On Jan 27, 2013, at 08:33 , Emily Sessa wrote: > Hi all, > > I am trying to use the scan function in an R script that I am calling from > the command line on a Mac; at the shell prompt I type: > > $ Rscript get_q_values.R LRT_codeml_output > > in the hope that LRT_codeml_output will get passed to the get_q_values R > script. The first line of that script is: > > chidata <- scan(file="") > > which, as I understand how scan works, will read the contents of the file > from the command line into the object chidata. I did this a few times and it > worked like a charm. And then, it stopped working. Now, every time I try to > do this, I get "Read 0 items" as the next line in the terminal window, and > the output produced by the script is empty, because it's apparently no longer > reading anything in. I don't think I changed anything in the script; it just > stopped being able to execute the scan function. Does anyone have any idea > how to fix this?? I did not have anything else in that scan line when it was > working before. I've updated R and restarted my computer in the hope that it > would help, but it hasn't. Any help would be much appreciated.
I don't see how that would ever work. The 2nd and further args to Rscript are passed to R and accesible via commandArgs(). There's no way that scan() can know what the arguments are. It might work with Rscript get_q_values.R < LRT_codeml_output though. Or you need to arrange explicitly for scan(file=commandArgs(TRUE)[1]). > > -ES > ______________________________________________ > 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. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd....@cbs.dk Priv: pda...@gmail.com ______________________________________________ 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.
