Re: [R] Runing R in a bash script
Prof Brian Ripley wrote:
> On Wed, 18 Apr 2007, Ulrik Stervbo wrote:
>
>> As I har problems installing the Cairo package, I went for Henriks solution
>> - and it works almost perfect. I would like to have been able to generate
>> transparent png.
>
> You cannot do transparency via postscript.
>
> I would suggest using pdf() and converting the output of that, which often
> works even better (and does have full transparency support).
Cairo also has full transparency support, both for png and pdf.
Ulrik, I presume the problem you ran into was the absence of the cairo
library dependency:
configure: error: Cannot find cairo.h! Please install cairo
(http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS
correspondingly.
which has it's own library dependencies as well. Most all Linux
distributions (I'm presuming you're running Linux) have ways to install
these dependencies easily: apt-get, rpm, etc.
Otherwise, if you had other problems installing Cairo, please let me
know and I can fix them.
Jeff
>
>> Thanks for the help
>> Ulrik
>>
>> On 18/04/07, Henrik Bengtsson <[EMAIL PROTECTED]> wrote:
>>> Or see png2() in R.utils, which imitates png() but uses bitmap(),
>>> which in turn uses postscript-to-png via ghostscript. BTW, personally
>>> I think PNGs generated via bitmap() look way better than the ones
>>> generated via png().
>
> As there are two separate versions of png() for different OSes, comments
> like that are very system-dependent. Other postings suggest this is
> Windows, and if png() is giving poor results there it suggests a problem
> with the way Windows' GDI is configured (which depends on the graphics
> card).
>
> And of course, PNGs don't 'look' at all: they are rendered by some other
> tool, and quite often the perceived problem with R graphical output is in
> fact with the rendering tool.
>
>>> /Henrik
>>>
>>> On 4/17/07, Jeffrey Horner <[EMAIL PROTECTED]> wrote:
Ulrik Stervbo wrote:
> Hello!
>
> I am having issues trying to plot to a ong (or jpg) when the R-code
>>> in a
> bash script is executed from cron.
>
> I can generate a pdf file, but when I try to write to a png, the file
>>> is
> created, but nothing is written. If I execute the bash script from my
> console, everything works file. Any ideas?
>
> In my cron I have SHELL=/bin/bash - otherwise /bin/shell is used and
>>> the
> folowing enery, so example is executed every minute
> * * * * * [path]/example.sh
>
> I am running
> R version 2.4.1 (2006-12-18)
>
> Here's a minimal example - two files one R-script ('example.r') and
>>> one
> bash-script ('example.sh')
>
> example.r
> # Example R-script
> x <- c(1:10)
> y <- x^2
> png(file="example2.png")
> #pdf(file="example2.pdf")
> plot(x,y)
> graphics.off()
>
> example.sh
> #/bin/bash
> #
> # Hello world is written to exhotext every time cron executes this
>>> script
> echo "Hello world" > echotext
> # This works, but not when executed from cron
> n=`R --save < example.r`
> # using exec as in `exec R --save < example.r` dosent work with cron
either
> # This also works, but nothing is written to the png when executed
from cron
> R --save < x <- c(1:10)
> y <- x^2
> png(file="example2.png")
> #pdf(file="example2.pdf")
> plot(x,y)
> graphics.off()
> #dev.off() dosent work at all when executed from cron
> RSCRIPT
The png() device requires an X server for the image rendering. You might
be able to get away with exporting the DISPLAY environment variable
export DISPLAY=:0.0 # try and connect to X server on display 0.0
within your script, but it will only work if the script is executed by
the same user as is running the X server, *and* the X server is running
at the time the script is executed.
There are a handful of packages that will create a png without the
presence of an X server, and I'm partial to Cairo (since I've done some
work on it). You can install the latest version like this:
install.packages("Cairo",,'http://rforge.net/',type='source')
Cairo can also outputs nice pdf's with embedded fonts... useful if you
want to embed high-quality OpenType or TrueType fonts.
Best,
Jeff
--
http://biostat.mc.vanderbilt.edu/JeffreyHorner
__
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] Runing R in a bash script
On Wed, 18 Apr 2007, Ulrik Stervbo wrote:
> As I har problems installing the Cairo package, I went for Henriks solution
> - and it works almost perfect. I would like to have been able to generate
> transparent png.
You cannot do transparency via postscript.
