[BioC] problem with \"readCufflinks\"

Dan Tenenbaum dtenenba at fhcrc.org
Mon Apr 21 06:50:57 CEST 2014

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:


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:


> 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:



> --
> Sent via the guest posting facility at bioconductor.org.
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor

More information about the Bioconductor mailing list