[BioC] 答复: 答复: problem with \"readCufflinks\"

[Dan Tenenbaum]

----- 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: 答复: 答复: [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
> ________________________________________
> 发件人: Dan Tenenbaum [dtenenba at fhcrc.org]
> 发送时间: 2014年4月22日 0:31
> 收件人: Zhou, Peng (CAFHS, Geelong AAHL)
> 抄送: bioconductor at r-project.org list
> 主题: Re: 答复: [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: 答复: [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
> >
> > ________________________________________
> > 发件人: Dan Tenenbaum [dtenenba at fhcrc.org]
> > 发送时间: 2014年4月21日 14:50
> > 收件人: Peng [guest]
> > 抄送: bioconductor at r-project.org; Zhou, Peng (CAFHS, Geelong AAHL)
> > 主题: 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.
> > >
> > > _______________________________________________
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> > >