Not display message when using system()
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_grt at 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'ex?cution 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'ex?cution 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'ex?cution 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
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