Re: [R] running R from PHP
Perhaps this is a interesting starting point for you? http://steve.stat.tku.edu.tw/R_PHP/doR.html regards,christian Am Dienstag, 3. Februar 2004 03:26 schrieb [EMAIL PROTECTED]: I would like to construct a PHP script that runs R to generate a graphics file. Running R itself is no problem. However, it seems impossible to instantiate one of the graphics devices to create output. For example, the normal bitmap devices (e.g., jpeg, png, etc.) are derived from X11, which requires a display. This seems true, even if no output is ever directed to a real display. For some reason, the postscript device seems to suffer from similar problems. Is there a trick to creating a graphics device in the absence of an actual display in order to create an image in a file? Thanks for your help. Cheers, Brook __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] running R from PHP
[EMAIL PROTECTED] writes: Below are 2 scripts (png.R and pdf.R) I am trying to run in R from PHP. # png.R x11(display=:5) png(filename=g.png) plot(1:5) graphics.off() # pdf.R pdf(file=g.pdf) plot(1:5) graphics.off() Both run from terminals and png.R will run without a normal X server if Xvfb is running. Neither runs under PHP, though (when invoked as R --no-save xxx.R). They yield the following errors (with the R startup banner deleted for compactness): x11(display=:5) png(filename=g.png) Error in X11(paste(png::, filename, sep = ), width, height, pointsize, : unable to start device PNG In addition: Warning message: could not open PNG file `g.png' Execution halted and pdf(file=/usr/pkg/share/httpd/htdocs/test-R/g.pdf) Error in PDF(file, old$family, old$encoding, old$bg, old$fg, width, height, : unable to start device pdf In addition: Warning message: cannot open `pdf' file argument `/usr/pkg/share/httpd/htdocs/test-R/g.pdf' Execution halted For reference, the R banner information includes the following: R : Copyright 2003, The R Development Core Team Version 1.6.2 (2003-01-10) Any help on how to get these scripts to work is greatly appreciated. Your R version is about a year out of date, but that's hardly the issue. I don't do PHP, but the error message in both cases has to do with file opening, so how about checking permissions on your current directory: Try sticking this into your script system(id; pwd; ls -la) Also notice that web applications often take special security measures and may change one or all of the following: working directory, root directory, user id, and group id. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] running R from PHP
[EMAIL PROTECTED] wrote: Both run from terminals and png.R will run without a normal X server if Xvfb is running. Neither runs under PHP, though (when invoked as R --no-save xxx.R). They yield the following errors (with the R startup banner deleted for compactness): could not open PNG file `g.png' cannot open `pdf' file argument `/usr/pkg/share/httpd/htdocs/test-R/g.pdf' From the evidence above, I'd guess a file permission error. The web server probably runs as the user apache or something similar -- does that user have write permission to the place where you are trying to create the images? Try writing to /tmp/g.png and /tmp/g.pdf and see if the files get created. HTH, Joe __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] running R from PHP
On Tue, 3 Feb 2004, Philippe Glaziou wrote: @biology.nmsu.edu [EMAIL PROTECTED] wrote: I would like to construct a PHP script that runs R to generate a graphics file. Running R itself is no problem. However, it seems impossible to instantiate one of the graphics devices to create output. For example, the normal bitmap devices (e.g., jpeg, png, etc.) are derived from X11, which requires a display. This seems true, even if no output is ever directed to a real display. It _is_ documented on the help page, and output _is_ directed to a real display: you just mever see it. It is possible make use a virtual display such as that provided by Xvfb. For some reason, the postscript device seems to suffer from similar problems. Is there a trick to creating a graphics device in the absence of an actual display in order to create an image in a file? If you need a bitmap graphic file, I would suggest the use of ImageMagick: You may as well use the bitmap() device built into R, which is also a wrapper for the use of ghostscript. That too is described on the help page. I have never seen a reported problem with getting postscript output from a script. After reading the posting guide, please give us some useful details of what happened. cunegonde:~/tmp ls foo cunegonde:~/tmp cat foo pdf(file=g.pdf) plot(1:5) dev.off() cunegonde:~/tmp R --no-save foo/dev/null convert g.pdf g.png cunegonde:~/tmp ls -g -rw---1 glaziou 3374 2004-02-03 11:58 g.pdf -rw---1 glaziou 4115 2004-02-03 11:58 g.png -rw---1 glaziou80 2004-02-03 11:58 foo This works from a unix console without X running (the postcript device works similarly on my machine). R can easily be fed this way with a file and parameters passed from a php script. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] running R from PHP
[EMAIL PROTECTED] wrote: Is there a trick to creating a graphics device in the absence of an actual display in order to create an image in a file? Look for Xvfb (X virtual frame buffer). Not sure what OS you are running, but on RH9 and Fedora, at least, there is a package called XFree86-Xvfb. I use Xvfb with the following command: /usr/X11R6/bin/Xvfb :5 -screen 0 1024x768x16 More specifically I wrote an init script and set Xvfb up to start as a service on boot. Then in R I use: x11(display=:5) HTH, Joe __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] running R from PHP
@biology.nmsu.edu [EMAIL PROTECTED] wrote: I would like to construct a PHP script that runs R to generate a graphics file. Running R itself is no problem. However, it seems impossible to instantiate one of the graphics devices to create output. For example, the normal bitmap devices (e.g., jpeg, png, etc.) are derived from X11, which requires a display. This seems true, even if no output is ever directed to a real display. For some reason, the postscript device seems to suffer from similar problems. Is there a trick to creating a graphics device in the absence of an actual display in order to create an image in a file? If you need a bitmap graphic file, I would suggest the use of ImageMagick: cunegonde:~/tmp ls foo cunegonde:~/tmp cat foo pdf(file=g.pdf) plot(1:5) dev.off() cunegonde:~/tmp R --no-save foo/dev/null convert g.pdf g.png cunegonde:~/tmp ls -g -rw---1 glaziou 3374 2004-02-03 11:58 g.pdf -rw---1 glaziou 4115 2004-02-03 11:58 g.png -rw---1 glaziou80 2004-02-03 11:58 foo This works from a unix console without X running (the postcript device works similarly on my machine). R can easily be fed this way with a file and parameters passed from a php script. -- Philippe Glaziou, MD Epidemiologist Institut Pasteur du Cambodge __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
