Dear Henrik and list-members,
Thanks for your proposition but it is the same:
For example, no error message but no result:
> pathfile <- system2(command="find", args="$HOME -type f -name
'PuertoSanJose.csv'", stderr = FALSE, stdout="")
/Users/marc/Dropbox/DropBoxPerso/Data_Ale/Original/PuertoSanJose.csv
> pathfile
[1] 1
Example 2 with error message but I get the result !
> pathfile <- system2(command="find", args="$HOME -type f -name
'PuertoSanJose.csv'", stderr = FALSE, stdout=TRUE)
Message d'avis :
l'exécution de la commande ''find' $HOME -type f -name
'PuertoSanJose.csv' 2>/dev/null' renvoie un statut 1
> pathfile
[1] "/Users/marc/Dropbox/DropBoxPerso/Data_Ale/Original/PuertoSanJose.csv"
attr(,"status")
[1] 1
I try another solution with options(warn=2) and try(xxx, silent=TRUE) to
convert the warning in error and mask the error, but I cannot get the
result anymore:
> options(warn=2)
> pathfile <- try(system2(command="find", args="$HOME -type f -name
'PuertoSanJose.csv'", stderr = FALSE, stdout=TRUE), silent=TRUE)
> pathfile
[1] "Error : (converti depuis l'avis) l'exécution de la commande ''find'
$HOME -type f -name 'PuertoSanJose.csv' 2>/dev/null' renvoie un statut 1\n"
attr(,"class")
[1] "try-error"
attr(,"condition")
<simpleError: (converti depuis l'avis) l'exécution de la commande
''find' $HOME -type f -name 'PuertoSanJose.csv' 2>/dev/null' renvoie un
statut 1>
I try also this combinations but without success:
> pathfile <- ""
> try(assign("pathfile", system2(command="find", args="$HOME -type f
-name 'PuertoSanJose.csv'", stderr = FALSE, stdout=TRUE),
envir=globalenv()), silent=TRUE)
> pathfile
[1] ""
> try({pathfile <<- system2(command="find", args="$HOME -type f -name
'PuertoSanJose.csv'", stderr = FALSE, stdout=TRUE)}, silent=TRUE)
> pathfile
[1] ""
Sooo... any other idea ?
Thanks a lot
Marc
Le 29/08/2014 22:33, Henrik Bengtsson a écrit :
>
> As a start try to use system2() instead and look at its argument for
> how to capture stdout and/or stderr. It's a neater function.
>
> It may be that those messages cannot be captured easily, but hopefully
> they are.
>
> My $0.02
>
> Henrik
>
> On Aug 29, 2014 12:21 PM, "Marc Girondot" <marc_...@yahoo.fr
> <mailto:marc_...@yahoo.fr>> wrote:
>
> Dear list members,
>
> My question concerns the use of system() in R version 3.1.1
> patched and MacosX 10.9.4.
> I want capture the result of a system command without displaying
> error message. I give exemple.
>
> In terminal, if I do this command:
> find $HOME -type f -name 'PuertoSanJose.csv'
>
> I get the correct answer but also a message about Permission
> denied for one directory:
> /Users/marc/Dropbox/DropBoxPerso/Data_Ale/Original/PuertoSanJose.csv
> find: /Users/marc/Library/Saved Application
> State/com.adobe.flashplayer.installmanager.savedState/data.data:
> Permission denied
>
> I want get the output of this command in R; then I do:
> > pathfile <- system("find $HOME -type f -name
> 'PuertoSanJose.csv'", intern=TRUE, ignore.stderr = TRUE)
> Message d'avis :
> l'exécution de la commande 'find $HOME -type f -name
> 'PuertoSanJose.csv' 2>/dev/null' renvoie un statut 1
>
> In pathfile, I have the correct answer but I have also a message
> that I don't want.
>
> My question is then: How to prevent display this message?
>
> I try the following:
> > pathfile <- capture.output(system("find $HOME -type f -name
> 'PuertoSanJose.csv'", intern=TRUE, ignore.stderr = TRUE))
> Message d'avis :
> l'exécution de la commande 'find $HOME -type f -name
> 'PuertoSanJose.csv' 2>/dev/null' renvoie un statut 1
>
> The same
>
> I try also:
> > pathfile <- suppressMessages(system("find $HOME -type f -name
> 'PuertoSanJose.csv'", intern=TRUE, ignore.stderr = TRUE))
> Message d'avis :
> l'exécution de la commande 'find $HOME -type f -name
> 'PuertoSanJose.csv' 2>/dev/null' renvoie un statut 1
>
> The same
>
> The only solution to not see this message is:
> > pathfile <- system("find $HOME -type f -name
> 'PuertoSanJose.csv'", intern=FALSE, ignore.stderr = TRUE)
> /Users/marc/Dropbox/DropBoxPerso/Data_Ale/Original/PuertoSanJose.csv
> > pathfile
> [1] 1
>
> But pathfile does not capture the output.
>
> And the use of capture.output() does not help:
> > pathfile <- capture.output(system("find $HOME -type f -name
> 'PuertoSanJose.csv'", intern=FALSE, ignore.stderr = TRUE))
> /Users/marc/Dropbox/DropBoxPerso/Data_Ale/Original/PuertoSanJose.csv
> > pathfile
> character(0)
>
>
> I really don't know how to not see this message...
> If someone knows, I will appreciate !
>
> Marc
>
> ______________________________________________
> R-help@r-project.org <mailto:R-help@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.
>
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