Dear Scott (and all),
Thanks for sharing your idea - it helped me solve the problem. The issue
was actually the "nmfe6.bat" itself - there was plenty of references
such as "%dir%", "%nmdir%", etc. I replaced them all with full paths.
Additionally, I put all the PATH settings from "NMdirectories.bat" into
the "nmfe6.bat" to save on number of files that I have to call. I also
deleted most of the error-checking code and left only the lines calling
directly to the NONMEM components.
If anyone is interested, I replaced both the ":tran" and ":compile"
parts of the "nmfe6.bat" with the following code:
------------------------------------------------
:tran
K:\NONMEMCourse\nmvi\tr\nmtran.exe < %1 > FMSG
type FMSG
copy fsubs fsubs.for > nul
makeg77bat
call g77compile
echo Starting nonmem execution ...
nonmem.exe
echo Stop Time: >>%2
date /t >>%2
time /t >>%2
goto exit
------------------------------------------------
When run in R, it displays a warning: "...execution failed with error
code 1", nevertheless NONMEM actually produces the tables. I placed the
edited "nmfe6.bat" in my project folder and used the following R
commands to execute it:
------------------------------------------------
setwd("K:\\PROJECT1\\")
shell("nmfe6 control.txt output.txt", wait=T)
------------------------------------------------
Therefore, this works for me, for now. Nevertheless, if anyone has an
idea on what causes the warning message and how to make it run smoothly,
please share with me.
--
Michal J. Figurski, PhD
HUP, Pathology & Laboratory Medicine
Biomarker Research Laboratory
3400 Spruce St. 7 Maloney
Philadelphia, PA 19104
tel. (215) 662-3413
Scott Sherrill-Mix wrote:
I believe R does system calls from its current working directory
(getwd() will tell you where that is). This may not be the same
directory you designed your .bat for. What if you use the full path
for your files in the batch file? e.g.
call K:\nmvi\nmfe6 "K:\nmvi\path\control.txt" "K:\nmvi\path\output.txt"
Alternatively, you could make sure R is working in the right directory. e.g.
setwd('K:\nmvi')
Scott
Scott Sherrill-Mix
Department of Microbiology
University of Pennsylvania
402B Johnson Pavilion
3610 Hamilton Walk
Philadelphia, PA 19104-6076
Phone: 215-573-3141
On Wed, Aug 5, 2009 at 11:24 AM, Michal
Figurski<figur...@mail.med.upenn.edu> wrote:
Hello,
I have made an R script that prepares a NONMEM dataset and I would like to
start the NONMEM run right after the dataset is ready.
I am using windows XP, R 2.9.1 and NONMEM 6.
I have prepared a run.bat file that looks like this:
----------------------------------------
call K:\nmvi\NMdirectories.bat
call K:\nmvi\nmfe6 "path\control.txt" "path\output.txt"
----------------------------------------
The first call sets up all paths and directories, the second call starts
NONMEM. If I run this run.bat file directly in cmd window, it runs
correctly. However, if I use the R command:
shell("K:\\path\\run.bat", wait=T)
the first call runs correctly, but then the second produces and error "The
system cannot find the path specified." - completely as if the computer has
forgotten all the paths and settings from the first call.
Does anyone know a solution to this problem?
--
Michal J. Figurski, PhD
HUP, Pathology & Laboratory Medicine
Biomarker Research Laboratory
3400 Spruce St. 7 Maloney
Philadelphia, PA 19104
tel. (215) 662-3413
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and provide commented, minimal, self-contained, reproducible code.
