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Keith Jewell

2010-Jun-10 10:31 UTC

[R] Capturing buffered output from Rterm

In MS Windows I
  a) invoke Rterm from a batch file (test.bat)
  b) to execute commands from a script (m:\test.rsc)
  c) capturing output in a log file (m:\test.log)
BUT if the script results in an error the error message is NOT written to 
the log file, leaving me problems when the error is from a complicated 
function.

Simplified example:.

test.bat ------------------------
REM ensure 'R' is in path
path \\Server02\stats\R\R-Current\bin\;%PATH%
Rterm  --no-init-file --no-restore-data --no-save --silent < m:\test.rsc >
m:\test.log
---------------------

m:\test.rsc -----------------
print("this is a test")
#generate an error
nls()
------------------

The error message:
  "Error in .Internal(inherits(x, what, which)) : 'x' is
missing"
is is NOT written to the log file, which just ends

m:\test.log --------------------------
  <snip>> print("this is a test")
[1] "this is a test"> #generate an error
> nls()---------------------

I surmise this is due to output buffering (?). In an S-Plus version I turned 
off buffering with
  guiSetOption(option.name="BufferOutputWindows",
value.string="F")
but I don't think this is available in R (?).

Has anyone any suggestions?

Thanks in advance,

Keith Jewell
--please do not edit the information below--

R Version:
 platform = i386-pc-mingw32
 arch = i386
 os = mingw32
 system = i386, mingw32
 status  major = 2
 minor = 11.0
 year = 2010
 month = 04
 day = 22
 svn rev = 51801
 language = R
 version.string = R version 2.11.0 (2010-04-22)

Windows Server 2003 x64 (build 3790) Service Pack 2

Locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United 
Kingdom.1252;LC_MONETARY=English_United 
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

Search Path:
 .GlobalEnv, package:datasets, CBRIForecast, package:RODBC, package:tree, 
package:locfit, package:lattice, package:akima, package:nlme, package:MASS, 
package:grDevices, package:geometry, KJRutils, package:xlsReadWrite, 
package:svSocket, package:TinnR, package:R2HTML, package:Hmisc, 
package:survival, package:splines, package:graphics, package:stats, 
CBRIutils, package:utils, package:tcltk, package:tools, package:methods, 
TempEnv, Autoloads, package:base

Duncan Murdoch

2010-Jun-10 10:47 UTC

head link

[R] Capturing buffered output from Rterm

Keith Jewell wrote:> In MS Windows I
>   a) invoke Rterm from a batch file (test.bat)
>   b) to execute commands from a script (m:\test.rsc)
>   c) capturing output in a log file (m:\test.log)
> BUT if the script results in an error the error message is NOT written to 
> the log file, leaving me problems when the error is from a complicated 
> function.
>
> Simplified example:.
>
> test.bat ------------------------
> REM ensure 'R' is in path
> path \\Server02\stats\R\R-Current\bin\;%PATH%
> Rterm  --no-init-file --no-restore-data --no-save --silent < m:\test.rsc
>
> m:\test.log
> ---------------------
>
> m:\test.rsc -----------------
> print("this is a test")
> #generate an error
> nls()
> ------------------
>
> The error message:
>   "Error in .Internal(inherits(x, what, which)) : 'x' is
missing"
> is is NOT written to the log file, which just ends
>
> m:\test.log --------------------------
>   <snip>
>   
>> print("this is a test")
>>     
> [1] "this is a test"
>   
>> #generate an error
>> nls()
>>     
> ---------------------
>
> I surmise this is due to output buffering (?). In an S-Plus version I
turned
> off buffering with
>   guiSetOption(option.name="BufferOutputWindows",
value.string="F")
> but I don't think this is available in R (?).
>
> Has anyone any suggestions?
It's not output buffering, it's because error messages go to a different
file handle than regular ones.  You need to redirect both stdout and stderr.

I'm not sure of the syntax to do that in Windows CMD, but R CMD BATCH 
test.rsc instead of Rterm would do it.  (The output should go to test.Rout.)

Duncan Murdoch

Prof Brian Ripley

2010-Jun-10 12:42 UTC

head link

[R] Capturing buffered output from Rterm

On Thu, 10 Jun 2010, Keith Jewell wrote:
> In MS Windows I
>  a) invoke Rterm from a batch file (test.bat)
>  b) to execute commands from a script (m:\test.rsc)
>  c) capturing output in a log file (m:\test.log)
>
> BUT if the script results in an error the error message is NOT written to
> the log file, leaving me problems when the error is from a complicated
> function.
Sure, warning and errors are written to stderr, which you did not 
redirect.  This is covered in rw-FAQ Q2.12.  Using R CMD BATCH would 
have done this for you ....

This is not to do with 'buffered output': in any case R uses minimal 
buffering so stdout and stderr can be mixed nicely on a single log 
file.
> Simplified example:.
>
> test.bat ------------------------
> REM ensure 'R' is in path
> path \\Server02\stats\R\R-Current\bin\;%PATH%
> Rterm  --no-init-file --no-restore-data --no-save --silent < m:\test.rsc
>
> m:\test.log
> ---------------------
>
> m:\test.rsc -----------------
> print("this is a test")
> #generate an error
> nls()
> ------------------
>
> The error message:
>  "Error in .Internal(inherits(x, what, which)) : 'x' is
missing"
> is is NOT written to the log file, which just ends
>
> m:\test.log --------------------------
>  <snip>
>> print("this is a test")
> [1] "this is a test"
>> #generate an error
>> nls()
> ---------------------
>
> I surmise this is due to output buffering (?). In an S-Plus version I
turned
> off buffering with
>  guiSetOption(option.name="BufferOutputWindows",
value.string="F")
> but I don't think this is available in R (?).
>
> Has anyone any suggestions?
>
> Thanks in advance,
>
> Keith Jewell
> --please do not edit the information below--
>
> R Version:
> platform = i386-pc-mingw32
> arch = i386
> os = mingw32
> system = i386, mingw32
> status > major = 2
> minor = 11.0
> year = 2010
> month = 04
> day = 22
> svn rev = 51801
> language = R
> version.string = R version 2.11.0 (2010-04-22)
>
> Windows Server 2003 x64 (build 3790) Service Pack 2
>
> Locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> Search Path:
> .GlobalEnv, package:datasets, CBRIForecast, package:RODBC, package:tree,
> package:locfit, package:lattice, package:akima, package:nlme, package:MASS,
> package:grDevices, package:geometry, KJRutils, package:xlsReadWrite,
> package:svSocket, package:TinnR, package:R2HTML, package:Hmisc,
> package:survival, package:splines, package:graphics, package:stats,
> CBRIutils, package:utils, package:tcltk, package:tools, package:methods,
> TempEnv, Autoloads, package:base
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
-- 
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 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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