Keeping the bioconductor list on the thread. See below: ----- Original Message ----- > From: "Peng Zhou" <peng.zhou at="" csiro.au=""> > To: dtenenba at fhcrc.org > Sent: Monday, April 21, 2014 3:38:48 AM > Subject: ??: [BioC] problem with \"readCufflinks\" > > > library(cummeRbund) > Loading required package: BiocGenerics > Loading required package: parallel > Attaching package: ?BiocGenerics? > The following objects are masked from ?package:parallel?: > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, clusterMap, parApply, parCapply, parLapply, > parLapplyLB, parRapply, parSapply, parSapplyLB > The following object is masked from ?package:stats?: > xtabs > The following objects are masked from ?package:base?: > anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, > Filter, Find, get, intersect, lapply, Map, mapply, match, mget, > order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, > rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, > tapply, union, unique, unlist > Loading required package: RSQLite > Loading required package: DBI > Loading required package: ggplot2 > Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = > vI[[i]]) : > there is no package called ?plyr? THis is telling you that you need to install 'plyr'. So do biocLite("plyr") and try again. Dan > Error: package ?ggplot2? could not be loaded > > cuff_data<-readCufflinks('D:\\AAA-Peng > > Zhou\\R-3.0.1\\library\\AAAAAA') > Error: could not find function "readCufflinks" > > > > > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-w64-mingw32/x64 (64-bit) > locale: > [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 > [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936 > [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 > [4] LC_NUMERIC=C > [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936 > attached base packages: > [1] parallel stats graphics grDevices utils datasets > methods base > other attached packages: > [1] RSQLite_0.11.4 DBI_0.2-7 BiocGenerics_0.6.0 > loaded via a namespace (and not attached): > [1] digest_0.6.4 grid_3.0.1 gtable_0.1.2 > > > Hi, see above, the problem still exist. > > Cheer, > Peng > > ________________________________________ > ???: Dan Tenenbaum [dtenenba at fhcrc.org] > ????: 2014?4?21? 14:50 > ???: Peng [guest] > ??: bioconductor at r-project.org; Zhou, Peng (CAFHS, Geelong AAHL) > ??: Re: [BioC] problem with \"readCufflinks\" > > 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 > >