Re: [R] unable to view vignette in R

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Sun, 16 Nov 2008 06:50:43 +0000 (GMT)

Why not ask on r-sig-debian?: presumably it is a setting in the binary install of R you are using that is inappropriate on your systems.

On Sat, 15 Nov 2008, Erik Iverson wrote:

> I never could figure this out, I had the exact same issue though. My
> solution was to simply set
>
> options(pdfviewer = "evince")
>
> in my .Rprofile. Presumably, you could set it to whatever PDF viewer is your
> favorite. I never looked further into why the default was doing what it was
> doing.

You could also set the environment variable R_PDFVIEWER .

> Lionel Brooks wrote:
>> Hello All R-Gurus:
>>
>> ISSUE:
>> Cannot view R vignettes due in Ubuntu Linux (a debian variant).
>> note: this issue has been posted to this list before with no responses
>> given
>> see https://stat.ethz.ch/pipermail/r-help/2007-September/141178.html
>>
>> DETAILS:
>> I am trying to view an R vignette.
>> Here is the situation: I issue the openvignette(), then select the vignette
>> I wish to view...and the system returns:
>>
>> "Could not get a file descriptor referring to the console."
>>
>> This action should spawn a ps viewer displaying the contents of the
>> vignette for my enjoyment.
>> I suspect it may have something to do with the call to the postscript
>> viewer application.
>> Is there a simple way to change this behavior within R?
>>
>> Any Thoughts?
>>
>> Here is the copy paste of my session
>>
>> Code:
>>
>> > openVignette()
>> Please select a vignette:
>> 1: annotate - Annotation Overview
>> 2: annotate - Basic GO Usage
>> 3: annotate - HowTo: Get HTML Output
>> 4: annotate - HowTo: use chromosomal information
>> 5: annotate - HOWTO: Use the online query tools
>> 6: annotate - Using Affymetrix Probe Level Data
>> 7: annotate - Using Data Packages
>> 8: annotate - Using the homology package
>> 9: AnnotationDbi - AnnotationDbi
>> 10: AnnotationDbi - SQLForge
>> 11: Biobase - An introduction to Biobase and ExpressionSets
>> 12: Biobase - Bioconductor Overview
>> 13: Biobase - esApply Introduction
>> 14: Biobase - Notes for eSet developers
>> 15: Biobase - Notes for writing introductory 'how to' documents
>> 16: Biobase - quick views of eSet instances
>> 17: geneplotter - How to assemble a chromLocation object
>> 18: geneplotter - Visualization of Microarray Data
>> 19: xtable - xtable Gallery
>>
>> Selection: 17)
>> Opening
>> /home/lbthrice/R/i486-pc-linux-gnu-library/2.8/geneplotter/doc/byChroms.pdf
>> > Couldnt get a file descriptor referring to the console
>> Could not get a file descriptor referring to the console
>>
>> ______________________________________________
>> R-help_at_r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Brian D. Ripley,                  ripley_at_stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Received on Sun 16 Nov 2008 - 06:57:18 GMT

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