I could not use R commands on Mac OS X, so, like with GRASS, I decided to analyze the Python scripts and the sextante log to understand what happens
This time, no error in the log but no results either, no resulting shapefile in /Users/martinlaloux/sextante/tempdata. The temporary script /Users/martinlaloux/sextante/*sextante_script.r* has been created so the problem is again in the parameters of the Python module subprocess in * Rutils.py* (line 58): command = ["R", "CMD","BATCH", "--vanilla", RUtils.getRScriptFilename(), RUtils.getConsoleOutputFilename()] proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stdin=subprocess.PIPE,stderr=subprocess.STDOUT, universal_newlines=True) Usually when I want to run an R script in Python, I use the command (see "QGIS: run Python scripts from the Python Console or with Script Runner (without creating an extension)" (in french QGIS : lancer des scripts Python ou des commandes Shell depuis la Console Python ou avec Script Runner <http://www.portailsig.org/content/qgis-lancer-des-scripts-python-ou-des-commandes-shell-depuis-la-console-python-ou-avec-scrip> ):<http://www.portailsig.org/content/qgis-lancer-des-scripts-python-ou-des-commandes-shell-depuis-la-console-python-ou-avec-scrip> subprocess.Popen(['Rscript','sextante_script.r'],stdout=subprocess.PIPE)) -> *works* *But what about the solution of the script ?* If I try to run the procedure directly in the Python shell (with sextante_script.r obtained by the script): >>> import subprocess >>> doc=subprocess.Popen(['R', 'CMD', 'BATCH', 'sextante_script.r'],stdout=subprocess.PIPE) -> *works* >>> doc=subprocess.Popen(['R', 'CMD', 'BATCH', 'sextante_script.r'],stdout=subprocess.PIPE, stdin=subprocess.PIPE,stderr=subprocess.STDOUT, universal_newlines=True) -> *works* >>> doc=subprocess.Popen(['R', 'CMD', 'BATCH', 'sextante_script.r'], shell= True, stdout=subprocess.PIPE, stdin=subprocess.PIPE,stderr=subprocess.STDOUT, universal_newlines=True) -> *no result * *Why ? * * The problem is shell= True* *with Unix systems. *I have already encountered this problem many times in my work **A good explanation is given in the stackoverflow.com question: Getting output from Python script in Python tests<http://stackoverflow.com/questions/9095733/getting-output-from-python-script-in-python-tests/9096104#9096104> * "If you're using shell=True, don't pass the program and its arguments as a list*" *but whith a string* - replacing the line 58 of Rutil.py by *command = "R CMD BATCH --vanilla " + RUtils.getRScriptFilename() + " "+ RUtils.getConsoleOutputFilename()* proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stdin=subprocess.PIPE,stderr=subprocess.STDOUT, universal_newlines=True) * works because the result of command is a string* - or command = ["R", "CMD","BATCH", "--vanilla", RUtils.getRScriptFilename(), RUtils.getConsoleOutputFilename()] *proc = subprocess.Popen(command, stdout=subprocess.PIPE, stdin=subprocess.PIPE,stderr=subprocess.STDOUT, universal_newlines=True)* *works also because shell=false.* The complete explanation is (from the question of stackoverflow): > *On Unix, with shell=True: If args is a string, it specifies the command > string to execute through the shell. This means that the string must be > formatted exactly as it would be when typed at the shell prompt. This > includes, for example, quoting or backslash escaping filenames with spaces > in them. If args is a sequence, the first item specifies the command > string, and any additional items will be treated as additional arguments to > the shell itself.* > > I hope you understand why the original script does not work on Mac OS X, a > Unix system. By modifying line 58, no more problem
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