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  • RVJ12
    Junior Member
    • Feb 2011
    • 1

    #1

    how to install spp chip-seq package in linux?

    Hello, I am trying to install 'spp' package by Krachenko etal. I am in a linux system. I installed boost c++ libraries to a local directory '/home/user/boost' and ran 'R CMD INSTALL spp_1.8.tar.gz' but its giving the folowing error

    Installing to library '/home/RVJ12/R/x86_64-unknown-linux-gnu-library/2.8'
    * Installing *source* package 'spp' ...
    checking for gcc... gcc
    checking for C compiler default output file name... a.out
    checking whether the C compiler works... yes
    checking whether we are cross compiling... no
    checking for suffix of executables...
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking for BZ2_bzDecompressInit in -lbz2... no
    configure: creating ./config.status
    config.status: creating src/Makevars
    ** libs
    /usr/bin/g++ -I/share/opt/R/2.8.1/gcc/lib64/R/include -I/usr/local/include -D_FASTMAP -DMAQ_LONGREADS -fpic -O3 -g -c bed2vector.C -o bed2vector.o
    In file included from /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/backward/strstream:51,
    from bed2vector.C:8:
    /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/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.
    bed2vector.C:14:31: error: boost/tokenizer.hpp: No such file or directory
    bed2vector.C: In function 'SEXPREC* read_bed_ends(SEXPREC*)':
    .
    .
    .
    bed2vector.C:2477: error: 'sit' was not declared in this scope
    bed2vector.C:2477: error: 'tok' was not declared in this scope
    make: *** [bed2vector.o] Error 1
    chmod: cannot access `/home/RVJ12/R/x86_64-unknown-linux-gnu-library/2.8/spp/libs/*': No such file or directory
    ERROR: compilation failed for package 'spp'
    ** Removing '/home/RVJ12/R/x86_64-unknown-linux-gnu-library/2.8/spp'


    before executing this I set up the LD_LIBRARY_PATH by
    setenv LD_LIBRARY_PATH /home/RVJ12/boost:${LD_LIBRARY_PATH}

    I am not familiar with linux commands and setting up paths etc.

    Can anybody suggest a solution or suggestion to install spp??

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