Difficulties using the r module

Difficulties using the r module

[Matthew Routley]

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

...

Re: Difficulties using the r module

[Johan Sandblom]

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 <matthew.routley@gmail.com>:
> 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

Re: Difficulties using the r module

[Matthew Routley]

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

Re: Difficulties using the r module

[Matthew Routley]

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

Re: Difficulties using the r module

[Aditya Mahajan]

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

Re: Difficulties using the r module

[Johan Sandblom]

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 <matthew.routley@gmail.com>:
> 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
>
> _______________________________________________
> 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

Re: Difficulties using the r module

[Matthew Routley]

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

Re: Difficulties using the r module

[Johan Sandblom]

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 <jsandblom@gmail.com>:
> 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 <matthew.routley@gmail.com>:
> > 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
> >
> >
> >
> > _______________________________________________
> > 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
>


-- 
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

Re: Difficulties using the r module

[Johan Sandblom]

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 <matthew.routley@gmail.com>:
> 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
>
>
>
> _______________________________________________
> 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

Re: Difficulties using the r module

[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

Re: Difficulties using the r module

[Hans Hagen]

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

Re: Difficulties using the r module

[Johan Sandblom]

\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 <pragma@wxs.nl>:
> Olaf Mersmann wrote:
> > Hi Hans,
> >
> > * Hans Hagen <pragma@wxs.nl> [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
> -----------------------------------------------------------------
>
> _______________________________________________
> 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

Re: Difficulties using the r module

[Hans Hagen]

Olaf Mersmann wrote:
> Hi Hans,
>
> * Hans Hagen <pragma@wxs.nl> [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
-----------------------------------------------------------------

Re: Difficulties using the r module

[Johan Sandblom]

2006/7/2, Hans Hagen <pragma@wxs.nl>:
> 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

Re: Difficulties using the r module

[Olaf Mersmann]

Hi Hans,

* Hans Hagen <pragma@wxs.nl> [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

Re: Difficulties using the r module

[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

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
-----------------------------------------------------------------

Re: Difficulties using the r module

[Johan Sandblom]

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 <matthew.routley@gmail.com>:
> 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

Difficulties using the r module

[Matthew Routley]

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