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.
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
>
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