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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793