[Useq-users] help ( USeq - ChIPSeq Cannot find the required R libraries)

[Ashutosh S. <ash...@cc...>]

 Dear All,

I am trying to use USeq package for ChIP-Seq analysis. I have installed required packages DESeq2 , gplots and qvalue in a user local library ("~/R/x86_64-unknown-linux-gnu-library/3.1").
When I open R in command line, i could see library(DESeq2),library(gplots) and library(qvalue) are present there. Now, when I try to run ChIPSeq  using command

$ java -Xmx2G -jar /home/pb/USeq_8.8.1/Apps/ChIPSeq -y novoalign -v S_cerevisiae_Apr_2011 -t /home/pb/Desktop/test/ -c /home/pb/Desktop/control/ -s /home/pb/Desktop/SAVE/

I get the following error:

Checking parameters...

The following problems were encountered when processing your parameter file.  Correct and restart. -> 

Error: Cannot find the required R libraries.  Did you install DESeq2, gplots, and qvalue? Once installed, launch an R terminal and type 'library(DESeq2); library(qvalue); library(gplots)' to see if it is present. Error message:
		Error in library(DESeq2) : there is no package called ‘DESeq2’ Execution halted

is this error because of ChIPSeq only works with global R library? but not with library in my local folders.

-- to check this problem i even tried to install all the required packages and dependencies one after another in /usr/local/lib/R/site-library but i got the following error 

Checking parameters...

The following problems were encountered when processing your parameter file.  Correct and restart. -> 

Error: Cannot find the required R libraries.  Did you install DESeq2, gplots, and qvalue? Once installed, launch an R terminal and type 'library(DESeq2); library(qvalue); library(gplots)' to see if it is present. Error message:
		Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/local/lib/R/site-library/RcppArmadillo/libs/RcppArmadillo.so': libRlapack.so: cannot open shared object file: No such file or directory Error: package ‘RcppArmadillo’ could not be loaded Execution halted.

am i doing something wrong with the commands and package installations ? I am basically a biologist who recently started learning Linux and R. so please bear me , if I am asking a trivial question. any elaborated help would by highly appreciated.

Thanks for help 
-- 
Ashutosh Shukla
Senior Research Fellow
W313, West wing, IInd floor,
Centre For Cellular & Molecular Biology
Hyderabad -500007
India.