I would suggest using pdf() and converting the output of that, which often
works even better (and does have full transparency support).
> Thanks for the help
> Ulrik
>
> On 18/04/07, Henrik Bengtsson <[EMAIL PROTECTED]> wrote:
>>
>> Or see png2() in R.utils, which imitates png() but uses bitmap(),
>> which in turn uses postscript-to-png via ghostscript. BTW, personally
>> I think PNGs generated via bitmap() look way better than the ones
>> generated via png().
As there are two separate versions of png() for different OSes, comments
like that are very system-dependent. Other postings suggest this is
Windows, and if png() is giving poor results there it suggests a problem
with the way Windows' GDI is configured (which depends on the graphics
card).
And of course, PNGs don't 'look' at all: they are rendered by some other
tool, and quite often the perceived problem with R graphical output is in
fact with the rendering tool.
>> /Henrik
>>
>> On 4/17/07, Jeffrey Horner <[EMAIL PROTECTED]> wrote:
>>> Ulrik Stervbo wrote:
>>> > Hello!
>>> >
>>> > I am having issues trying to plot to a ong (or jpg) when the R-code
>> in a
>>> > bash script is executed from cron.
>>> >
>>> > I can generate a pdf file, but when I try to write to a png, the file
>> is
>>> > created, but nothing is written. If I execute the bash script from my
>>> > console, everything works file. Any ideas?
>>> >
>>> > In my cron I have SHELL=/bin/bash - otherwise /bin/shell is used and
>> the
>>> > folowing enery, so example is executed every minute
>>> > * * * * * [path]/example.sh
>>> >
>>> > I am running
>>> > R version 2.4.1 (2006-12-18)
>>> >
>>> > Here's a minimal example - two files one R-script ('example.r') and
>> one
>>> > bash-script ('example.sh')
>>> >
>>> > example.r
>>> > # Example R-script
>>> > x <- c(1:10)
>>> > y <- x^2
>>> > png(file="example2.png")
>>> > #pdf(file="example2.pdf")
>>> > plot(x,y)
>>> > graphics.off()
>>> >
>>> > example.sh
>>> > #/bin/bash
>>> > #
>>> > # Hello world is written to exhotext every time cron executes this
>> script
>>> > echo "Hello world" > echotext
>>> > # This works, but not when executed from cron
>>> > n=`R --save < example.r`
>>> > # using exec as in `exec R --save < example.r` dosent work with cron
>>> either
>>> > # This also works, but nothing is written to the png when executed
>>> from cron
>>> > R --save <>> > x <- c(1:10)
>>> > y <- x^2
>>> > png(file="example2.png")
>>> > #pdf(file="example2.pdf")
>>> > plot(x,y)
>>> > graphics.off()
>>> > #dev.off() dosent work at all when executed from cron
>>> > RSCRIPT
>>>
>>> The png() device requires an X server for the image rendering. You might
>>> be able to get away with exporting the DISPLAY environment variable
>>>
>>> export DISPLAY=:0.0 # try and connect to X server on display 0.0
>>>
>>> within your script, but it will only work if the script is executed by
>>> the same user as is running the X server, *and* the X server is running
>>> at the time the script is executed.
>>>
>>> There are a handful of packages that will create a png without the
>>> presence of an X server, and I'm partial to Cairo (since I've done some
>>> work on it). You can install the latest version like this:
>>>
>>> install.packages("Cairo",,'http://rforge.net/',type='source')
>>>
>>> Cairo can also outputs nice pdf's with embedded fonts... useful if you
>>> want to embed high-quality OpenType or TrueType fonts.
>>>
>>> Best,
>>>
>>> Jeff
>>> --
>>> http://biostat.mc.vanderbilt.edu/JeffreyHorner
>>>
>>> __
>>> 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.
>>>
>>
>
> [[alternative HTML version deleted]]
>
> __
> 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.
>
--
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] Runing R in a bash script
As I har problems installing the Cairo package, I went for Henriks solution
- and it works almost perfect. I would like to have been able to generate
transparent png.
Thanks for the help
Ulrik
On 18/04/07, Henrik Bengtsson <[EMAIL PROTECTED]> wrote:
>
> Or see png2() in R.utils, which imitates png() but uses bitmap(),
> which in turn uses postscript-to-png via ghostscript. BTW, personally
> I think PNGs generated via bitmap() look way better than the ones
> generated via png().
