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

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor