[BioC] intern=TRUE seems not working in system command in Mac OS

[Harris A. Jaffee]

As far as I know, 'intern=TRUE' only captures standard output, and
not standard error unless you do something explicitly to put that on
standard output.  In this case, they won't be distinguishable, but
at least you can see both.

# here I get the same thing you do
> x = system("java -version", intern=TRUE)
java version "1.6.0_29"
Java(TM) SE Runtime Environment (build 1.6.0_29-b11-402-10M3527)
Java HotSpot(TM) Client VM (build 20.4-b02-402, mixed mode)

# put stderr on stdout
> x = system("java -version 2>&1", intern=TRUE)
> x
[1] "java version \"1.6.0_29\""                                       
[2] "Java(TM) SE Runtime Environment (build 1.6.0_29-b11-402-10M3527)"
[3] "Java HotSpot(TM) Client VM (build 20.4-b02-402, mixed mode)"     

On Jan 30, 2012, at 5:17 AM, rcaloger wrote:

> Hi,
> I am trying to save the output produced from the following command in Mac :
> 
> > tmp.java <- system("java -version", intern=TRUE)
> java version "1.6.0_29"
> Java(TM) SE Runtime Environment (build 1.6.0_29-b11-402-11M3527)
> Java HotSpot(TM) 64-Bit Server VM (build 20.4-b02-402, mixed mode)
> > tmp.java
> character(0)
> 
> The intern command work perfectly under windows and linux .
> Is there any other option to get manage to save the output of system command in a variable?
> 
> Cheers
> Raffaele
> 
> > sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> 
> 
> -- 
> 
> ----------------------------------------
> Prof. Raffaele A. Calogero
> Bioinformatics and Genomics Unit
> MBC Centro di Biotecnologie Molecolari
> Via Nizza 52, Torino 10126
> tel.   ++39 0116706457
> Fax    ++39 0112366457
> Mobile ++39 3333827080
> email: raffaele.calogero at unito.it
>       raffaele[dot]calogero[at]gmail[dot]com
> www:   http://www.bioinformatica.unito.it
> 
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