[R-sig-Debian] ubuntu configuration problem "Couldnt get a file descriptior referring to the console"
Dirk Eddelbuettel
edd at debian.org
Mon Jun 15 16:18:46 CEST 2009
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?
[ 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
|
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