Re: [NTG-context] Difficulties using the r module
The resolution to my problem was specific to Mac OS X and had nothing to do with the R module in particular. In case others have a similar problem, here is my solution. First, write18 must be enabled. As described by Aditya Mahajan, edit /usr/local/teTeX/texmf.cnf so that shell_escape = t. Second, create a texmfstart script as described in the Configuration of texmfstart section of http://wiki.contextgarden.net/Mac_Installation. I modified this slightly by placing the script in ~/bin so that I didn't interfere with the installed teTeX tree. Now the r module works. Thanks for everyone's help with this. Matt ___ ntg-context mailing list ntg-context@ntg.nl http://www.ntg.nl/mailman/listinfo/ntg-context
Re: [NTG-context] Difficulties using the r module
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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Re: [NTG-context] Difficulties using the r module
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 [EMAIL PROTECTED]:
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 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
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Re: [NTG-context] Difficulties using the r module
I now discovered a side effect of using the R CMD BATCH invocation
instead of the piping. With the CMD R outputs the setting of options
in the first line and the result of proc.time at the end. Perhaps not
a problem, but it does require three more typed lines per R block.
Johan
2006/7/5, Johan Sandblom [EMAIL PROTECTED]:
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 [EMAIL PROTECTED]:
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 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
--
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
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Re: [NTG-context] Difficulties using the r module
I get no such output, either to stdout or in the log, in fact nothing
even similar. Does the ...disabled indicate that it is not run,
possibly because of something TeX/ConTeXt-related?
Johan
2006/7/5, Matthew Routley [EMAIL PROTECTED]:
Johan Sandblom jsandblom at gmail.com 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
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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
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Re: [NTG-context] Difficulties using the r module
On Wed, 5 Jul 2006, Matthew Routley wrote:
Johan Sandblom jsandblom at gmail.com 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
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Re: [NTG-context] Difficulties using the r module
Aditya Mahajan adityam at umich.edu writes: 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 This worked for enabling the commands. Of course, this revealed a new problem. texmfstart was not being called correctly. Replacing texmfstart with: ruby /usr/local/teTeX/share/texmf.local/scripts/context/ruby/texmfstart.rb , which is my path to texmfstart.rb, in \runR solved the problem. I had followed the Other method from the ConTeXt wiki for enabling texmfstart on my system. This works fine for calling commands from the command line, but (as suggested in the wiki) doesn't necessarily work for other methods. Once I sort out all of these OS X specific details, I'll post back to my original message with a solution. Thanks, Matt ___ ntg-context mailing list ntg-context@ntg.nl http://www.ntg.nl/mailman/listinfo/ntg-context
Re: [NTG-context] Difficulties using the r module
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
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Re: [NTG-context] Difficulties using the r module
2006/7/2, Hans Hagen [EMAIL PROTECTED]: 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-of-R 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 ___ ntg-context mailing list ntg-context@ntg.nl http://www.ntg.nl/mailman/listinfo/ntg-context
Re: [NTG-context] Difficulties using the r module
Hi Hans, * Hans Hagen [EMAIL PROTECTED] [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 -- Olaf ___ ntg-context mailing list ntg-context@ntg.nl http://www.ntg.nl/mailman/listinfo/ntg-context
Re: [NTG-context] Difficulties using the r module
Olaf Mersmann wrote:
Hi Hans,
* Hans Hagen [EMAIL PROTECTED] [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
-
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Re: [NTG-context] Difficulties using the r module
\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.
