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(): > cuff_data<-readCufflinks('D:\\AAA-Peng Zhou\\R-3.0.1\\library\\AAAAAA') Error: could not find function "readCufflinks" > biocLite("readCufflinks") 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) -- Sent via the guest posting facility at bioconductor.org.

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 > -- > 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 >