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R not responding (must force quit) when saving graphic to PDF (bug?)

4 messages · Neil French Collier, Wolfgang Huber, Henrik Bengtsson

#
Dear colleagues,

I wish to report a problem I encounter when trying to save a graphic to
file. When I produce a graphic and try to save it R becomes unresponsive
and I must force quit, and then restart R. The problem occurs when I try to
overwrite an existing graphic: for example when I made changes to the
graphic and want to save the graphic using the original file name. It only
happens when I use the menus to save files, not using script. It doesn't
happen when I save it as a new file. So, like this:

1. Make the graphic
2. Click File -> Save -> click on existing file name
3. Colour wheel appears and R is unresponsive.

Reproducible example:

x <- seq(1,10)
y <- x^2
plot(x,y, type="l") # Save as new file, all fine.

#Change plot and save as old plot file name:

plot(x,y, type="l", col=2)

# Click File -> Save
# 'Save quartz to PDF file' box opens
# Click on existing file name
# Colour wheel

Here is the sessionInfo():

R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.1 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

I'm not sure if this is worthy of reporting but I was encouraged to submit
a report. It doesn't really make a huge impact on my workflow, but it can
be annoying.
#
Dear Neil

Have you tried with completely uninstalling your R, and reinstalling a more recent version (e.g. 3.2.4 right now).
And then the same with your operating system - OS X is currently at 10.11.4.
There is likely not much interest (or benefit) in chasing such things in obsolete versions.

And I think R-help would be the more appropriate place for this kind of question.
	Wolfgang
Wolfgang

Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
Genome Biology Unit
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

wolfgang.huber at embl.de
http://www.huber.embl.de
#
Dear Wolfgang,

Thanks for your response.

No, I haven't tried doing the complete reinstallation as you suggest. If I
recall correctly, this has happened on previous occasions but like I said
in my email it's not all that disruptive to my workflow. It's more like a
'first world problem'.

I was encouraged to submit the query because I had correspondence with
someone involved with R development: "this shouldn't be happening" was the
advice I received. I use R a lot but I'm not deeply knowledgable about it's
inner workings.

To be frank, I really don't care if this is resolved. I was just trying to
help the R development group after receiving advice that it might be
important.

Again, thanks for your help.

Cheers

Neil
On Mon, Apr 11, 2016 at 6:41 PM, Wolfgang Huber <whuber at embl.de> wrote:

            

  
    
#
I'm not an OS X user, but two things you might look into/help you troubleshoot:

1. Because you said it only happens when you try to overwrite an
existing PDF, could it be that there is another process holding onto
(=locking) the PDF file that you're trying to write to?  For instance,
are you viewing it at the same time?

2. What happens if you create a dummy dummy.txt file, and then try to
overwrite that (with the same name - so no *.pdf)?  Does that work/not
work?  If it works, it means there's something special with *.pdf
files.  If not, then ... ?!?.

My $.02

/Henrik

PS. I think Wolfgang's point is that few people will spent time
troubleshooting obsolete versions of R (unless they're on the same
version), meaning the chances for feedback/troubleshooting on this is
much smaller than if it could be confirmed we a more up-to-date
version of R.  Because if it does given a problem in a new version,
there is nothing really to fix.  Having said this, any feedback that
might >= 1 person is always useful.


On Mon, Apr 11, 2016 at 2:35 PM, Neil French Collier
<neilandertal at gmail.com> wrote: