Here is Dr. Leisch's advice for dealing with open handles (and it works):
On 4/5/2012 4:22 AM, Friedrich Leisch wrote:
...
You need to close the pdf device, not an open connection:
R Sweave(test.Rnw)
Writing to file test.tex
Processing code chunks with options ...
1 : keep.source term
On 04/04/2012 3:25 PM, Alexander Shenkin wrote:
Hello Folks,
When I run the document below through sweave, rgui.exe/rsession.exe
leaves a file handle open to the sweave-001.pdf graphic (as verified by
process explorer). Pdflatex.exe then crashes (with a Permission Denied
error) because the
Thanks for the nice ideas, Duncan. I think that would work nicely in
most cases. The major issue with that workflow in my case is that the
scripts to set up my workspace take around a half-hour to run (I really
wish CUDA was working with my setup!), so running R each time in that
case is
In terms of editors, I think RStudio is pretty good
(http://www.rstudio.org/download/preview). Or LyX
(http://yihui.name/knitr/demo/lyx/), or TeXmaker, WinEdit
(http://yihui.name/knitr/demo/editors/)... All of them start a new R
session when weaving the document, and all support one-click
Yep, I'm using RStudio, and have used Tinn-R in the past. RStudio does
start a new R session when processing a sweave document via the RStudio
GUI. In my case, this presented a problem for the reasons I stated
before (i.e. that I need to run sweave in the main environment, not a
new one).
Well, I do not think it is a good practice (in terms of reproducible
research) to keep on running Sweave in the same R session, because
your previous run and your current workspace could pollute your next
run. To make sure a document compiles on its own, it is better always
to start a new clean R
Reproducibility is important, and as I mentioned in a previous email,
there are probably ways I could avoid running the entire script over and
over again with each sweave compilation. Still, relying on saved
workspaces, temporary files or caches still has some of the issues that
working in the
Things are not that gory with knitr. You only need to use the option
cache=TRUE and it will take care of most of the things you mentioned.
For example, objects in a chunk are automatically saved and lazy
loaded; when code is modified, old cache will be automatically removed
and new cache will be
Hello Folks,
When I run the document below through sweave, rgui.exe/rsession.exe
leaves a file handle open to the sweave-001.pdf graphic (as verified by
process explorer). Pdflatex.exe then crashes (with a Permission Denied
error) because the graphic file is locked.
This only seems to happen
See ?closeAllConnections
Suggestion to the maintainer of Sweave: atomify the figure
generation, e.g. use { pdf(); on.exit(dev.off()); {...}; } or similar,
instead of { pdf(); {...}; dev.off(); } possibly by leaving a copy of
the fault figure file for troubleshooting.
/Henrik
On Wed, Apr 4, 2012
Thanks for the reply, Henrik. Process Explorer still shows the file
handle as being open, but R only shows the following:
showConnections(all=TRUE)
description class mode text isopen can read can write
0 stdin terminal r text opened yesno
1 stdoutterminal w text opened
Herik's suggestion is an absolutely good practice which guarantees the
device is always closed. That is what I did in the knitr package, so
you can probably take a look at http://yihui.name/knitr/
Regards,
Yihui
--
Yihui Xie xieyi...@gmail.com
Phone: 515-294-2465 Web: http://yihui.name
Department
12 matches
Mail list logo
