Johan Sandblom wrote:

I can't really think why it wouldn't work then. Perhaps it is to do with \write18 and the right of TeX to run external programs? Or maybe R on the mac does not take the same command-line options? In that case the output of the texexec run should be revealing. R takes more than a second to start up so there are noticable breaks in the output after which error messages from R appear. Btw, the reason it does not work on contextgarden is likely that R is not installed there.

one problem could be that R has this piping; i wonder why a program that takes a 50 meg installation does not support something --output or i must have missed something Hans -- ----------------------------------------------------------------- Hans Hagen | PRAGMA ADE Ridderstraat 27 | 8061 GH Hasselt | The Netherlands tel: 038 477 53 69 | fax: 038 477 53 74 | www.pragma-ade.com | www.pragma-pod.nl -----------------------------------------------------------------

Olaf Mersmann wrote:

Hi Hans,

* Hans Hagen [060702 13:25]:

...

one problem could be that R has this piping; i wonder why a program that takes a 50 meg installation does not support something --output or i must have missed something

R does support redirecting output to a file. Use

R CMD BATCH [options] <infile> <outfile>

currently we use: \def\runR {\executesystemcommand{texmfstart --ifchanged=\Rfile\space --direct R "-q --save --restore < \Rfile\space > \Rfile.out"}} so how should it look then? Hans ----------------------------------------------------------------- Hans Hagen | PRAGMA ADE Ridderstraat 27 | 8061 GH Hasselt | The Netherlands tel: 038 477 53 69 | fax: 038 477 53 74 | www.pragma-ade.com | www.pragma-pod.nl -----------------------------------------------------------------

Johan Sandblom wrote:

\def\runR {\executesystemcommand{texmfstart --ifchanged=\Rfile\space --direct R CMD BATCH "-q --save --restore \Rfile\space \Rfile.out"}}

or some such, I do not really understand the quoting. The invocation should change, options should not and redirectors should go away. Not sure if this is better or worse in any way.

the quoting tells texmfstart not split this, < > | are passes ok that way" did you test it? Hans

I think some quoting is required: \def\runR {\executesystemcommand{texmfstart --ifchanged=\Rfile\space --direct R CMD BATCH "-q --save --restore \Rfile\space \Rfile.out"}} works here, but then I am on Linux. I think eventually Mac expertise may be required. Johan 2006/7/5, Matthew Routley :

I can confirm that this works from the command line:

R CMD BATCH -q --save --restore rsample-r-1.tmp rsample-r-1.tmp.out

using the sample file from the r module. Running this command for each of the r segments will produce the desired output. What I haven't determined is how to modify the r module \runR command. Simply replacing the current \runR with

\def\runR {\executesystemcommand{texmfstart --ifchanged=\Rfile\space --direct R CMD BATCH -q --save --restore \Rfile\space \Rfile.out}}

was not successful. But I'm quite unfamilier with ConTeXt at this level.

As far as I can determine, the appropriate .out files are not being created, which the log file correctly indicates. The .tmp files are successfully extracted from the source file.

Thanks for the help with this.

Matt

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Johan Sandblom writes:

I think some quoting is required:

\def\runR {\executesystemcommand{texmfstart --ifchanged=\Rfile\space --direct R CMD BATCH "-q --save --restore \Rfile\space \Rfile.out"}}

works here, but then I am on Linux. I think eventually Mac expertise may be required.

Unfortunately, the quoting doesn't help. Closer inspection of the log file reveals lines such as: system(texmfstart --ifchanged=test-r-1.tmp --direct R CMD BATCH "-q --save --restore test-r-1.tmp test-r-1.tmp.out")...disabled. with both the original \runR and new, batch mode. Matt

On Wed, 5 Jul 2006, Matthew Routley wrote:

Johan Sandblom writes:

...

I think some quoting is required:

\def\runR {\executesystemcommand{texmfstart --ifchanged=\Rfile\space --direct R CMD BATCH "-q --save --restore \Rfile\space \Rfile.out"}}

works here, but then I am on Linux. I think eventually Mac expertise may be required.

Unfortunately, the quoting doesn't help. Closer inspection of the log file reveals lines such as:

system(texmfstart --ifchanged=test-r-1.tmp --direct R CMD BATCH "-q --save --restore test-r-1.tmp test-r-1.tmp.out")...disabled.

with both the original \runR and new, batch mode.

This means that write18 is disabled on your system, so tex cannot execute any system commands. This is a security feature and most intallation disable write18 by default. You need to edit your texmf.cnf file to enable it. Search for texmf.cnf using texmfstart --locate texmf.cnf open that file in your favourite editor. Search for shell_escape and set it to true by shell_escape = t Save the file and write18 should work. Rerun texexec on your file and look at the log file. You should get system(....) executed. Aditya

2006/7/2, Hans Hagen :

Johan Sandblom wrote:

...

I can't really think why it wouldn't work then. Perhaps it is to do with \write18 and the right of TeX to run external programs? Or maybe R on the mac does not take the same command-line options? In that case the output of the texexec run should be revealing. R takes more than a second to start up so there are noticable breaks in the output after which error messages from R appear. Btw, the reason it does not work on contextgarden is likely that R is not installed there.

one problem could be that R has this piping; i wonder why a program that takes a 50 meg installation does not support something --output or i must have missed something

I think R is most commonly used interactively in which case it is not needed. Anyway, OS X is a unix-alike so it should work fine. It even works on Windoze! The R MAC FAQ http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Command-line-version-o... indicates that this approach should work. Johan

Hans

--

----------------------------------------------------------------- Hans Hagen | PRAGMA ADE Ridderstraat 27 | 8061 GH Hasselt | The Netherlands tel: 038 477 53 69 | fax: 038 477 53 74 | www.pragma-ade.com | www.pragma-pod.nl -----------------------------------------------------------------

-- Johan Sandblom N8, MRC, Karolinska sjh t +46851776108 17176 Stockholm m +46735521477 Sweden "What is wanted is not the will to believe, but the will to find out, which is the exact opposite" - Bertrand Russell