Johan
2006/7/2, Hans Hagen [EMAIL PROTECTED]:
Olaf Mersmann wrote:
Hi Hans,
* Hans Hagen [EMAIL PROTECTED] [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
-
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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
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Re: [NTG-context] Difficulties using the r module
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. Sorry I could not be of more assistance, Johan 2006/6/30, Matthew Routley [EMAIL PROTECTED]: Johan, It appears R is not found. Is it on the path? Does it have the same name on the Mac? Yes, R is in the bath and is found in /usr/bin/R which is a link to /Library/Frameworks/R.framework/Resources/bin/R. Thanks for your help with this. Take care, Matt -- Matthew Routley http://matt.routleynet.org ___ ntg-context mailing list ntg-context@ntg.nl http://www.ntg.nl/mailman/listinfo/ntg-context -- 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 ___ ntg-context mailing list ntg-context@ntg.nl http://www.ntg.nl/mailman/listinfo/ntg-context
[NTG-context] Difficulties using the r module
I spotted the announcement of the use of R in ConTeXt and was quite interested in trying it out. However, so far I haven't been able to get it to work. It appears that R is not being called by texexec and the .tmp.out are not being found, despite the fact that they are being produced. Are there more details on installing and using this module? I think it would be quite useful. Thanks for any advice, Matt Some details are that I am using Mac OS X 10.4.7, R-2.3.1, and ConTeXt ver: 2006.06.28 from gwTeX and running the sample file contained in m-r.tex. I have also tried using context live @ contextgarden.net with the same results as on my personal machine. Here is some output from the log file: system : module r loaded (/usr/local/teTeX/share/texmf.local/tex/context/base/m-r.tex) ... systems : begin file r at line 11 r-r-1.tmp (/usr/local/teTeX/share/texmf.local/tex/context/base/pdfr-ec.tex) verbatim : file r-r-1.tmp.out does not exist r-r-2.tmp verbatim : file r-r-2.tmp.out does not exist r-r-3.tmp r-r-4.tmp verbatim : file r-r-4.tmp.out does not exist r-r-5.tmp verbatim : file r-r-5.tmp.out does not exist r-r.tmp (./r-r.tmp figures : figure ushape can not be found floatblocks : 1 placed ) r-r-6.tmp verbatim : file r-r-6.tmp.out does not exist r-r.tmp (./r-r.tmp figures : figure lattice can not be found floatblocks : 2 placed ) r-r-7.tmp verbatim : file r-r-7.tmp.out does not exist ... ___ ntg-context mailing list ntg-context@ntg.nl http://www.ntg.nl/mailman/listinfo/ntg-context
Re: [NTG-context] Difficulties using the r module
It appears R is not found. Is it on the path? Does it have the same name on the Mac? Regards, Johan 2006/6/28, Matthew Routley [EMAIL PROTECTED]: I spotted the announcement of the use of R in ConTeXt and was quite interested in trying it out. However, so far I haven't been able to get it to work. It appears that R is not being called by texexec and the .tmp.out are not being found, despite the fact that they are being produced. Are there more details on installing and using this module? I think it would be quite useful. Thanks for any advice, Matt Some details are that I am using Mac OS X 10.4.7, R-2.3.1, and ConTeXt ver: 2006.06.28 from gwTeX and running the sample file contained in m-r.tex. I have also tried using context live @ contextgarden.net with the same results as on my personal machine. Here is some output from the log file: system : module r loaded (/usr/local/teTeX/share/texmf.local/tex/context/base/m-r.tex) ... systems : begin file r at line 11 r-r-1.tmp (/usr/local/teTeX/share/texmf.local/tex/context/base/pdfr-ec.tex) verbatim : file r-r-1.tmp.out does not exist r-r-2.tmp verbatim : file r-r-2.tmp.out does not exist r-r-3.tmp r-r-4.tmp verbatim : file r-r-4.tmp.out does not exist r-r-5.tmp verbatim : file r-r-5.tmp.out does not exist r-r.tmp (./r-r.tmp figures : figure ushape can not be found floatblocks : 1 placed ) r-r-6.tmp verbatim : file r-r-6.tmp.out does not exist r-r.tmp (./r-r.tmp figures : figure lattice can not be found floatblocks : 2 placed ) r-r-7.tmp verbatim : file r-r-7.tmp.out does not exist ... ___ ntg-context mailing list ntg-context@ntg.nl http://www.ntg.nl/mailman/listinfo/ntg-context -- 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 ___ ntg-context mailing list ntg-context@ntg.nl http://www.ntg.nl/mailman/listinfo/ntg-context
