1 root root 11K ago 11 10:09 build.make
                            -rw-r--r-- 1 root root 421 ago 11 10:09 cmake_clean.cmake
                            -rw-r--r-- 1 root root 954 ago 11 10:09 DependInfo.cmake
                            -rw-r--r-- 1 root root 97 ago 11 10:09 depend.make
                            -rw-r--r-- 1 root root 529 ago 11 10:09 flags.make
                            -rw-r--r-- 1 root root 791 ago 11 10:09 link.txt
                            -rw-r--r-- 1 root root 64 ago 11 10:09 progress.make

                            /root/breakdancer/build/build/test/lib/io:
                            total 32K
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles
                            -rw-r--r-- 1 root root 1,2K ago 11 10:09 cmake_install.cmake
                            -rw-r--r-- 1 root root 406 ago 11 10:09 CTestTestfile.cmake
                            -rw-r--r-- 1 root root 18K ago 11 10:09 Makefile

                            /root/breakdancer/build/build/test/lib/io/CMakeFiles:
                            total 12K
                            -rw-r--r-- 1 root root 971 ago 11 10:09 CMakeDirectoryInformation.cmake
                            -rw-r--r-- 1 root root 3 ago 11 10:09 progress.marks
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 TestIoLib.dir

                            /root/breakdancer/build/build/test/lib/io/CMakeFiles/TestIoLib.dir:
                            total 52K
                            -rw-r--r-- 1 root root 28K ago 11 10:09 build.make
                            -rw-r--r-- 1 root root 783 ago 11 10:09 cmake_clean.cmake
                            -rw-r--r-- 1 root root 2,1K ago 11 10:09 DependInfo.cmake
                            -rw-r--r-- 1 root root 93 ago 11 10:09 depend.make
                            -rw-r--r-- 1 root root 529 ago 11 10:09 flags.make
                            -rw-r--r-- 1 root root 1,3K ago 11 10:09 link.txt
                            -rw-r--r-- 1 root root 218 ago 11 10:09 progress.make

                            /root/breakdancer/build/CMakeFiles:
                            total 152K
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 boost-libs.dir
                            -rw-r--r-- 1 root root 1,4K ago 11 10:09 CMakeCCompiler.cmake
                            -rw-r--r-- 1 root root 85 ago 11 10:09 cmake.check_cache
                            -rw-r--r-- 1 root root 1,6K ago 11 10:09 CMakeCXXCompiler.cmake
                            -rwxr-xr-x 1 root root 8,3K ago 11 10:09 CMakeDetermineCompilerABI_C.bin
                            -rwxr-xr-x 1 root root 8,3K ago 11 10:09 CMakeDetermineCompilerABI_CXX.bin
                            -rw-r--r-- 1 root root 971 ago 11 10:09 CMakeDirectoryInformation.cmake
                            -rw-r--r-- 1 root root 2,4K ago 11 10:09 CMakeError.log
                            -rw-r--r-- 1 root root 27K ago 11 10:09 CMakeOutput.log
                            -rw-r--r-- 1 root root 2,1K ago 11 10:09 CMakeRuleHashes.txt
                            -rw-r--r-- 1 root root 402 ago 11 10:09 CMakeSystem.cmake
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeTmp
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 CompilerIdC
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 CompilerIdCXX
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 deps.dir
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 gtest160.dir
                            -rw-r--r-- 1 root root 25K ago 11 10:09 Makefile2
                            -rw-r--r-- 1 root root 5,5K ago 11 10:09 Makefile.cmake
                            -rw-r--r-- 1 root root 3 ago 11 10:09 progress.marks
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 samtools-lib.dir
                            -rw-r--r-- 1 root root 700 ago 11 10:09 TargetDirectories.txt

                            /root/breakdancer/build/CMakeFiles/boost-libs.dir:
                            total 20K
                            -rw-r--r-- 1 root root 7,6K ago 11 10:09 build.make
                            -rw-r--r-- 1 root root 593 ago 11 10:09 cmake_clean.cmake
                            -rw-r--r-- 1 root root 346 ago 11 10:09 DependInfo.cmake
                            -rw-r--r-- 1 root root 177 ago 11 10:09 progress.make

                            /root/breakdancer/build/CMakeFiles/CMakeTmp:
                            total 4,0K
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles

                            /root/breakdancer/build/CMakeFiles/CMakeTmp/CMakeFiles:
                            total 4,0K
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 cmTryCompileExec.dir

                            /root/breakdancer/build/CMakeFiles/CMakeTmp/CMakeFiles/cmTryCompileExec.dir:
                            total 0

                            /root/breakdancer/build/CMakeFiles/CompilerIdC:
                            total 20K
                            -rwxr-xr-x 1 root root 8,3K ago 11 10:09 a.out
                            -rw-r--r-- 1 root root 5,9K ago 11 10:09 CMakeCCompilerId.c

                            /root/breakdancer/build/CMakeFiles/CompilerIdCXX:
                            total 20K
                            -rwxr-xr-x 1 root root 8,3K ago 11 10:09 a.out
                            -rw-r--r-- 1 root root 5,6K ago 11 10:09 CMakeCXXCompilerId.cpp

