SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SPP -- ChIP-seq program installation?? ewilbanks Bioinformatics 10 06-19-2013 06:41 AM
ChIP-Seq: DIME: R-package for Identifying Differential ChIP-seq Based on an Ensemble Newsbot! Literature Watch 0 04-08-2011 02:00 AM
Install spp (chip-seq processing pipeline) bbl Bioinformatics 0 10-27-2010 07:02 AM
ChIP-Seq: ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip dat Newsbot! Literature Watch 0 05-13-2010 02:00 AM
Error -- SPP package, MSER -- could you please help abmmki Introductions 0 11-15-2009 03:17 AM

Reply
 
Thread Tools
Old 02-21-2011, 11:01 AM   #1
RVJ12
Junior Member
 
Location: VA

Join Date: Feb 2011
Posts: 1
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 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??
RVJ12 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:34 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO