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*gmapR option name for returning system calls is now "systemCallMode"

*asSystemCall.R added

*previous code that calls .system had to account for the case of when
getOption("systemCallMode") is TRUE. Since exception is now being
thrown, this logic was removed from gsnap() function

*LungCancerLines no longer mentioned in NAMESPACE

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69338 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 11/09/2012 22:12:30
Showing 1 changed files

R/asSystemCall.R

History View file @ 297de88

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                                     +##written to get the string of the system call rather than having the
                                     +##system call actually executed. Initial motivation was for unit
                                     +##testing.
                                     +asSystemCall <- function(x) {
                                     +  expr <- substitute(x)
                                     +  options(systemCallMode = TRUE)
                                     +  on.exit(options(systemCallMode = FALSE))
                                     +  error <- tryCatch(eval(expr, parent.frame()),
                                     +                         error = function(e) return(e))
                                     +  error$systemCall
                                     +}