                            /root/breakdancer/build/CMakeFiles/deps.dir:
                            total 16K
                            -rw-r--r-- 1 root root 1,8K ago 11 10:09 build.make
                            -rw-r--r-- 1 root root 193 ago 11 10:09 cmake_clean.cmake
                            -rw-r--r-- 1 root root 346 ago 11 10:09 DependInfo.cmake
                            -rw-r--r-- 1 root root 1 ago 11 10:09 progress.make

                            /root/breakdancer/build/CMakeFiles/gtest160.dir:
                            total 20K
                            -rw-r--r-- 1 root root 7,2K ago 11 10:09 build.make
                            -rw-r--r-- 1 root root 559 ago 11 10:09 cmake_clean.cmake
                            -rw-r--r-- 1 root root 346 ago 11 10:09 DependInfo.cmake
                            -rw-r--r-- 1 root root 177 ago 11 10:09 progress.make

                            /root/breakdancer/build/CMakeFiles/samtools-lib.dir:
                            total 20K
                            -rw-r--r-- 1 root root 7,7K ago 11 10:09 build.make
                            -rw-r--r-- 1 root root 627 ago 11 10:09 cmake_clean.cmake
                            -rw-r--r-- 1 root root 346 ago 11 10:09 DependInfo.cmake
                            -rw-r--r-- 1 root root 177 ago 11 10:09 progress.make

                            /root/breakdancer/build/debian:
                            total 8,0K
                            -rwxr-xr-x 1 root root 1,3K ago 11 10:09 postinst
                            -rwxr-xr-x 1 root root 1,1K ago 11 10:09 prerm

                            /root/breakdancer/build/integration-test:
                            total 24K
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 CMakeFiles
                            -rw-r--r-- 1 root root 1,2K ago 11 10:09 cmake_install.cmake
                            -rw-r--r-- 1 root root 547 ago 11 10:09 CTestTestfile.cmake
                            -rw-r--r-- 1 root root 6,4K ago 11 10:09 Makefile
                            -rw-r--r-- 1 root root 52 ago 11 10:09 testdata.py

                            /root/breakdancer/build/integration-test/CMakeFiles:
                            total 8,0K
                            -rw-r--r-- 1 root root 971 ago 11 10:09 CMakeDirectoryInformation.cmake
                            -rw-r--r-- 1 root root 2 ago 11 10:09 progress.marks

                            /root/breakdancer/build/perl:
                            total 16K
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 CMakeFiles
                            -rw-r--r-- 1 root root 1,7K ago 11 10:09 cmake_install.cmake
                            -rw-r--r-- 1 root root 6,4K ago 11 10:09 Makefile

                            /root/breakdancer/build/perl/CMakeFiles:
                            total 8,0K
                            -rw-r--r-- 1 root root 957 ago 11 10:09 CMakeDirectoryInformation.cmake
                            -rw-r--r-- 1 root root 2 ago 11 10:09 progress.marks

                            /root/breakdancer/build/test-bin:
                            total 0

                            /root/breakdancer/build/test-data:
                            total 4,0K
                            -rw-r--r-- 1 root root 619 ago 11 10:09 TestData.hpp

                            /root/breakdancer/build/vendor:
                            total 20K
                            drwxr-xr-x 3 root root 4,0K ago 11 10:09 boost
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 gtest160-build
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 samtools
                            drwxr-xr-x 6 root root 4,0K ago 11 10:09 src
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 tmp

                            /root/breakdancer/build/vendor/boost:
                            total 4,0K
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 boost-src

                            /root/breakdancer/build/vendor/boost/boost-src:
                            total 0

                            /root/breakdancer/build/vendor/gtest160-build:
                            total 0

                            /root/breakdancer/build/vendor/samtools:
                            total 0

                            /root/breakdancer/build/vendor/src:
                            total 16K
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 boost-libs-stamp
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 gtest160
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 gtest160-stamp
                            drwxr-xr-x 2 root root 4,0K ago 11 10:09 samtools-lib-stamp

                            /root/breakdancer/build/vendor/src/boost-libs-stamp:
                            total 12K
                            -rw-r--r-- 1 root root 105 ago 11 10:09 boost-libs-urlinfo.txt
                            -rw-r--r-- 1 root root 1,6K ago 11 10:09 extract-boost-libs.cmake
                            -rw-r--r-- 1 root root 1,2K ago 11 10:09 verify-boost-libs.cmake

                            /root/breakdancer/build/vendor/src/gtest160:
                            total 0

                            /root/breakdancer/build/vendor/src/gtest160-stamp:
                            total 12K
                            -rw-r--r-- 1 root root 1,6K ago 11 10:09 extract-gtest160.cmake
                            -rw-r--r-- 1 root root 107 ago 11 10:09 gtest160-urlinfo.txt
                            -rw-r--r-- 1 root root 1,2K ago 11 10:09 verify-gtest160.cmake

