[BioC] cummeRbund

[Dan Du]

Hi Valentina,

The dependent Gviz is only available for R >=2.15, as stated in the
warning msg,

> In getDependencies(pkgs, dependencies, available, lib) :
>   package ‘Gviz’ is not available (for R version 2.14.1)

You should have your R installation upgraded.

cheers,
Dan

On Fri, 2013-03-08 at 01:57 -0800, valentina indio [guest] wrote:
> 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.
> 
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