[BioC] problem with \"readCufflinks\"

[Dan Tenenbaum]

Hi Peng,


----- Original Message -----
> From: "Peng [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, "peng zhou" <peng.zhou at csiro.au>
> Sent: Sunday, April 20, 2014 9:30:56 PM
> Subject: [BioC] problem with \"readCufflinks\"
> 
> 
> Hi,
> I have used cummeRbund a bit recently with Cuffdiff outputs from runs
> on Galaxy. It has worked ok but the last few days it does not. I
> have tried to install the package again but no success. Please see
> below for my problems, the function "readCufflilnks" does not work,
> know why? Many thanks!
> 
> R 3.0.1
> 
>  -- output of sessionInfo():
> 

By the way, sessionInfo() is an R command that gives information about your version of R, operating system, and installed packages. Including the output of this function can help us figure out problems and answer questions.

> > cuff_data<-readCufflinks('D:\\AAA-Peng
> > Zhou\\R-3.0.1\\library\\AAAAAA')
> Error: could not find function "readCufflinks"


This might be simply that you haven't loaded the cummeRbund package, so try this first:

library(cummeRbund)

If that does not give an error, then try your readCuffLinks command again.

> > biocLite("readCufflinks")

biocLite() is the command for installing packages. So if cummeRbund is not installed, you can try this:

biocLite("cummeRbund")



> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.12 (BiocInstaller 1.10.4), R version
> 3.0.1.
> Installing package(s) 'readCufflinks'
> Warning message:
> package ‘readCufflinks’ is not available (for R version 3.0.1)
> 

That's because readCufflinks is a function, not a package.

So all of this should work:

source("http://bioconductor.org/biocLite.R")
biocLite("cummeRbund")
cuff_data<-readCufflinks('D:\\AAA-PengZhou\\R-3.0.1\\library\\AAAAAA')

Dan




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