                            /root/breakdancer/build/vendor/src/samtools-lib-stamp:
                            total 12K
                            -rw-r--r-- 1 root root 1,6K ago 11 10:09 extract-samtools-lib.cmake
                            -rw-r--r-- 1 root root 98 ago 11 10:09 samtools-lib-urlinfo.txt
                            -rw-r--r-- 1 root root 1,1K ago 11 10:09 verify-samtools-lib.cmake

                            /root/breakdancer/build/vendor/tmp:
                            total 24K
                            -rw-r--r-- 1 root root 21 ago 11 10:09 boost-libs-cfgcmd.txt
                            -rw-r--r-- 1 root root 12 ago 11 10:09 boost-libs-cfgcmd.txt.in
                            -rw-r--r-- 1 root root 128 ago 11 10:09 gtest160-cfgcmd.txt
                            -rw-r--r-- 1 root root 12 ago 11 10:09 gtest160-cfgcmd.txt.in
                            -rw-r--r-- 1 root root 93 ago 11 10:09 samtools-lib-cfgcmd.txt
                            -rw-r--r-- 1 root root 12 ago 11 10:09 samtools-lib-cfgcmd.txt.in

                            /root/breakdancer/build/version:
                            total 4,0K
                            -rw-r--r-- 1 root root 197 ago 11 10:09 version.h
                            root@ubuntulab:~/breakdancer/build# make
                            Scanning dependencies of target boost-libs
                            [ 1%] Creating directories for 'boost-libs'
                            [ 3%] Performing download step (verify and extract) for 'boost-libs'
                            -- verifying file...
                            file='/root/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
                            -- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
                            -- extracting...
                            src='/root/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
                            dst='/root/breakdancer/build/vendor/boost/boost-src'
                            -- extracting... [tar xfz]
                            -- extracting... [analysis]
                            -- extracting... [rename]
                            -- extracting... [clean up]
                            -- extracting... done
                            [ 5%] No patch step for 'boost-libs'
                            [ 7%] No update step for 'boost-libs'
                            [ 8%] Performing configure step for 'boost-libs'
                            Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86_64/b2
                            Detecting Python version... 2.7
                            Detecting Python root... /usr
                            Unicode/ICU support for Boost.Regex?... not found.
                            Generating Boost.Build configuration in project-config.jam...

                            Bootstrapping is done. To build, run:

                            ./b2

                            To adjust configuration, edit 'project-config.jam'.
                            Further information:

                            - Command line help:
                            ./b2 --help

                            - Getting started guide:


                            - Boost.Build documentation:


                            [ 10%] Performing build step for 'boost-libs'
                            [ 12%] No install step for 'boost-libs'
                            [ 14%] Completed 'boost-libs'
                            [ 14%] Built target boost-libs
                            Scanning dependencies of target samtools-lib
                            [ 15%] Creating directories for 'samtools-lib'
                            [ 17%] Performing download step (verify and extract) for 'samtools-lib'
                            -- verifying file...
                            file='/root/breakdancer/vendor/samtools-0.1.19.tar.gz'
                            -- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
                            -- extracting...
                            src='/root/breakdancer/vendor/samtools-0.1.19.tar.gz'
                            dst='/root/breakdancer/build/vendor/samtools'
                            -- extracting... [tar xfz]
                            -- extracting... [analysis]
                            -- extracting... [rename]
                            -- extracting... [clean up]
                            -- extracting... done
                            [ 19%] No patch step for 'samtools-lib'
                            [ 21%] No update step for 'samtools-lib'
                            [ 22%] Performing configure step for 'samtools-lib'
                            Building samtools, build log at /root/breakdancer/build/vendor/samtools/build.log
                            [ 24%] Performing build step for 'samtools-lib'
                            make[2]: *** [vendor/src/samtools-lib-stamp/samtools-lib-build] Error 2
                            make[1]: *** [CMakeFiles/samtools-lib.dir/all] Error 2
                            make: *** [all] Error 2

                            What do you think about? Can you help me?

                            Comment


                            • #15
                              Hi Genomax,
                              I restart the installation procedure.
                              These are command line and I also included a recursive list of directory.

