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

[Henrik Bengtsson]

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
 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  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 <
>> neilander...@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 Lüneburg
>> > Rotenbleicher Weg 67
>> > 21335 Lueneburg
>> > Germany
>> >
>> > Twitter: @foodsecbio
>> > email: coll...@leuphana.de
>> > Google Scholar
>> > <
>> https://scholar.google.com.au/citations?hl=en=xVdc-dsJ_op=list_works=pubdate
>> >
>> > Ideas for Sustainability 
>> >
>> >   [[alternative HTML version deleted]]
>> >
>> > __
>> > R-devel@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.hu...@embl.de
>> http://www.huber.embl.de
>>
>>
>>
>>
>>
>>
>>
>>

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

[Neil French Collier]

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  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 <
> neilander...@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 Lüneburg
> > Rotenbleicher Weg 67
> > 21335 Lueneburg
> > Germany
> >
> > Twitter: @foodsecbio
> > email: coll...@leuphana.de
> > Google Scholar
> > <
> https://scholar.google.com.au/citations?hl=en=xVdc-dsJ_op=list_works=pubdate
> >
> > Ideas for Sustainability 
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-devel@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.hu...@embl.de
> http://www.huber.embl.de
>
>
>
>
>
>
>
>
>
>


-- 
Cheers,

Neil

Neil French Collier, PhD
Faculty of Sustainability
Leuphana University Lüneburg
Rotenbleicher Weg 67
21335 Lueneburg
Germany

Twitter: @foodsecbio
email: coll...@leuphana.de
Google Scholar

Ideas for Sustainability 

[[alternative HTML version deleted]]

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

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

[Wolfgang Huber]

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  
> 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 Lüneburg
> Rotenbleicher Weg 67
> 21335 Lueneburg
> Germany
> 
> Twitter: @foodsecbio
> email: coll...@leuphana.de
> Google Scholar
> 
> Ideas for Sustainability 
> 
>   [[alternative HTML version deleted]]
> 
> __
> R-devel@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.hu...@embl.de
http://www.huber.embl.de

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

[Neil French Collier]

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 Lüneburg
Rotenbleicher Weg 67
21335 Lueneburg
Germany

Twitter: @foodsecbio
email: coll...@leuphana.de
Google Scholar

Ideas for Sustainability 

[[alternative HTML version deleted]]

__
R-devel@r-project.org mailing list
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