----- Original Message ----- > From: "Peng Zhou" <peng.zhou at="" csiro.au=""> > To: dtenenba at fhcrc.org > Sent: Saturday, April 26, 2014 11:30:57 PM > Subject: ??: ??: ??: [BioC] problem with \"readCufflinks\" > > Hi, Dan, looks like I only need to update some of the packages, they > have been too old but still necessary to the function > "readCufflinks". After update, everything turn out to be normal. > This would be a good lesson for new users who have the same problem. Glad to hear the problem is resolved. I'm cc'ing the bioconductor list. Dan > Cheers, > Peng > > > ________________________________________ > ???: Dan Tenenbaum [dtenenba at fhcrc.org] > ????: 2014?4?24? 9:14 > ???: Zhou, Peng (CAFHS, Geelong AAHL) > ??: bioconductor at r-project.org > ??: Re: ??: ??: [BioC] problem with \"readCufflinks\" > > Hi Peng, > > ----- Original Message ----- > > From: "Peng Zhou" <peng.zhou at="" csiro.au=""> > > To: dtenenba at fhcrc.org > > Cc: bioconductor at r-project.org > > Sent: Wednesday, April 23, 2014 4:09:40 PM > > Subject: RE: ??: ??: [BioC] problem with \"readCufflinks\" > > > > Same to last time: Error: could not find function "readCufflinks" > > It did show that "plyr" has been installed. > > > > You have to provide the complete transcript of the session, meaning > the commands you typed in and ALL of the output of R in response. > > Really, all you should have to do is: > > source("http://bioconductor.org.biocLite.R") > biocLite("cummeRbund") > library(cummeRbund) > > cuff_data<-readCufflinks('D:\\AAA- PengZhou\\R-3.0.1\\library\\AAAAAA') > > > Dan > > > > Cheers, > > Peng > > > > -----Original Message----- > > From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] > > Sent: Thursday, 24 April 2014 12:43 AM > > To: Zhou, Peng (CAFHS, Geelong AAHL) > > Cc: bioconductor at r-project.org list > > Subject: Re: ??: ??: [BioC] problem with \"readCufflinks\" > > > > > > > > ----- Original Message ----- > > > From: "Peng Zhou" <peng.zhou at="" csiro.au=""> > > > To: dtenenba at fhcrc.org > > > Sent: Wednesday, April 23, 2014 12:11:22 AM > > > Subject: ??: ??: [BioC] problem with \"readCufflinks\" > > > > > > Thanks Dan! Unfortunately not working after I installed the > > > package > > > "plyr". I guess I may need to uninstall R and start everything > > > from > > > begining. > > > > > > > What is the error message you are getting this time? > > > > Dan > > > > > > > Cheers, > > > Peng > > > ________________________________________ > > > ???: Dan Tenenbaum [dtenenba at fhcrc.org] > > > ????: 2014?4?22? 0:31 > > > ???: Zhou, Peng (CAFHS, Geelong AAHL) > > > ??: bioconductor at r-project.org list > > > ??: Re: ??: [BioC] problem with \"readCufflinks\" > > > > > > 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 > > > > > > >