                              root@ubuntulab:~# git clone --recursive https://github.com/genome/breakdancer.git
                              Cloning into 'breakdancer'...
                              remote: Counting objects: 4238, done.
                              remote: Total 4238 (delta 0), reused 0 (delta 0), pack-reused 4238
                              Receiving objects: 100% (4238/4238), 9.42 MiB | 2.93 MiB/s, done.
                              Resolving deltas: 100% (2004/2004), done.
                              root@ubuntulab:~# ls -lhR /root/breakdancer/vendor/
                              /root/breakdancer/vendor/:
                              total 5,8M
                              -rw-r--r-- 1 root root 5,2M ago 11 10:07 boost-1.54-breakdancer.tar.gz
                              -rw-r--r-- 1 root root 551K ago 11 10:07 samtools-0.1.19.tar.gz
                              root@ubuntulab:~# cd breakdancer/
                              root@ubuntulab:~/breakdancer# ls
                              build-common CMakeLists.txt gmt gmt.yml integration-test perl src test-data version
                              cmake debian gmt-web INSTALL.md PackageInfo.cmake README test vendor
                              root@ubuntulab:~/breakdancer# mkdir build
                              root@ubuntulab:~/breakdancer# cd build
                              root@ubuntulab:~/breakdancer/build# cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local
                              -- 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
                              Score floating point type: double
                              -- Looking for include files CMAKE_HAVE_PTHREAD_H
                              -- Looking for include files CMAKE_HAVE_PTHREAD_H - found
                              -- Looking for pthread_create in pthreads
                              -- Looking for pthread_create in pthreads - not found
                              -- Looking for pthread_create in pthread
                              -- Looking for pthread_create in pthread - found
                              -- Found Threads: TRUE
                              -- Performing Test CXX11_FLAG0
                              -- Performing Test CXX11_FLAG0 - Failed
                              -- Performing Test CXX11_FLAG1
                              -- Performing Test CXX11_FLAG1 - Success
                              -- C++11 support enabled via -std=c++0x
                              -- Performing Test CXX11_STDLIB_FLAG0
                              -- Performing Test CXX11_STDLIB_FLAG0 - Success
                              -- Sufficient C++11 library support found with flag ' '
                              -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.3.4")
                              -- Configuring done
                              -- Generating done
                              -- Build files have been written to: /root/breakdancer/build
                              root@ubuntulab:~/breakdancer/build# ls -lhR /root/breakdancer/build/
                              /root/breakdancer/build/:
                              total 92K
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 bin
                              drwxr-xr-x 4 root root 4,0K ago 11 10:09 build
                              -rw-r--r-- 1 root root 13K ago 11 10:09 CMakeCache.txt
                              drwxr-xr-x 9 root root 4,0K ago 11 10:09 CMakeFiles
                              -rw-r--r-- 1 root root 2,4K ago 11 10:09 cmake_install.cmake
                              -rw-r--r-- 1 root root 5,4K ago 11 10:09 CPackConfig.cmake
                              -rw-r--r-- 1 root root 5,8K ago 11 10:09 CPackSourceConfig.cmake
                              -rw-r--r-- 1 root root 517 ago 11 10:09 CTestTestfile.cmake
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 debian
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 integration-test
                              -rw-r--r-- 1 root root 11K ago 11 10:09 Makefile
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 perl
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 test-bin
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 test-data
                              drwxr-xr-x 7 root root 4,0K ago 11 10:09 vendor
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 version

                              /root/breakdancer/build/bin:
                              total 0

                              /root/breakdancer/build/build:
                              total 8,0K
                              drwxr-xr-x 4 root root 4,0K ago 11 10:09 src
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 test

                              /root/breakdancer/build/build/src:
                              total 8,0K
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 exe
                              drwxr-xr-x 5 root root 4,0K ago 11 10:09 lib

                              /root/breakdancer/build/build/src/exe:
                              total 4,0K
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 breakdancer-max

                              /root/breakdancer/build/build/src/exe/breakdancer-max:
                              total 20K
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles
                              -rw-r--r-- 1 root root 2,1K ago 11 10:09 cmake_install.cmake
                              -rw-r--r-- 1 root root 8,3K ago 11 10:09 Makefile

                              /root/breakdancer/build/build/src/exe/breakdancer-max/CMakeFiles:
                              total 12K
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 breakdancer-max.dir
                              -rw-r--r-- 1 root root 957 ago 11 10:09 CMakeDirectoryInformation.cmake
                              -rw-r--r-- 1 root root 3 ago 11 10:09 progress.marks

                              /root/breakdancer/build/build/src/exe/breakdancer-max/CMakeFiles/breakdancer-max.dir:
                              total 32K
                              -rw-r--r-- 1 root root 6,7K ago 11 10:09 build.make
                              -rw-r--r-- 1 root root 320 ago 11 10:09 cmake_clean.cmake
                              -rw-r--r-- 1 root root 858 ago 11 10:09 DependInfo.cmake
                              -rw-r--r-- 1 root root 99 ago 11 10:09 depend.make
                              -rw-r--r-- 1 root root 493 ago 11 10:09 flags.make
                              -rw-r--r-- 1 root root 747 ago 11 10:09 link.txt
                              -rw-r--r-- 1 root root 23 ago 11 10:09 progress.make

                              /root/breakdancer/build/build/src/lib:
                              total 12K
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 breakdancer
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 common
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 io

                              /root/breakdancer/build/build/src/lib/breakdancer:
                              total 20K
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles
                              -rw-r--r-- 1 root root 1,2K ago 11 10:09 cmake_install.cmake
                              -rw-r--r-- 1 root root 12K ago 11 10:09 Makefile

                              /root/breakdancer/build/build/src/lib/breakdancer/CMakeFiles:
                              total 12K
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 breakdancer.dir
                              -rw-r--r-- 1 root root 957 ago 11 10:09 CMakeDirectoryInformation.cmake
                              -rw-r--r-- 1 root root 2 ago 11 10:09 progress.marks

