Re: [Useq-users] USeq installation problem w R

[David N. <dav...@gm...>]

Hello Zeynep,

No that is correct.  The checker returns null or a non empty error message
when things go wrong.

I suspect that R is not aware of the environmental variables in your .bashrc
when called from java.  It¹s as if these don¹t exist.  I recommend you
install a local copy of R in your home directory and then load the libraries
into that local copy.  Alternatively, get someone with root access to
install DESeq into the global R.  To test if this is working, comment out
your R_HOME and R_LIBS and launch R and type the library(DESeq).

The thing that is puzzling to me is the :

> WARNING: ignoring environment value of R_HOME

This says that R did see your R_HOME  upon launch but is ignoring it.
Weird!

-cheers, D

-- 
David Austin Nix, PhD | Bioinformatics Shared Resource | Huntsman Cancer
Institute | 2000 Circle of Hope | SLC, UT 84112 | Rm: 3165 | Vc:
801.587.4611 | Fx: 801.585.6458 | dav...@hc... | Skype/iChat:
LiveNix | WebSite: http://bioserver.hci.utah.edu | DAS/2:
http://bioserver.hci.utah.edu:8080/DAS2DB/genome





On 9/25/10 5:46 PM, "Zeynep Hulya Gumus" <zey...@gm...> wrote:

> Hi
> 
> It looks like in the sourcecode for ChIPSeq.java, there may be a bug that
> causes the error I described in my previous email: I highlighted how this can
> be changed to fix the error message with ***:
> 
>  else {
>                         String errors =
> IO.runRCommandLookForError("library(DESeq)", rApplication, resultsDirectory);
>                         *** Do you mean errors != null (instead of
> errors==null)? ***
>                         if (errors == null || errors.length() !=0){
>                                 passed = false;
>                                 notes.append("\nError: Cannot find the
> required R library.  Did you install DESeq " +
>                                               
>  "(http://www-huber.embl.de/users/anders/DESeq/)?  See the author's websites
> for installation instructions. Once installed, " +
>                                                 "launch an R terminal and type
> 'library(DESeq)' to see if it is present. Error
> message:\n\t\t"+errors+"\n\n");
>                         }
>                 }
> 
> 
> However, I don't know how to re-compile this within the application and make
> it into the jar ChIPseq. Help would be appreciated! Thank you! - Z
> 
> 
> 
> 
> 
> On Sat, Sep 25, 2010 at 3:37 PM, Zeynep Hulya Gumus <zey...@gm...>
> wrote:
>> > Hi
>> >
>> > I've installed USeq and also DESeq. When I open R in my local
>> > directory, and library(DESeq), I see that it is there.
>> > Now, when I try to run ChIPSeq, I get the following error:
>> >
>> > mimi@panda TEST_MIMI $ java -Xmx2G -jar ../ChIPSeq -y sam -v
>> > M_musculus_Jul_2007 -t ../../../MOUSE_SEQ/TRT_H3K4me/ -c
>> > ../../../MOUSE_SEQ/TRT_Input/ -r
>> > /softlib/exe/x86_64/pkg/R/2.11.1/gcc_64/bin/R -s TEST
>> >
>> > Checking parameters...
>> > WARNING: ignoring environment value of R_HOME
>> >
>> > The following problems were encountered when processing your parameter
>> > file.  Correct and restart. ->
>> >
>> > Error: Cannot find the required R library.  Did you install DESeq
>> > (http://www-huber.embl.de/users/anders/DESeq/)?  See the author's
>> > websites for installation instructions. Once installed, launch an R
>> > terminal and type 'library(DESeq)' to see if it is present. Error
>> > message:
>> >                null
>> >
>> > ---
>> > I am running it in a linux cluster, where R.11.1 is installed
>> > globally. However, I install the libraries locally, such that my
>> > .bashrc file is:
>> >
>> > # to install R:
>> > export R_HOME=/softlib/exe/x86_64/pkg/R/2.11.1/gcc_64
>> > export PATH=$R_HOME/bin${PATH+:$PATH}
>> > export R_LIBS=/panda_scratch_homes002/mimi/.R/mylibrary
>> >
>> > How can I make ChIPSeq correctly? Is this a problem with my paths in
>> > .bashrc (note that it works when I open R in the command line)?
>> > ChIPSeq seems to go to the global network library as opposed to
>> > mylibrary in my local folders.
>> >
>> > Thank you for your help!
>> > - Z
>> >
> 
> 
> 
> 
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