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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