                              /root/breakdancer/build/build/src/lib/breakdancer/CMakeFiles/breakdancer.dir:
                              total 44K
                              -rw-r--r-- 1 root root 14K ago 11 10:09 build.make
                              -rw-r--r-- 1 root root 423 ago 11 10:09 cmake_clean.cmake
                              -rw-r--r-- 1 root root 43 ago 11 10:09 cmake_clean_target.cmake
                              -rw-r--r-- 1 root root 1,1K ago 11 10:09 DependInfo.cmake
                              -rw-r--r-- 1 root root 95 ago 11 10:09 depend.make
                              -rw-r--r-- 1 root root 493 ago 11 10:09 flags.make
                              -rw-r--r-- 1 root root 245 ago 11 10:09 link.txt
                              -rw-r--r-- 1 root root 89 ago 11 10:09 progress.make

                              /root/breakdancer/build/build/src/lib/common:
                              total 20K
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles
                              -rw-r--r-- 1 root root 1,2K ago 11 10:09 cmake_install.cmake
                              -rw-r--r-- 1 root root 8,8K ago 11 10:09 Makefile

                              /root/breakdancer/build/build/src/lib/common/CMakeFiles:
                              total 12K
                              -rw-r--r-- 1 root root 957 ago 11 10:09 CMakeDirectoryInformation.cmake
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 common.dir
                              -rw-r--r-- 1 root root 2 ago 11 10:09 progress.marks

                              /root/breakdancer/build/build/src/lib/common/CMakeFiles/common.dir:
                              total 36K
                              -rw-r--r-- 1 root root 7,4K ago 11 10:09 build.make
                              -rw-r--r-- 1 root root 295 ago 11 10:09 cmake_clean.cmake
                              -rw-r--r-- 1 root root 38 ago 11 10:09 cmake_clean_target.cmake
                              -rw-r--r-- 1 root root 687 ago 11 10:09 DependInfo.cmake
                              -rw-r--r-- 1 root root 90 ago 11 10:09 depend.make
                              -rw-r--r-- 1 root root 493 ago 11 10:09 flags.make
                              -rw-r--r-- 1 root root 130 ago 11 10:09 link.txt
                              -rw-r--r-- 1 root root 45 ago 11 10:09 progress.make

                              /root/breakdancer/build/build/src/lib/io:
                              total 28K
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles
                              -rw-r--r-- 1 root root 1,2K ago 11 10:09 cmake_install.cmake
                              -rw-r--r-- 1 root root 18K ago 11 10:09 Makefile

                              /root/breakdancer/build/build/src/lib/io/CMakeFiles:
                              total 12K
                              -rw-r--r-- 1 root root 957 ago 11 10:09 CMakeDirectoryInformation.cmake
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 io.dir
                              -rw-r--r-- 1 root root 3 ago 11 10:09 progress.marks

                              /root/breakdancer/build/build/src/lib/io/CMakeFiles/io.dir:
                              total 56K
                              -rw-r--r-- 1 root root 27K ago 11 10:09 build.make
                              -rw-r--r-- 1 root root 655 ago 11 10:09 cmake_clean.cmake
                              -rw-r--r-- 1 root root 34 ago 11 10:09 cmake_clean_target.cmake
                              -rw-r--r-- 1 root root 1,9K ago 11 10:09 DependInfo.cmake
                              -rw-r--r-- 1 root root 86 ago 11 10:09 depend.make
                              -rw-r--r-- 1 root root 493 ago 11 10:09 flags.make
                              -rw-r--r-- 1 root root 458 ago 11 10:09 link.txt
                              -rw-r--r-- 1 root root 245 ago 11 10:09 progress.make

                              /root/breakdancer/build/build/test:
                              total 4,0K
                              drwxr-xr-x 5 root root 4,0K ago 11 10:09 lib

                              /root/breakdancer/build/build/test/lib:
                              total 12K
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 breakdancer
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 common
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 io

                              /root/breakdancer/build/build/test/lib/breakdancer:
                              total 24K
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles
                              -rw-r--r-- 1 root root 1,2K ago 11 10:09 cmake_install.cmake
                              -rw-r--r-- 1 root root 424 ago 11 10:09 CTestTestfile.cmake
                              -rw-r--r-- 1 root root 9,4K ago 11 10:09 Makefile

                              /root/breakdancer/build/build/test/lib/breakdancer/CMakeFiles:
                              total 12K
                              -rw-r--r-- 1 root root 971 ago 11 10:09 CMakeDirectoryInformation.cmake
                              -rw-r--r-- 1 root root 3 ago 11 10:09 progress.marks
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 TestBdLib.dir

                              /root/breakdancer/build/build/test/lib/breakdancer/CMakeFiles/TestBdLib.dir:
                              total 36K
                              -rw-r--r-- 1 root root 9,0K ago 11 10:09 build.make
                              -rw-r--r-- 1 root root 362 ago 11 10:09 cmake_clean.cmake
                              -rw-r--r-- 1 root root 851 ago 11 10:09 DependInfo.cmake
                              -rw-r--r-- 1 root root 93 ago 11 10:09 depend.make
                              -rw-r--r-- 1 root root 529 ago 11 10:09 flags.make
                              -rw-r--r-- 1 root root 815 ago 11 10:09 link.txt
                              -rw-r--r-- 1 root root 43 ago 11 10:09 progress.make

