ubuntu configuration problem "Couldnt get a file descriptior referring to the console"

Paul,

| Greetings to everybody in r-sig-debian land.
| 
| I hope I have found the right place to ask this. If not, please refer me on...

No this is the right place. So welcome!
 
| I run R 2.9 on Ubuntu 9.04.  

That was 'a little underspecified'. "Whose R"? I.e. where did the binary come
from?  CRAN? Or from sources and you built it yourself?  What is the
architecture?

[ Ok, I figured it out comparing amd64 (at work) to i386 (at home). My
R-on-Ubuntu at home has the same problem. ]

| I believe many people have seen this
| problem, but because the error message is hard to understand, they
| have not traced it back to the R install in the distribution.  I think
| it ought to be fixed in the R packaging process, but I do not know if
| the problem begins with the Debian packaging or if someone at Ubuntu
| has caused it.
| 
| As far as I can see, any program that tries to spawn a pdf viewer
| fails with this somewhat uninformative error message:
| 
| > RShowDoc("frame", package="grid")
| > Couldnt get a file descriptor referring to the console
| 
| I've traced this back to  a setting in /etc/R/Renviron:
| 
| ## Default PDF viewer
| R_PDFVIEWER=${R_PDFVIEWER-'/bin/open'}

On my Ubuntu system at work (amd64, 2.9.0 binaries from CRAN using Vicent and
Michael's "Ubuntu re-builds" of my Debian packages) I have

$ grep -i pdf /etc/R/Renviron
R_PDFLATEXCMD=${R_PDFLATEXCMD-${PDFLATEX-'/usr/bin/pdflatex'}}
R_RD4PDF=${R_RD4PDF-'times,hyper'}
## Default PDF viewer
R_PDFVIEWER=${R_PDFVIEWER-'/usr/bin/xpdf'}
$

The '/usr/bin/xpdf' is actually an explicit setting, and we ensure xpdf is
present at built time.

On my Ubuntu system at home (i386, binaries from CRAN as well) I have the
same problem you diagnosed.  Now, I don;t use that machine much for R so I
never noticed...

This seems to be a genuine bug in the i386 CRAN builds, and I trust Vincent
and Michael will try to fix it.

| That setting causes the trouble--if it is changed to a valid pdf
| viewer, then the strange error message does not appear.  If your
| system has the OpenDesktop mime system in place, this setting will
| work:
| 
| # Default PDF viewer
| R_PDFVIEWER=${R_PDFVIEWER-'/usr/bin/xdg-open'}
| 
| I've also learned that within a session a pdf viewer can be set with options:
| 
| options(pdfviewer = "evince")

See help(Startup) -- you can also make that 'permanent' via the files in
either $(HOME) or below /etc/R/.

| Why does the existing configuration refer to /bin/open?  Can this be
| fixed by the packager so that users don't have to make this change?

We sure should try to fix it, esp as it comes from a pre-packaged binary.

Thanks,  Dirk


 
| Here is the post that says this is a debian-sig issue:
| http://www.nabble.com/Re:-unable-to-view-vignette-in-R-p20522903.html
| And I believe this problem has existed for a long time because:
| https://stat.ethz.ch/pipermail/r-help/2007-September/141178.html
| PJ
| 
| -- 
| Paul E. Johnson
| Professor, Political Science
| 1541 Lilac Lane, Room 504
| University of Kansas
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Three out of two people have difficulties with fractions.

Paul,

On 15 June 2009 at 08:49, Paul Johnson wrote:
| Greetings to everybody in r-sig-debian land.
|
| I hope I have found the right place to ask this. If not, please refer me on...

No this is the right place. So welcome!

| I run R 2.9 on Ubuntu 9.04.

That was 'a little underspecified'. "Whose R"? I.e. where did the binary come
from? ?CRAN? Or from sources and you built it yourself? ?What is the
architecture?

Ah, I'm using the ubuntu package from CRAN, I think. I download it
from the Iowa state mirror:

deb http://rh-mirror.linux.iastate.edu/CRAN/bin/linux/ubuntu jaunty/ #iastate R

[ Ok, I figured it out comparing amd64 (at work) to i386 (at home). My
R-on-Ubuntu at home has the same problem. ]

I've downloaded the R source code and I see where the problem
originates.  I think the DEB packages for ubuntu must be built on a
system that does not have any of the expected pdf viewers.  If you
look in the R configure script, it sets a macro variable for the
viewer

## PDF viewer
for ac_prog in ${R_PDFVIEWER} acroread acroread4 evince xpdf gv
gnome-gv ggv kghostview open gpdf

When I buld R on my system, it finds acroread and that gets put into
the /etc/R/Renviron file for the  PDFVIEWER.

On the system where R is built for CRAN, it must not find acroread,
evince, or anything until "open".

I *THINK* it might be slightly more "in style" to make the preferred
pdf viewer xdg-open.  I've had some ups and downs with xdg-open
because it is poorly documented (that's another trauma discussed
elsewhere).  But, if you are going by the Ubuntu community standard,
xdg-open should be first.

pj

Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas