Re: [R] command option for R CMD BATCH
Thanks.
R.
On Thursday 23 November 2006 16:32, Prof Brian Ripley wrote:
On Thu, 23 Nov 2006, Ramon Diaz-Uriarte wrote:
On Thursday 23 November 2006 15:44, Prof Brian Ripley wrote:
Try this:
gannet% cat month.R
x - commandArgs()
print(x[length(x)])
gannet% R --slave --args January month.R
[1] January
Is the above
R --slave --args January month.R
the preferred way of using it?
Yes it is. That's exactly what --args was added to allow.
I tend to use
R --slave month.R January
instead (as a consequence of reconverting former scripts that used R CMD
BATCH). The second call produces a ARGUMENT 'January' __ignored__ but
otherwise seems to do the same thing.
--
Ramón Díaz-Uriarte
Bioinformatics
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900
http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
(http://ligarto.org/rdiaz/0xE89B3462.asc)
**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en s...{{dropped}}
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[R] command option for R CMD BATCH
I wish to use R CMD BATCH to run a small R function which reads a text
file and plots a single graph to a PDF file.
version
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 4.0
year 2006
month 10
day03
svn rev39566
language R
version.string R version 2.4.0 (2006-10-03)
The text files are monthly data, (called lyrical names like
October.txt or November.txt) and the end result of each run will be a
PDF file called October.pdf, etc.
It's simple enough to make a separate file for each month which has
the command to call the R function, e.g. October.r would be
plot.month(October.txt)
and use it like so:
R CMD BATCH October.r /dev/null
(the R function creates the name for the PDF file)
or slightly more elegantly, a one line shell script that takes an argument:
R CMD BATCH $1.r /dev/null
(so that the script name and the name of the month will make a PDF
file for that month)
What I'd like to do is avoid the need to make the Month.r files and
have the script pass the month information directly to the function
that a single .r file would call. If I brushed up on a bit of Perl, I
might work out how to modify the shell script to do such a thing, but
I suspect it should be simpler than that.
I had thought of using litter for such a thing, but as I looked into
it, I get the impression that's not the idea of litter. (I'm also a
bit reluctant to recompile R.)
Ideas welcome.
Thanks
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_Middle minds discuss events
(:_~*~_:)Small minds discuss people
(_)-(_) . Anon
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] command option for R CMD BATCH
Patrick Connolly p_connolly at ihug.co.nz writes: What I'd like to do is avoid the need to make the Month.r files and have the script pass the month information directly to the function that a single .r file would call. ?commandArgs __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] command option for R CMD BATCH
Try this: gannet% cat month.R x - commandArgs() print(x[length(x)]) gannet% R --slave --args January month.R [1] January On Thu, 23 Nov 2006, Patrick Connolly wrote: I wish to use R CMD BATCH to run a small R function which reads a text file and plots a single graph to a PDF file. version _ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 4.0 year 2006 month 10 day03 svn rev39566 language R version.string R version 2.4.0 (2006-10-03) The text files are monthly data, (called lyrical names like October.txt or November.txt) and the end result of each run will be a PDF file called October.pdf, etc. It's simple enough to make a separate file for each month which has the command to call the R function, e.g. October.r would be plot.month(October.txt) and use it like so: R CMD BATCH October.r /dev/null (the R function creates the name for the PDF file) or slightly more elegantly, a one line shell script that takes an argument: R CMD BATCH $1.r /dev/null (so that the script name and the name of the month will make a PDF file for that month) What I'd like to do is avoid the need to make the Month.r files and have the script pass the month information directly to the function that a single .r file would call. If I brushed up on a bit of Perl, I might work out how to modify the shell script to do such a thing, but I suspect it should be simpler than that. I had thought of using litter for such a thing, but as I looked into it, I get the impression that's not the idea of litter. (I'm also a bit reluctant to recompile R.) Ideas welcome. Thanks -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] command option for R CMD BATCH
On Thursday 23 November 2006 15:44, Prof Brian Ripley wrote:
Try this:
gannet% cat month.R
x - commandArgs()
print(x[length(x)])
gannet% R --slave --args January month.R
[1] January
Is the above
R --slave --args January month.R
the preferred way of using it?
I tend to use
R --slave month.R January
instead (as a consequence of reconverting former scripts that used R CMD
BATCH). The second call produces a ARGUMENT 'January' __ignored__ but
otherwise seems to do the same thing.
Thanks,
R.
On Thu, 23 Nov 2006, Patrick Connolly wrote:
I wish to use R CMD BATCH to run a small R function which reads a text
file and plots a single graph to a PDF file.
version
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 4.0
year 2006
month 10
day03
svn rev39566
language R
version.string R version 2.4.0 (2006-10-03)
The text files are monthly data, (called lyrical names like
October.txt or November.txt) and the end result of each run will be a
PDF file called October.pdf, etc.
It's simple enough to make a separate file for each month which has
the command to call the R function, e.g. October.r would be
plot.month(October.txt)
and use it like so:
R CMD BATCH October.r /dev/null
(the R function creates the name for the PDF file)
or slightly more elegantly, a one line shell script that takes an
argument: R CMD BATCH $1.r /dev/null
(so that the script name and the name of the month will make a PDF
file for that month)
What I'd like to do is avoid the need to make the Month.r files and
have the script pass the month information directly to the function
that a single .r file would call. If I brushed up on a bit of Perl, I
might work out how to modify the shell script to do such a thing, but
I suspect it should be simpler than that.
I had thought of using litter for such a thing, but as I looked into
it, I get the impression that's not the idea of litter. (I'm also a
bit reluctant to recompile R.)
Ideas welcome.
Thanks
--
Ramón Díaz-Uriarte
Bioinformatics
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900
http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
(http://ligarto.org/rdiaz/0xE89B3462.asc)
**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en s...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] command option for R CMD BATCH
On Thu, 23 Nov 2006, Ramon Diaz-Uriarte wrote: On Thursday 23 November 2006 15:44, Prof Brian Ripley wrote: Try this: gannet% cat month.R x - commandArgs() print(x[length(x)]) gannet% R --slave --args January month.R [1] January Is the above R --slave --args January month.R the preferred way of using it? Yes it is. That's exactly what --args was added to allow. I tend to use R --slave month.R January instead (as a consequence of reconverting former scripts that used R CMD BATCH). The second call produces a ARGUMENT 'January' __ignored__ but otherwise seems to do the same thing. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] command option for R CMD BATCH
On Thu, 23-Nov-2006 at 02:44PM +, Prof Brian Ripley wrote:
| Try this:
|
| gannet% cat month.R
| x - commandArgs()
| print(x[length(x)])
|
| gannet% R --slave --args January month.R
| [1] January
That's exactly what I needed. Thank you Brian for a concise and
thorough answer.
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_Middle minds discuss events
(:_~*~_:)Small minds discuss people
(_)-(_) . Anon
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