                              /root/breakdancer/build/build/test/lib/common:
                              total 24K
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles
                              -rw-r--r-- 1 root root 1,2K ago 11 10:09 cmake_install.cmake
                              -rw-r--r-- 1 root root 426 ago 11 10:09 CTestTestfile.cmake
                              -rw-r--r-- 1 root root 11K ago 11 10:09 Makefile

                              /root/breakdancer/build/build/test/lib/common/CMakeFiles:
                              total 12K
                              -rw-r--r-- 1 root root 971 ago 11 10:09 CMakeDirectoryInformation.cmake
                              -rw-r--r-- 1 root root 3 ago 11 10:09 progress.marks
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 TestCommonLib.dir

                              /root/breakdancer/build/build/test/lib/common/CMakeFiles/TestCommonLib.dir:
                              total 36K
                              -rw-r--r-- 1 root root 11K ago 11 10:09 build.make
                              -rw-r--r-- 1 root root 421 ago 11 10:09 cmake_clean.cmake
                              -rw-r--r-- 1 root root 954 ago 11 10:09 DependInfo.cmake
                              -rw-r--r-- 1 root root 97 ago 11 10:09 depend.make
                              -rw-r--r-- 1 root root 529 ago 11 10:09 flags.make
                              -rw-r--r-- 1 root root 791 ago 11 10:09 link.txt
                              -rw-r--r-- 1 root root 64 ago 11 10:09 progress.make

                              /root/breakdancer/build/build/test/lib/io:
                              total 32K
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles
                              -rw-r--r-- 1 root root 1,2K ago 11 10:09 cmake_install.cmake
                              -rw-r--r-- 1 root root 406 ago 11 10:09 CTestTestfile.cmake
                              -rw-r--r-- 1 root root 18K ago 11 10:09 Makefile

                              /root/breakdancer/build/build/test/lib/io/CMakeFiles:
                              total 12K
                              -rw-r--r-- 1 root root 971 ago 11 10:09 CMakeDirectoryInformation.cmake
                              -rw-r--r-- 1 root root 3 ago 11 10:09 progress.marks
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 TestIoLib.dir

                              /root/breakdancer/build/build/test/lib/io/CMakeFiles/TestIoLib.dir:
                              total 52K
                              -rw-r--r-- 1 root root 28K ago 11 10:09 build.make
                              -rw-r--r-- 1 root root 783 ago 11 10:09 cmake_clean.cmake
                              -rw-r--r-- 1 root root 2,1K ago 11 10:09 DependInfo.cmake
                              -rw-r--r-- 1 root root 93 ago 11 10:09 depend.make
                              -rw-r--r-- 1 root root 529 ago 11 10:09 flags.make
                              -rw-r--r-- 1 root root 1,3K ago 11 10:09 link.txt
                              -rw-r--r-- 1 root root 218 ago 11 10:09 progress.make

                              /root/breakdancer/build/CMakeFiles:
                              total 152K
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 boost-libs.dir
                              -rw-r--r-- 1 root root 1,4K ago 11 10:09 CMakeCCompiler.cmake
                              -rw-r--r-- 1 root root 85 ago 11 10:09 cmake.check_cache
                              -rw-r--r-- 1 root root 1,6K ago 11 10:09 CMakeCXXCompiler.cmake
                              -rwxr-xr-x 1 root root 8,3K ago 11 10:09 CMakeDetermineCompilerABI_C.bin
                              -rwxr-xr-x 1 root root 8,3K ago 11 10:09 CMakeDetermineCompilerABI_CXX.bin
                              -rw-r--r-- 1 root root 971 ago 11 10:09 CMakeDirectoryInformation.cmake
                              -rw-r--r-- 1 root root 2,4K ago 11 10:09 CMakeError.log
                              -rw-r--r-- 1 root root 27K ago 11 10:09 CMakeOutput.log
                              -rw-r--r-- 1 root root 2,1K ago 11 10:09 CMakeRuleHashes.txt
                              -rw-r--r-- 1 root root 402 ago 11 10:09 CMakeSystem.cmake
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeTmp
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 CompilerIdC
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 CompilerIdCXX
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 deps.dir
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 gtest160.dir
                              -rw-r--r-- 1 root root 25K ago 11 10:09 Makefile2
                              -rw-r--r-- 1 root root 5,5K ago 11 10:09 Makefile.cmake
                              -rw-r--r-- 1 root root 3 ago 11 10:09 progress.marks
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 samtools-lib.dir
                              -rw-r--r-- 1 root root 700 ago 11 10:09 TargetDirectories.txt

                              /root/breakdancer/build/CMakeFiles/boost-libs.dir:
                              total 20K
                              -rw-r--r-- 1 root root 7,6K ago 11 10:09 build.make
                              -rw-r--r-- 1 root root 593 ago 11 10:09 cmake_clean.cmake
                              -rw-r--r-- 1 root root 346 ago 11 10:09 DependInfo.cmake
                              -rw-r--r-- 1 root root 177 ago 11 10:09 progress.make

