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]]

I just found a more elegant and permanent way to set the pdfviewer : just edit in the /etc/R/Renviron config file, the R_PDFVIEWER variable, e.g. R_PDFVIEWER=${R_PDFVIEWER-'evince'} Karl On Tue, Jun 3, 2008 at 4:50 PM, Karl Forner <karl.forner@gmail.com> wrote: > 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]]