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Old 02-21-2011, 12:01 PM   #1
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Join Date: Feb 2011
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Default 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 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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