[R-pkg-devel] R CMD BATCH plot output

[Josiah Parry]

Hey folks! I am working with R CMD BATCH and providing a providing a
logfile output e.g.

R CMD BATCH main.R 2024-07-28.log

This creates the desired log file with the contents of stdout and stderr.

However, if plots are generated in the process, the plots are stored in
Rplots.pdf.

Is there a way via command line arguments to change the name of the pdf
output.

There might be multiple runs of this script and it would be ideal to store
the plot output independently.

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Re: [R-pkg-devel] R CMD BATCH plot output

[Duncan Murdoch]

On 2024-07-28 1:48 p.m., Josiah Parry wrote:

Hey folks! I am working with R CMD BATCH and providing a providing a
logfile output e.g.

R CMD BATCH main.R 2024-07-28.log

This creates the desired log file with the contents of stdout and stderr.

However, if plots are generated in the process, the plots are stored in
Rplots.pdf.

Is there a way via command line arguments to change the name of the pdf
output.

There might be multiple runs of this script and it would be ideal to store
the plot output independently.


That's the default filename if you open a PDF device.  Open it 
explicitly and you can specify any file you like.


That is,

  plot(rnorm(100))

will call dev.new() which in a non-interactive session calls pdf().  If 
you specify


  dev.new(file = "something.pdf")
  plot(rnorm(100))

the "file" argument will be ignored in an interactive session, but will 
be used in a non-interactive one.


Duncan Murdoch

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Re: [R-pkg-devel] R CMD BATCH plot output

[Josiah Parry]

Thanks, Duncan!

Is there a way to override this using the command line arguments?

I'd like to be able to have a generalizable way to address this without
having to modify R source code.

My understanding is that when there is a plot output, R CMD BATCH uses the
PDF device which is a fair default.

However, there is not any use of `dev.new()` or `pdf()` called anywhere in
the code.

On Sun, Jul 28, 2024 at 3:44 PM Duncan Murdoch 
wrote:

> On 2024-07-28 1:48 p.m., Josiah Parry wrote:
> > Hey folks! I am working with R CMD BATCH and providing a providing a
> > logfile output e.g.
> >
> > R CMD BATCH main.R 2024-07-28.log
> >
> > This creates the desired log file with the contents of stdout and stderr.
> >
> > However, if plots are generated in the process, the plots are stored in
> > Rplots.pdf.
> >
> > Is there a way via command line arguments to change the name of the pdf
> > output.
> >
> > There might be multiple runs of this script and it would be ideal to
> store
> > the plot output independently.
>
> That's the default filename if you open a PDF device.  Open it
> explicitly and you can specify any file you like.
>
> That is,
>
>plot(rnorm(100))
>
> will call dev.new() which in a non-interactive session calls pdf().  If
> you specify
>
>dev.new(file = "something.pdf")
>plot(rnorm(100))
>
> the "file" argument will be ignored in an interactive session, but will
> be used in a non-interactive one.
>
> Duncan Murdoch
>
>
>

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Re: [R-pkg-devel] R CMD BATCH plot output

[Ben Bolker]

Dirk Eddelbuettel would tell you to use his 'little r' script instead,
though not sure if it has this particular flexibility. You could wrap R CMD
BATCH in your own script that moved Rplots.pdf where you wanted it ...

On Sun, Jul 28, 2024, 4:05 PM Josiah Parry  wrote:

> Thanks, Duncan!
>
> Is there a way to override this using the command line arguments?
>
> I'd like to be able to have a generalizable way to address this without
> having to modify R source code.
>
> My understanding is that when there is a plot output, R CMD BATCH uses the
> PDF device which is a fair default.
>
> However, there is not any use of `dev.new()` or `pdf()` called anywhere in
> the code.
>
> On Sun, Jul 28, 2024 at 3:44 PM Duncan Murdoch 
> wrote:
>
> > On 2024-07-28 1:48 p.m., Josiah Parry wrote:
> > > Hey folks! I am working with R CMD BATCH and providing a providing a
> > > logfile output e.g.
> > >
> > > R CMD BATCH main.R 2024-07-28.log
> > >
> > > This creates the desired log file with the contents of stdout and
> stderr.
> > >
> > > However, if plots are generated in the process, the plots are stored in
> > > Rplots.pdf.
> > >
> > > Is there a way via command line arguments to change the name of the pdf
> > > output.
> > >
> > > There might be multiple runs of this script and it would be ideal to
> > store
> > > the plot output independently.
> >
> > That's the default filename if you open a PDF device.  Open it
> > explicitly and you can specify any file you like.
> >
> > That is,
> >
> >plot(rnorm(100))
> >
> > will call dev.new() which in a non-interactive session calls pdf().  If
> > you specify
> >
> >dev.new(file = "something.pdf")
> >plot(rnorm(100))
> >
> > the "file" argument will be ignored in an interactive session, but will
> > be used in a non-interactive one.
> >
> > Duncan Murdoch
> >
> >
> >
>
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>
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>

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Re: [R-pkg-devel] R CMD BATCH plot output

[Duncan Murdoch]

On 2024-07-28 4:05 p.m., Josiah Parry wrote:

Thanks, Duncan!

Is there a way to override this using the command line arguments?


I assume you could do that using commandArgs() in the dev.new() call, 
but I don't use BATCH.


I'd like to be able to have a generalizable way to address this without 
having to modify R source code.


Take a look at the source to dev.new().  It tries various things, maybe 
one of those will suit you.


My understanding is that when there is a plot output, R CMD BATCH uses 
the PDF device which is a fair default.


However, there is not any use of `dev.new()` or `pdf()` called anywhere 
in the code.


Not explicitly, but if you try to call a plot function with no device 
active, the graphics system will call dev.new().


Duncan Murdoch



On Sun, Jul 28, 2024 at 3:44 PM Duncan Murdoch > wrote:


On 2024-07-28 1:48 p.m., Josiah Parry wrote:
 > Hey folks! I am working with R CMD BATCH and providing a providing a
 > logfile output e.g.
 >
 > R CMD BATCH main.R 2024-07-28.log
 >
 > This creates the desired log file with the contents of stdout and
stderr.
 >
 > However, if plots are generated in the process, the plots are
stored in
 > Rplots.pdf.
 >
 > Is there a way via command line arguments to change the name of
the pdf
 > output.
 >
 > There might be multiple runs of this script and it would be ideal
to store
 > the plot output independently.

That's the default filename if you open a PDF device.  Open it
explicitly and you can specify any file you like.

That is,

    plot(rnorm(100))

will call dev.new() which in a non-interactive session calls pdf().  If
you specify

    dev.new(file = "something.pdf")
    plot(rnorm(100))

the "file" argument will be ignored in an interactive session, but will
be used in a non-interactive one.

Duncan Murdoch




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Re: [R-pkg-devel] R CMD BATCH plot output

[Dirk Eddelbuettel]

On 28 July 2024 at 15:44, Duncan Murdoch wrote:
| On 2024-07-28 1:48 p.m., Josiah Parry wrote:
| > However, if plots are generated in the process, the plots are stored in
| > Rplots.pdf.
| > 
| > Is there a way via command line arguments to change the name of the pdf
| > output.
| > 
| > There might be multiple runs of this script and it would be ideal to store
| > the plot output independently.
| 
| That's the default filename if you open a PDF device.  Open it

It's the default (and fallback) device and filename you fail to specify
something else. Ie 'Rscript -e "plot(1:10)"' will create it too.

My preferred alternative is to wrap call to plot() with actual device create
(something like 'if (!interactive()) pdf(my_filename, 8. 6)' with a
corresponding 'if (!interactive()) dev.off()' to ensure the file finalised
and close.

If we cannot (or do not want to) modify the given main.R, I would suggest
something along the lines of

  Rscript -e 'pdf(myfilenamevar); source("main.R"); dev.off()' | tee 
2024-07-28.log

and Bob's your uncle now in terms of how you spec the filename.

In short, I would let go of `R CMD BATCH` if it does not do what you want.

Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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