                              /root/breakdancer/build/CMakeFiles/CMakeTmp:
                              total 4,0K
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 CMakeFiles

                              /root/breakdancer/build/CMakeFiles/CMakeTmp/CMakeFiles:
                              total 4,0K
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 cmTryCompileExec.dir

                              /root/breakdancer/build/CMakeFiles/CMakeTmp/CMakeFiles/cmTryCompileExec.dir:
                              total 0

                              /root/breakdancer/build/CMakeFiles/CompilerIdC:
                              total 20K
                              -rwxr-xr-x 1 root root 8,3K ago 11 10:09 a.out
                              -rw-r--r-- 1 root root 5,9K ago 11 10:09 CMakeCCompilerId.c

                              /root/breakdancer/build/CMakeFiles/CompilerIdCXX:
                              total 20K
                              -rwxr-xr-x 1 root root 8,3K ago 11 10:09 a.out
                              -rw-r--r-- 1 root root 5,6K ago 11 10:09 CMakeCXXCompilerId.cpp

                              /root/breakdancer/build/CMakeFiles/deps.dir:
                              total 16K
                              -rw-r--r-- 1 root root 1,8K ago 11 10:09 build.make
                              -rw-r--r-- 1 root root 193 ago 11 10:09 cmake_clean.cmake
                              -rw-r--r-- 1 root root 346 ago 11 10:09 DependInfo.cmake
                              -rw-r--r-- 1 root root 1 ago 11 10:09 progress.make

                              /root/breakdancer/build/CMakeFiles/gtest160.dir:
                              total 20K
                              -rw-r--r-- 1 root root 7,2K ago 11 10:09 build.make
                              -rw-r--r-- 1 root root 559 ago 11 10:09 cmake_clean.cmake
                              -rw-r--r-- 1 root root 346 ago 11 10:09 DependInfo.cmake
                              -rw-r--r-- 1 root root 177 ago 11 10:09 progress.make

                              /root/breakdancer/build/CMakeFiles/samtools-lib.dir:
                              total 20K
                              -rw-r--r-- 1 root root 7,7K ago 11 10:09 build.make
                              -rw-r--r-- 1 root root 627 ago 11 10:09 cmake_clean.cmake
                              -rw-r--r-- 1 root root 346 ago 11 10:09 DependInfo.cmake
                              -rw-r--r-- 1 root root 177 ago 11 10:09 progress.make

                              /root/breakdancer/build/debian:
                              total 8,0K
                              -rwxr-xr-x 1 root root 1,3K ago 11 10:09 postinst
                              -rwxr-xr-x 1 root root 1,1K ago 11 10:09 prerm

                              /root/breakdancer/build/integration-test:
                              total 24K
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 CMakeFiles
                              -rw-r--r-- 1 root root 1,2K ago 11 10:09 cmake_install.cmake
                              -rw-r--r-- 1 root root 547 ago 11 10:09 CTestTestfile.cmake
                              -rw-r--r-- 1 root root 6,4K ago 11 10:09 Makefile
                              -rw-r--r-- 1 root root 52 ago 11 10:09 testdata.py

                              /root/breakdancer/build/integration-test/CMakeFiles:
                              total 8,0K
                              -rw-r--r-- 1 root root 971 ago 11 10:09 CMakeDirectoryInformation.cmake
                              -rw-r--r-- 1 root root 2 ago 11 10:09 progress.marks

                              /root/breakdancer/build/perl:
                              total 16K
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 CMakeFiles
                              -rw-r--r-- 1 root root 1,7K ago 11 10:09 cmake_install.cmake
                              -rw-r--r-- 1 root root 6,4K ago 11 10:09 Makefile

                              /root/breakdancer/build/perl/CMakeFiles:
                              total 8,0K
                              -rw-r--r-- 1 root root 957 ago 11 10:09 CMakeDirectoryInformation.cmake
                              -rw-r--r-- 1 root root 2 ago 11 10:09 progress.marks

                              /root/breakdancer/build/test-bin:
                              total 0

                              /root/breakdancer/build/test-data:
                              total 4,0K
                              -rw-r--r-- 1 root root 619 ago 11 10:09 TestData.hpp

                              /root/breakdancer/build/vendor:
                              total 20K
                              drwxr-xr-x 3 root root 4,0K ago 11 10:09 boost
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 gtest160-build
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 samtools
                              drwxr-xr-x 6 root root 4,0K ago 11 10:09 src
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 tmp

                              /root/breakdancer/build/vendor/boost:
                              total 4,0K
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 boost-src

                              /root/breakdancer/build/vendor/boost/boost-src:
                              total 0

                              /root/breakdancer/build/vendor/gtest160-build:
                              total 0

                              /root/breakdancer/build/vendor/samtools:
                              total 0

                              /root/breakdancer/build/vendor/src:
                              total 16K
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 boost-libs-stamp
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 gtest160
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 gtest160-stamp
                              drwxr-xr-x 2 root root 4,0K ago 11 10:09 samtools-lib-stamp

