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  • SPP -- ChIP-seq program installation 2??

    Hi guys,
    I've tried install spp (http://compbio.med.harvard.edu/Supplements/ChIP-seq/) to my macbook pro or my ubuntu, met the same error. Stcuking for ages!! hope anyone can help

    Here is some detailed infor:
    macbook pro 10.7.4 OSX Lion
    ubuntu 12.04
    I've successfully installed boost C++, and R( both are the most recent one).

    below is the error message I got, every time, and on both machine :

    ----------------------
    g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -I./ -D_FASTMAP -DMAQ_LONGREADS -fPIC -g -O2 -c bamread.cpp -o bamread.o
    In file included from /usr/include/c++/4.2.1/backward/strstream:51,
    from bamread.cpp:8:
    /usr/include/c++/4.2.1/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
    bamread.cpp:14:31: error: boost/tokenizer.hpp: No such file or directory
    bamread.cpp: In function ‘SEXPREC* read_bam(SEXPREC*, SEXPREC*)’:
    bamread.cpp:71: error: ‘boost’ has not been declared
    bamread.cpp:71: error: expected initializer before ‘<’ token
    bamread.cpp:72: error: ‘boost’ has not been declared
    bamread.cpp:72: error: expected primary-expression before ‘char’
    bamread.cpp:72: error: expected `;' before ‘char’
    bamread.cpp:73: error: ‘boost’ has not been declared
    bamread.cpp:73: error: expected primary-expression before ‘char’
    bamread.cpp:73: error: expected `;' before ‘char’
    make: *** [bamread.o] Error 1
    ERROR: compilation failed for package ‘spp’
    * removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/spp’

    --------------------


    PS. I've looked up in the forum, a relative post (http://seqanswers.com/forums/showthr...&highlight=spp) has similar problem, but not quite same, and the link of patch is brocken.

    Many thanks.
    Attached Files

  • #2
    Hi Potatoo,

    I am getting exactly the same error message when I tried installing spp version version 1.11 on my Mac and Linux pc. Any luck in fixing this bug?

    Louella
    Last edited by Louella; 10-03-2012, 09:25 AM.

    Comment


    • #3
      Hi,
      You are missing the boost library. Install the boost library and try again. Here are my notes from a while back:

      # install dependencies
      sudo yum update
      sudo yum install gcc-c++.x86_64
      sudo yum install gcc-gfortran.x86_64
      sudo yum install readline-static.x86_64
      sudo yum install make.x86_64
      sudo yum install zlib-devel.x86_64
      sudo yum install boost-devel.x86_64

      # install R
      wget http://cran.r-project.org/src/base/R-2/R-2.14.1.tar.gz

      tar xvf R-2.14.1.tar.gz
      cd R-2.14.1
      # configure R with no X
      sudo ./configure --with-x=no

      sudo make
      sudo make install


      # Run R then install the following
      install.packages("bitops")
      install.packages("caTools")


      # get spp
      wget http://www.ebi.ac.uk/~anshul/public/...package.tar.gz
      tar xvf spp_package.tar.gz
      cd spp_package
      sudo R CMD INSTALL spp_1.10.1.tar.gz

      Q

      Comment


      • #4
        Hi,

        I also struggled on this issue, hope this can help (on mac OSX 10.8.5)

        download latest version of spp (1.11) from http://compbio.med.harvard.edu/Supplements/ChIP-seq/

        download the source for boost library and compile:

        ./bootstrap.sh
        ./b2
        ## do not forget the last step !
        sudo ./b2 install

        R CMD INSTALL spp_1.11.tar.gz

        Morgane

        Comment

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