>
> /Henrik
>
> On 4/17/07, Jeffrey Horner <[EMAIL PROTECTED]> wrote:
> > Ulrik Stervbo wrote:
> > > Hello!
> > >
> > > I am having issues trying to plot to a ong (or jpg) when the R-code
> in a
> > > bash script is executed from cron.
> > >
> > > I can generate a pdf file, but when I try to write to a png, the file
> is
> > > created, but nothing is written. If I execute the bash script from my
> > > console, everything works file. Any ideas?
> > >
> > > In my cron I have SHELL=/bin/bash - otherwise /bin/shell is used and
> the
> > > folowing enery, so example is executed every minute
> > > * * * * * [path]/example.sh
> > >
> > > I am running
> > > R version 2.4.1 (2006-12-18)
> > >
> > > Here's a minimal example - two files one R-script ('example.r') and
> one
> > > bash-script ('example.sh')
> > >
> > > example.r
> > > # Example R-script
> > > x <- c(1:10)
> > > y <- x^2
> > > png(file="example2.png")
> > > #pdf(file="example2.pdf")
> > > plot(x,y)
> > > graphics.off()
> > >
> > > example.sh
> > > #/bin/bash
> > > #
> > > # Hello world is written to exhotext every time cron executes this
> script
> > > echo "Hello world" > echotext
> > > # This works, but not when executed from cron
> > > n=`R --save < example.r`
> > > # using exec as in `exec R --save < example.r` dosent work with cron
> > either
> > > # This also works, but nothing is written to the png when executed
> > from cron
> > > R --save < > > x <- c(1:10)
> > > y <- x^2
> > > png(file="example2.png")
> > > #pdf(file="example2.pdf")
> > > plot(x,y)
> > > graphics.off()
> > > #dev.off() dosent work at all when executed from cron
> > > RSCRIPT
> >
> > The png() device requires an X server for the image rendering. You might
> > be able to get away with exporting the DISPLAY environment variable
> >
> > export DISPLAY=:0.0 # try and connect to X server on display 0.0
> >
> > within your script, but it will only work if the script is executed by
> > the same user as is running the X server, *and* the X server is running
> > at the time the script is executed.
> >
> > There are a handful of packages that will create a png without the
> > presence of an X server, and I'm partial to Cairo (since I've done some
> > work on it). You can install the latest version like this:
> >
> > install.packages("Cairo",,'http://rforge.net/',type='source')
> >
> > Cairo can also outputs nice pdf's with embedded fonts... useful if you
> > want to embed high-quality OpenType or TrueType fonts.
> >
> > Best,
> >
> > Jeff
> > --
> > http://biostat.mc.vanderbilt.edu/JeffreyHorner
> >
> > __
> > 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.
> >
>
[[alternative HTML version deleted]]
__
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] Runing R in a bash script
Or see png2() in R.utils, which imitates png() but uses bitmap(),
which in turn uses postscript-to-png via ghostscript. BTW, personally
I think PNGs generated via bitmap() look way better than the ones
generated via png().
/Henrik
On 4/17/07, Jeffrey Horner <[EMAIL PROTECTED]> wrote:
> Ulrik Stervbo wrote:
> > Hello!
> >
> > I am having issues trying to plot to a ong (or jpg) when the R-code in a
> > bash script is executed from cron.
> >
> > I can generate a pdf file, but when I try to write to a png, the file is
> > created, but nothing is written. If I execute the bash script from my
> > console, everything works file. Any ideas?
> >
> > In my cron I have SHELL=/bin/bash - otherwise /bin/shell is used and the
> > folowing enery, so example is executed every minute
> > * * * * * [path]/example.sh
> >
> > I am running
> > R version 2.4.1 (2006-12-18)
> >
> > Here's a minimal example - two files one R-script ('example.r') and one
> > bash-script ('example.sh')
> >
> > example.r
> > # Example R-script
> > x <- c(1:10)
> > y <- x^2
> > png(file="example2.png")
> > #pdf(file="example2.pdf")
> > plot(x,y)
> > graphics.off()
> >
> > example.sh
> > #/bin/bash
> > #
> > # Hello world is written to exhotext every time cron executes this script
> > echo "Hello world" > echotext
> > # This works, but not when executed from cron
> > n=`R --save < example.r`
> > # using exec as in `exec R --save < example.r` dosent work with cron
> either
> > # This also works, but nothing is written to the png when executed
> from cron
> > R --save < > x <- c(1:10)
> > y <- x^2
> > png(file="example2.png")
> > #pdf(file="example2.pdf")
> > plot(x,y)
> > graphics.off()
> > #dev.off() dosent work at all when executed from cron
> > RSCRIPT
>
> The png() device requires an X server for the image rendering. You might
> be able to get away with exporting the DISPLAY environment variable
>
> export DISPLAY=:0.0 # try and connect to X server on display 0.0
>
> within your script, but it will only work if the script is executed by
> the same user as is running the X server, *and* the X server is running
> at the time the script is executed.
