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

[Dan Tenenbaum]

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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