[BioC] BiocLite eror

[Dan Tenenbaum]

Please keep the bioconductor list added (use Reply All) so that all can learn and contribute.

Please shut down ALL R sessions and then start a new one with R --vanilla. That should stop the R session that is "using" hgu133plus2.db.

Dan


----- Original Message -----
> From: "Rabia Johnson" <Rabia.Johnson at mrc.ac.za>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Sent: Thursday, April 3, 2014 12:07:03 AM
> Subject: RE: [BioC] BiocLite eror
> 
> Dear Dan,
> No unfortunately it does not. This is the error that I am getting:
> 
> 
> > source("http://bioconductor.org/biocLite.R")
> Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
> > biocLite("hgu133plus2.db")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version
> 3.0.3.
> Installing package(s) 'hgu133plus2.db'
> Warning: package ‘hgu133plus2.db’ is in use and will not be installed
> Warning message:
> installed directory not writable, cannot update packages 'boot',
> 'class',
> 'cluster', 'foreign', 'KernSmooth', 'MASS', 'Matrix', 'mgcv', 'nlme',
> 'nnet',
> 'rpart', 'spatial'
> 
> Regards
> Rabia
> 
> -----Original Message-----
> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org]
> Sent: 02 April 2014 07:19 PM
> To: Rabia Johnson
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] BiocLite eror
> 
> 
> 
> ----- Original Message -----
> > From: "Rabia Johnson" <Rabia.Johnson at mrc.ac.za>
> > To: bioconductor at r-project.org
> > Sent: Wednesday, April 2, 2014 12:04:19 AM
> > Subject: [BioC] BiocLite eror
> > 
> > HI,
> > 
> > Object : problem with hgu133plus2.db you need to install this
> > package
> > to complete this step
> > 
> > If possible can anyone help. I am new to R and are working through
> > the
> > tutorial of Daniel Swan (Analysing microarray data in
> > BioConductor)
> > Upon writing the following command I get the following error:
> > 
> > > biocLite("hgu133plus2.db")
> > BioC_mirror: http://bioconductor.org
> > Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version
> > 3.0.3.
> > Installing package(s) 'hgu133plus2.db'
> > Warning: package 'hgu133plus2.db' is in use and will not be
> > installed
> > Warning message:
> > installed directory not writable, cannot update packages 'boot',
> > 'class',
> > 'cluster', 'foreign', 'KernSmooth', 'MASS', 'Matrix', 'mgcv',
> > 'nlme', 'nnet',
> > 'rpart', 'spatial'
> > 
> > 
> 
> Try quitting your R session and starting a fresh one like this:
> 
> R --vanilla
> 
> And then running
> 
> 
> source("http://bioconductor.org/biocLite.R")
> biocLite("hgu133plus2.db")
> 
> 
> Does that work?
> 
> Dan
> 
> 
> 
> > Thus, needless to say when I continue with the next command I get
> > more
> > errors:
> > 
> > > library(hgu133plus2.db)
> > > library(annotate)
> > > gene.symbols <- getSYMBOL(probeset.list$ID, "hgu133plus2")
> > Error in unlist(lookUp(x, data, "SYMBOL")) :
> > error in evaluating the argument 'x' in selecting a method for
> > function 'unlist': Error in lookUp(x, data, "SYMBOL") : No keys
> > provided
> > 
> > 
> > Can anyone help please
> > Regards
> > Rabia
> > 
> > 
> > _______________________________________
> > Rabia Johnson (PhD)
> > Senior Scientist
> > South African Medical Research Council Diabetes Discovery Platform
> > Building E Francie van Zijl Drive, Parow Valley, 7505, Cape Town
> > Cell: +27 82 0677296
> > Tel: +27 21 938 0866
> > Fax: +27 21 938 0456
> > E-mail: rabia.johnson at mrc.ac.za
> > 
> > 
> > Disclaimer\ \ The information contained in this
> > communic...{{dropped:20}}
> > 
> > _______________________________________________
> > 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
> > 
> 
> 
> 
> 
> Disclaimer
> 
> The information contained in this communication from the sender is
> confidential. It is intended solely for use by the recipient and
> others authorized to receive it. If you are not the recipient, you
> are hereby notified that any disclosure, copying, distribution or
> taking action in relation of the contents of this information is
> strictly prohibited and may be unlawful.
> 
> This email has been scanned for viruses and malware, and
> automatically archived by Mimecast SA (Pty) Ltd , an innovator in
> Software as a Service (SaaS) for business. Mimecast Unified Email
> Management ™ (UEM) offers email continuity, security, archiving and
> compliance with all current legislation. To find out more, contact
> Mimecast .