[Bioc-sig-seq] Probs installing dev version of Rsamtools

[Pratap, Abhishek]

Thanks Martin and Seth for your tricks. I have it working finally.

Cheers!
-Abhi

-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
Sent: Tuesday, December 08, 2009 6:52 PM
To: Pratap, Abhishek
Cc: bioc-sig-sequencing at r-project.org
Subject: Re: [Bioc-sig-seq] Probs installing dev version of Rsamtools

Hi Abhi --

Pratap, Abhishek wrote:
> Hi All
> 
>  
> 
> I am starting a new thread since the old issues I believe have been
> taken care of. I am trying to install dev version of Rsamtools and
> following is what I have done till now.    -Abhi
> 
>  
> 
>  
> 
> 1.       R devel install
> 
> 2.       BioC devel install ver 2.5.8
> 
>  
> 
> ..CMD:- Rdev CMD INSTALL --clean Rsamtools/
> 
>  
> 
> ****Error:*****
> 
> Warning in .completeClassSlots(ClassDef, where) :
> 
>   undefined slot classes in definition of "Alignments0":
> gapped_ranges(class "GappedRanges")
> 
> Error in setValidity2("Alignments0", .valid.Alignments0, where =
> asNamespace("Rsamtools")) : 
> 
>   unused argument(s) (where = asNamespace("Rsamtools"))
> 
> Error : unable to load R code in package 'Rsamtools'
> 
> ERROR: lazy loading failed for package 'Rsamtools'
> 

As mentioned, this package is under active development; your best bet is
to wait for it to mature. As a first step, you must use the 'devel'
version of R (sessionInfo below says 2.10.1 RC; you're looking for
2.11.0 Under development), and you'll need to ensure that you are using
svn versions of the package dependencies, particularly Biostrings and
IRanges. Having checked out IRanges, Biostrings, and Rsamtools, one
might

  svn up IRanges Biostrings Rsamtools
  R CMD INSTALL --clean IRanges Biostrings Rsamtools

even then, the packages may not be functional -- it is not even in
'devel' for a reason!

Again, your best bet is to wait for Rsamtools to become more stable.

Martin

> * removing
>
'/local/projects/grc/devel/apratap/softwares/R-devel/R-rc/lib64/R/librar
> y/Rsamtools'
> 
>  
> 
> ========
> 
>  
> 
>  
> 
> sessionInfo()
> 
> R version 2.10.1 RC (2009-12-06 r50688) 
> 
> x86_64-unknown-linux-gnu 
> 
>  
> 
> locale:
> 
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
> 
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
> 
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
> 
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
> 
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> 
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
> 
>  
> 
> attached base packages:
> 
> [1] stats     graphics  grDevices utils     datasets  methods   base

> 
>  
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793