You probably already know, but you can at least work around it as:
Sys.which2 <- function(cmd) {
stopifnot(length(cmd) == 1)
if (.Platform$OS.type == "windows") {
suppressWarnings({
pathname <- shell(sprintf("where %s 2> NUL", cmd), intern=TRUE)[1]
})
if (!is.na(pathname)) return(setNames(pathname, cmd))
}
Sys.which(cmd)
}
(it falls back to Sys.which() if 'where %s' doesn't give anything)
> Sys.which2("convert")
convert
"C:\\Program Files\\ImageMagick-6.8.3-Q16\\convert.exe"
> Sys.which("convert")
convert
"C:\\Windows\\system32\\convert.exe"
/Henrik
On Mon, May 18, 2015 at 11:08 AM, Yihui Xie <x...@yihui.name> wrote:
> +1 I have exactly the same problem.
>
> Regards,
> Yihui
> --
> Yihui Xie <xieyi...@gmail.com>
> Web: http://yihui.name
>
>
> On Mon, May 18, 2015 at 12:29 PM, Josh O'Brien <joshmobr...@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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>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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