                              /root/breakdancer/build/vendor/src/boost-libs-stamp:
                              total 12K
                              -rw-r--r-- 1 root root 105 ago 11 10:09 boost-libs-urlinfo.txt
                              -rw-r--r-- 1 root root 1,6K ago 11 10:09 extract-boost-libs.cmake
                              -rw-r--r-- 1 root root 1,2K ago 11 10:09 verify-boost-libs.cmake

                              /root/breakdancer/build/vendor/src/gtest160:
                              total 0

                              /root/breakdancer/build/vendor/src/gtest160-stamp:
                              total 12K
                              -rw-r--r-- 1 root root 1,6K ago 11 10:09 extract-gtest160.cmake
                              -rw-r--r-- 1 root root 107 ago 11 10:09 gtest160-urlinfo.txt
                              -rw-r--r-- 1 root root 1,2K ago 11 10:09 verify-gtest160.cmake

                              /root/breakdancer/build/vendor/src/samtools-lib-stamp:
                              total 12K
                              -rw-r--r-- 1 root root 1,6K ago 11 10:09 extract-samtools-lib.cmake
                              -rw-r--r-- 1 root root 98 ago 11 10:09 samtools-lib-urlinfo.txt
                              -rw-r--r-- 1 root root 1,1K ago 11 10:09 verify-samtools-lib.cmake

                              /root/breakdancer/build/vendor/tmp:
                              total 24K
                              -rw-r--r-- 1 root root 21 ago 11 10:09 boost-libs-cfgcmd.txt
                              -rw-r--r-- 1 root root 12 ago 11 10:09 boost-libs-cfgcmd.txt.in
                              -rw-r--r-- 1 root root 128 ago 11 10:09 gtest160-cfgcmd.txt
                              -rw-r--r-- 1 root root 12 ago 11 10:09 gtest160-cfgcmd.txt.in
                              -rw-r--r-- 1 root root 93 ago 11 10:09 samtools-lib-cfgcmd.txt
                              -rw-r--r-- 1 root root 12 ago 11 10:09 samtools-lib-cfgcmd.txt.in

                              /root/breakdancer/build/version:
                              total 4,0K
                              -rw-r--r-- 1 root root 197 ago 11 10:09 version.h
                              root@ubuntulab:~/breakdancer/build# make
                              Scanning dependencies of target boost-libs
                              [ 1%] Creating directories for 'boost-libs'
                              [ 3%] Performing download step (verify and extract) for 'boost-libs'
                              -- verifying file...
                              file='/root/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
                              -- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
                              -- extracting...
                              src='/root/breakdancer/vendor/boost-1.54-breakdancer.tar.gz'
                              dst='/root/breakdancer/build/vendor/boost/boost-src'
                              -- extracting... [tar xfz]
                              -- extracting... [analysis]
                              -- extracting... [rename]
                              -- extracting... [clean up]
                              -- extracting... done
                              [ 5%] No patch step for 'boost-libs'
                              [ 7%] No update step for 'boost-libs'
                              [ 8%] Performing configure step for 'boost-libs'
                              Building Boost.Build engine with toolset gcc... tools/build/v2/engine/bin.linuxx86_64/b2
                              Detecting Python version... 2.7
                              Detecting Python root... /usr
                              Unicode/ICU support for Boost.Regex?... not found.
                              Generating Boost.Build configuration in project-config.jam...

                              Bootstrapping is done. To build, run:

                              ./b2

                              To adjust configuration, edit 'project-config.jam'.
                              Further information:

                              - Command line help:
                              ./b2 --help

                              - Getting started guide:


                              - Boost.Build documentation:


                              [ 10%] Performing build step for 'boost-libs'
                              [ 12%] No install step for 'boost-libs'
                              [ 14%] Completed 'boost-libs'
                              [ 14%] Built target boost-libs
                              Scanning dependencies of target samtools-lib
                              [ 15%] Creating directories for 'samtools-lib'
                              [ 17%] Performing download step (verify and extract) for 'samtools-lib'
                              -- verifying file...
                              file='/root/breakdancer/vendor/samtools-0.1.19.tar.gz'
                              -- verifying file... warning: did not verify file - no URL_MD5 checksum argument? corrupt file?
                              -- extracting...
                              src='/root/breakdancer/vendor/samtools-0.1.19.tar.gz'
                              dst='/root/breakdancer/build/vendor/samtools'
                              -- extracting... [tar xfz]
                              -- extracting... [analysis]
                              -- extracting... [rename]
                              -- extracting... [clean up]
                              -- extracting... done
                              [ 19%] No patch step for 'samtools-lib'
                              [ 21%] No update step for 'samtools-lib'
                              [ 22%] Performing configure step for 'samtools-lib'
                              Building samtools, build log at /root/breakdancer/build/vendor/samtools/build.log
                              [ 24%] Performing build step for 'samtools-lib'
                              make[2]: *** [vendor/src/samtools-lib-stamp/samtools-lib-build] Error 2
                              make[1]: *** [CMakeFiles/samtools-lib.dir/all] Error 2
                              make: *** [all] Error 2

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