[BioC] cummeRbund

[valentina indio [guest]]

Hi,
I'm trying to install cummeRbund pakage in my R. In order to work on my RNA-seq data I need to obtain the cummeRbund_2.0.0 release.
When I type
source("http://bioconductor.org/biocLite.R")
biocLite("cummeRbund")
on my consolle I'm only able to download the cummeRbund_1.0.0 that lacks a lot of functions.
So I downloaded the source cummeRbund_2.0.0.tar.gz solving all the dependencies. But when I installed the pakage Gviz I'm not able to go on. This is my the Gviz error (see section ### 1 ###).

Moreover if I try to install from th R consolle the error is the following:(see section ### 2 ###)

Any idea to solve my problem???
Many thanks!
Valentina

 -- output of sessionInfo(): 

#######################   1    ###############################
valentina at valentina-desktop:~/Documenti/Tools/download$ sudo R CMD INSTALL Gviz_1.2.1.tar.gz
* installing to library ‘/usr/local/lib/R/site-library’
* installing *source* package ‘Gviz’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “file” in package ‘BiocGenerics’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “bzfile” in package ‘rtracklayer’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for class “characterORconnection” in package ‘rtracklayer’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “fifo” in package ‘rtracklayer’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “gzfile” in package ‘rtracklayer’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “pipe” in package ‘rtracklayer’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “sockconn” in package ‘rtracklayer’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “terminal” in package ‘rtracklayer’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “textConnection” in package ‘rtracklayer’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “unz” in package ‘rtracklayer’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class “url” in package ‘rtracklayer’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class
Error : requested methods not found in environment/package ‘GenomicRanges’: seqnameStyle
ERROR: lazy loading failed for package ‘Gviz’
* removing ‘/usr/local/lib/R/site-library/Gviz’



################    2    ############################
> source("http://bioconductor.org/biocLite.R")
BiocInstaller version 1.2.1, ?biocLite for help
> biocLite("Gviz")
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Installing package(s) 'Gviz'
Installing package(s) into ‘/usr/lib/R/library’
(as ‘lib’ is unspecified)
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘Gviz’ is not available (for R version 2.14.1)



This is the R version I used:
RKward Version 0.5.7 with KDE 4.8.5
And these are my OS information:
Linux valentina-desktop 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

--
Sent via the guest posting facility at bioconductor.org.