[Rd] How best to get around shadowing of executables by system()'s prepending of directories to Windows' PATH?

Roebuck,Paul L PLRoebuck at mdanderson.org
Tue May 19 20:12:27 CEST 2015

This is the code I use in my 'SuperCurve' R-Forge package:

## Merge output graphs with source tiff file, save it as JPG file
.mergeGraphsAndImage <- function(antibody,
                                 tiff) {
    ## Check arguments
    stopifnot(is.character(antibody)  && length(antibody) == 1)
    stopifnot(is.character(prefix)    && length(prefix) == 1)
    stopifnot(is.character(outputdir) && length(outputdir) == 1)
    stopifnot(is.character(tiff)      && length(tiff) == 1)

    ## Begin processing
    filename <- sprintf("%s_%s_1.png", prefix, antibody)
    pg1 <- file.path(outputdir, .portableFilename(filename))

    filename <- sprintf("%s_%s_2.png", prefix, antibody)
    pg2 <- file.path(outputdir, .portableFilename(filename))

    filename <- sprintf("%s.jpg", antibody)
    output <- file.path(outputdir, .portableFilename(filename))

    ## Use ImageMagick 'convert' binary to perform merge
    command <- paste("convert",
                     "-quality 100",
    rc <- switch(EXPR=.Platform$OS.type,
                 stop(sprintf("unrecognized operating system family %s",
    #cat("rc =", rc, ", command:", command, "\n")


Additionally, the package uses the .onLoad() method to verify
WHICH 'convert' would be used and alert user if missing (or
DOS command would be used instead of ImageMagick binary).

.onLoad <- function(libname, pkgname) {

    ## Preflight check use of ImageMagick 'convert' binary
    preflightCheck <- function() {
        command <- "convert --version"
                output <- switch(EXPR=.Platform$OS.type,
                grepl("ImageMagick", output[1], fixed=TRUE)
            error=function(e) {

    if (!preflightCheck()) {
        warning(sprintf("ImageMagick executable %s not installed or
unavailable via PATH",

    ## [SNIP unrelated additional code]

On 5/18/15 12:29 PM, "Josh O'Brien" <joshmobrien at gmail.com> wrote:

>My question:
>On Windows, R's system() command prepends several directories to those
>in the Windows Path variable.
>>From ?system
>     The search path for 'command' may be system-dependent: it will
>     include the R 'bin' directory, the working directory and the
>     Windows system directories before 'PATH'.
>This shadows any executables on the Path that share a name with, for
>example, one of the Windows commands.
>What should I do when I'd really like (the equivalent of) a call
>passed to system() that would be executed using the same Path that
>you'd get if working directly at the Windows command line? Is there a
>recommended workaround for situtations like this? (It _seems_ like it
>would be handy if system() et al. included an additional argument that
>optionally disabled the prepending of those extra directories, to give
>Windows users full control of the path seen by system(). Would adding
>such an argument have undesirable ramifications?)
>Motivation and reproducible example:
>I'm motivated here by a desire to use the function plotdiff() from
>Paul Murrell's gridGraphics package on my Windows laptop.  Getting
>that to work will require a few code fixes, of which the masking of
>ImageMagick's convert.exe by that in the C:/Windows/System32 seems to
>be the most challenging. plotdiff() relies on system2() calls to
>ImageMagick's 'convert'  function, as well as a call to
>Sys.which(c("convert", "compare")) that tests for the presence of
>ImageMagick on the Path. Even  if ImageMagick is placed early on the
>Path, though, both calls to Sys.which() and system2() find Windows'
>convert command  (which "Converts FAT volumes to NTFS") rather than
>ImageMagick's convert.
>Here's a reproducible example that shows what I'm seeing:
>    ## In R, make a pdf
>    pdf("a.pdf")
>    plot(rnorm(99), col="red")
>    dev.off()
>    ## At Windows cmd command line
>    where convert
>    ## C:\Program Files\ImageMagick-6.8.8-Q16\convert.exe
>    ## C:\Windows\System32\convert.exe
>    convert -density 100x100 a.pdf a.png
>    ## From R
>    ## Unqualified references to convert find the 'wrong' one
>    Sys.which("convert")
>    ##                               convert
>    ## "C:\\Windows\\system32\\convert.exe"
>     system2("convert",  "-density 100x100 a.pdf b.png")
>    ## Invalid Parameter - 100x100
>    ## Warning message:
>    ## running command '"convert" -density 100x100 a.pdf b.png' had
>status 4
>    ## A fully qualified reference does work
>    system2("C:/Program Files/ImageMagick-6.8.8-Q16/convert",
>"-density 100x100 a.pdf b.png")
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