[BioC] Problem viewing vignettes : openPDF and pdfviewer and possible fix

[Martin Morgan]

Thanks Karl, this is fixed in the development version of Biobase.

> options(pdfviewer='')
> openPDF()
Error in openPDF() : 
  getOption('pdfviewer') is ''; please use 'options(pdfviewer=...)'
> options(pdfviewer=NULL)
> openPDF()
Error in openPDF() : 
  getOption('pdfviewer') is NULL; please use 'options(pdfviewer=...)'

Martin

"Karl Forner" <karl.forner at gmail.com> writes:

> Hello,
>
> I'm using R 2.7.0 on Ubuntu 8.04 x86_64. I just installed bioconductor using
> the standard procedure, and I'm not able to see the vignettes.
>
>> openPDF("/usr/share/gnome/help/user-guide/C/user-guide.pdf")
> sh: /usr/share/gnome/help/user-guide/C/user-guide.pdf: Permission denied
>
>
> By looking at the openPDF code, the problem is that the "pdfviewer" option
> is set to "", instead of null or to the right value.
> So a fix is for example :
>> options(pdfviewer="evince")
>
> So I suppose there are 3 bugs :
>
>    1. the pdfviewer is not set to the appropriate value for the ubuntu
>    distrib (probably related to the packagers).
>    2. The empty strign value is not checked in the openPDF function.
>    3. The error message (triggered by a null pdfviewer option) seems
>    inaccurate :  "run the command setOptionPdfViewer()", because the
>    setOptionPdfViewer does not seem to be defined in my context.
>
> Karl
>
> 	[[alternative HTML version deleted]]
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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