Hello- Does anyone have a recommendation on how to call R from perl? I'm using the IPC::Open2 module, and running R with the --slave and --quiet options. The problem is that I can't predict how many lines of output I should try to read for each command-- if any! The ultimate goal is to use perl to provide a form-driven web interface, but have R do the underlying calculations. Thanks for any help! -John Barnett -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
perl advice
5 messages · Guido Masarotto, Jim Robison-Cox, Brian Ripley +1 more
On Mon, Dec 06, 1999 at 05:12:44PM -0500, John D. Barnett wrote:
Hello- Does anyone have a recommendation on how to call R from perl? I'm using the IPC::Open2 module, and running R with the --slave and --quiet options. The problem is that I can't predict how many lines of output I should try to read for each command-- if any! The ultimate goal is to use perl to provide a form-driven web interface, but have R do the underlying calculations.
A trick that I have used sometimes from tcl/tk is to redefine the prompt to some funny string (sending to the controlled process a 'option(prompt=...) command at the beginning) and then wait for the prompt on the output. If I remember also ESS works in a probably less weaker but similar approach (i.e., it waits for a particular regular expression on the standard output of the R process). Hoping this can help, guido -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
On Mon, 6 Dec 1999, John D. Barnett wrote:
Does anyone have a recommendation on how to call R from perl? I'm using the IPC::Open2 module, and running R with the --slave and --quiet options. The problem is that I can't predict how many lines of output I should try to read for each command-- if any! The ultimate goal is to use perl to provide a form-driven web interface, but have R do the underlying calculations.
Before you reinvent the wheel, look at Jeff Banfield's Rweb: http://www.math.montana.edu/Rweb/ You might contact him directly: jeff at math.montana.edu (I know he doesn't read R-help.) if you have more questions. Jim Jim Robison-Cox ____________ Department of Math Sciences | | phone: (406)994-5340 2-214 Wilson Hall \ BZN, MT | FAX: (406)994-1789 Montana State University | *_______| Bozeman, MT 59717-2400 \_| e-mail: jimrc at math.montana.edu -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
On Mon, 6 Dec 1999, Guido Masarotto wrote:
On Mon, Dec 06, 1999 at 05:12:44PM -0500, John D. Barnett wrote:
Hello- Does anyone have a recommendation on how to call R from perl? I'm using the IPC::Open2 module, and running R with the --slave and --quiet options. The problem is that I can't predict how many lines of output I should try to read for each command-- if any! The ultimate goal is to use perl to provide a form-driven web interface, but have R do the underlying calculations.
A trick that I have used sometimes from tcl/tk is to redefine the prompt to some funny string (sending to the controlled process a 'option(prompt=...) command at the beginning) and then wait for the prompt on the output. If I remember also ESS works in a probably less weaker but similar approach (i.e., it waits for a particular regular expression on the standard output of the R process). Hoping this can help,
Yes, ESS uses something like that. But, Programming Perl, p.345, warns you not to use IPC::Open2 for this purpose, because of buffering, but Comm.pl (from CPAN) instead. Emacs does use pseudo-ptys (on Unix, and tricks on Win32) to overcome the buffering problem. I am not sure that R always flushes its buffers, as although Rprintf seems to do so if it thinks it has an output file, R_WriteConsole does not. (Crashes in batch jobs do sometimes seem to have incomplete output on the output file.)
Brian D. Ripley, ripley at stats.ox.ac.uk 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 272860 (secr) Oxford OX1 3TG, UK Fax: +44 1865 272595 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Thanks; this is all very helpful. I looked into Comm.pl, but had problems using it. I found a message somewhere saying that Comm.pl was fairly specific to SunOS 4/5; there's a newer perl module with similar functionality, Expect.pm I've already written a routine to parse R output produced by dump(), but now that I'm able to interact directly, I'd like to parse R's normal output-- unless there's a way that I can send dump's output to STDOUT. Thanks again!
Prof Brian D Ripley wrote:
On Mon, 6 Dec 1999, Guido Masarotto wrote:
On Mon, Dec 06, 1999 at 05:12:44PM -0500, John D. Barnett wrote:
Hello- Does anyone have a recommendation on how to call R from perl? I'm using the IPC::Open2 module, and running R with the --slave and --quiet options. The problem is that I can't predict how many lines of output I should try to read for each command-- if any! The ultimate goal is to use perl to provide a form-driven web interface, but have R do the underlying calculations.
A trick that I have used sometimes from tcl/tk is to redefine the prompt to some funny string (sending to the controlled process a 'option(prompt=...) command at the beginning) and then wait for the prompt on the output. If I remember also ESS works in a probably less weaker but similar approach (i.e., it waits for a particular regular expression on the standard output of the R process). Hoping this can help,
Yes, ESS uses something like that. But, Programming Perl, p.345, warns you not to use IPC::Open2 for this purpose, because of buffering, but Comm.pl (from CPAN) instead. Emacs does use pseudo-ptys (on Unix, and tricks on Win32) to overcome the buffering problem. I am not sure that R always flushes its buffers, as although Rprintf seems to do so if it thinks it has an output file, R_WriteConsole does not. (Crashes in batch jobs do sometimes seem to have incomplete output on the output file.) -- Brian D. Ripley, ripley at stats.ox.ac.uk 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 272860 (secr) Oxford OX1 3TG, UK Fax: +44 1865 272595
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