[BioC] 答复: 答复: 答复: problem with \"readCufflinks\"
Dan Tenenbaum
dtenenba at fhcrc.org
Sun Apr 27 08:47:00 CEST 2014
----- 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: 答复: 答复: 答复: [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
>
>
> ________________________________________
> 发件人: Dan Tenenbaum [dtenenba at fhcrc.org]
> 发送时间: 2014年4月24日 9:14
> 收件人: Zhou, Peng (CAFHS, Geelong AAHL)
> 抄送: bioconductor at r-project.org
> 主题: Re: 答复: 答复: [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: 答复: 答复: [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: 答复: 答复: [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: 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.
> > > > >
> > > > > _______________________________________________
> > > > > 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
> > > > >
> >
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