From henrik.bengtsson at gmail.com  Tue Apr 12 01:12:04 2016
From: henrik.bengtsson at gmail.com (Henrik Bengtsson)
Date: Mon, 11 Apr 2016 16:12:04 -0700
Subject: [Rd] R not responding (must force quit) when saving graphic to
 PDF (bug?)
In-Reply-To: <CAOVghqrOtFxJbnNwO=Ffhu2gZ_9dbFJk2ay=Wjk44c-YXBCq6A@mail.gmail.com>
References: <CAOVghqoNkdpqtcQM6jiVSRHS2qyuavtD+jpX_9JpfVLfhEfxtA@mail.gmail.com>
	<72F4E33B-416F-4745-99B0-9AA6DD500261@embl.de>
	<CAOVghqrOtFxJbnNwO=Ffhu2gZ_9dbFJk2ay=Wjk44c-YXBCq6A@mail.gmail.com>
Message-ID: <CAFDcVCTMtfgDQ531uP3Lz1L1Dpn6bU2HEAvSMKRkuYte0=CGxA@mail.gmail.com>

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:
> 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:
>
>> 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
>>
>> > On Apr 11, 2016, at 18:37 GMT+2, Neil French Collier <
>> neilandertal at gmail.com> wrote:
>> >
>> > 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.
>> >
>> > --
>> > Cheers,
>> >
>> > Neil
>> >
>> > Neil French Collier, PhD
>> > Faculty of Sustainability
>> > Leuphana University L?neburg
>> > Rotenbleicher Weg 67
>> > 21335 Lueneburg
>> > Germany
>> >
>> > Twitter: @foodsecbio
>> > email: collier at leuphana.de
>> > Google Scholar
>> > <
>> https://scholar.google.com.au/citations?hl=en&user=xVdc-dsAAAAJ&view_op=list_works&sortby=pubdate
>> >
>> > Ideas for Sustainability <https://ideas4sustainability.wordpress.com>
>> >
>> >       [[alternative HTML version deleted]]
>> >
>> > ______________________________________________
>> > R-devel at r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>
> --
> Cheers,
>
> Neil
>
> Neil French Collier, PhD
> Faculty of Sustainability
> Leuphana University L?neburg
> Rotenbleicher Weg 67
> 21335 Lueneburg
> Germany
>
> Twitter: @foodsecbio
> email: collier at leuphana.de
> Google Scholar
> <https://scholar.google.com.au/citations?hl=en&user=xVdc-dsAAAAJ&view_op=list_works&sortby=pubdate>
> Ideas for Sustainability <https://ideas4sustainability.wordpress.com>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] R not responding (must force quit) when saving graphic to PDF (bug?)
Henrik Bengtsson