>
> There are a handful of packages that will create a png without the
> presence of an X server, and I'm partial to Cairo (since I've done some
> work on it). You can install the latest version like this:
>
> install.packages("Cairo",,'http://rforge.net/',type='source')
>
> Cairo can also outputs nice pdf's with embedded fonts... useful if you
> want to embed high-quality OpenType or TrueType fonts.
>
> Best,
>
> Jeff
> --
> http://biostat.mc.vanderbilt.edu/JeffreyHorner
>
> __
> 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.
>
__
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] Runing R in a bash script
Ulrik Stervbo wrote:
> Hello!
>
> I am having issues trying to plot to a ong (or jpg) when the R-code in a
> bash script is executed from cron.
>
> I can generate a pdf file, but when I try to write to a png, the file is
> created, but nothing is written. If I execute the bash script from my
> console, everything works file. Any ideas?
>
> In my cron I have SHELL=/bin/bash - otherwise /bin/shell is used and the
> folowing enery, so example is executed every minute
> * * * * * [path]/example.sh
>
> I am running
> R version 2.4.1 (2006-12-18)
>
> Here's a minimal example - two files one R-script ('example.r') and one
> bash-script ('example.sh')
>
> example.r
> # Example R-script
> x <- c(1:10)
> y <- x^2
> png(file="example2.png")
> #pdf(file="example2.pdf")
> plot(x,y)
> graphics.off()
>
> example.sh
> #/bin/bash
> #
> # Hello world is written to exhotext every time cron executes this script
> echo "Hello world" > echotext
> # This works, but not when executed from cron
> n=`R --save < example.r`
> # using exec as in `exec R --save < example.r` dosent work with cron
either
> # This also works, but nothing is written to the png when executed
from cron
> R --save < x <- c(1:10)
> y <- x^2
> png(file="example2.png")
> #pdf(file="example2.pdf")
> plot(x,y)
> graphics.off()
> #dev.off() dosent work at all when executed from cron
> RSCRIPT
The png() device requires an X server for the image rendering. You might
be able to get away with exporting the DISPLAY environment variable
export DISPLAY=:0.0 # try and connect to X server on display 0.0
within your script, but it will only work if the script is executed by
the same user as is running the X server, *and* the X server is running
at the time the script is executed.
There are a handful of packages that will create a png without the
presence of an X server, and I'm partial to Cairo (since I've done some
work on it). You can install the latest version like this:
install.packages("Cairo",,'http://rforge.net/',type='source')
Cairo can also outputs nice pdf's with embedded fonts... useful if you
want to embed high-quality OpenType or TrueType fonts.
Best,
Jeff
--
http://biostat.mc.vanderbilt.edu/JeffreyHorner
__
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.
[R] Runing R in a bash script
Hello!
I am having issues trying to plot to a ong (or jpg) when the R-code in a
bash script is executed from cron.
I can generate a pdf file, but when I try to write to a png, the file is
created, but nothing is written. If I execute the bash script from my
console, everything works file. Any ideas?
In my cron I have SHELL=/bin/bash - otherwise /bin/shell is used and the
folowing enery, so example is executed every minute
* * * * * [path]/example.sh
I am running
R version 2.4.1 (2006-12-18)
Here's a minimal example - two files one R-script ('example.r') and one
bash-script ('example.sh')
example.r
# Example R-script
x <- c(1:10)
y <- x^2
png(file="example2.png")
#pdf(file="example2.pdf")
plot(x,y)
graphics.off()
example.sh
#/bin/bash
#
# Hello world is written to exhotext every time cron executes this script
echo "Hello world" > echotext
# This works, but not when executed from cron
n=`R --save < example.r`
# using exec as in `exec R --save < example.r` dosent work with cron either
# This also works, but nothing is written to the png when executed from cron
R --save
