How to find correct executable with Sys.which on Windows - r

Question

What are the workarounds on Windows to make it so Sys.which finds the proper executables? Two cases that are reoccuring problems:
convert.exe which is both a windows program and the ImageMagik program, but Sys.which only finds the windows one which is never wanted from R no matter how I seem to arrange things on my PATH.
tar.exe is packaged along with various things like git or mingw or whatever, and even when I have Rtools and Rbuildtools first in my path, the tar program from Rtools is never found, for example when installing a package from source.
So, I have resorted to writing a wrapper that calls 7-zip instead whenever I am on windows. This can't be the thing to do can it?
Edit
Actually just adding an environment variable to .Renviron: TAR=path/to/tar.exe works fine for the install.packages example, and I am having trouble remembering where else the tar.exe was biting me, but Josh answered the main one, convert.exe.

Answer 1

I asked a +/- identical question earlier this year over on R-devel. Among the replies was this one, by Henrik Bengtsson, who kindly provided the following useful function:
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)
}
## Trying out Sys.which & Sys.which2 on my Windows box gives the following:
Sys.which("convert")
# convert
# "C:\\Windows\\system32\\convert.exe"
Sys.which2("convert")
# convert
# "C:\\Program Files\\ImageMagick-6.8.8-Q16\\convert.exe"
I'm really not sure why R-core don't just fix Sys.which() to make it actually portable, but they at least do document root cause of this behavior in ?system (whose functionality is afflicted by the same problem):
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'.

Answer 2

Because Sys.which() is vectorized–and since I think that is useful–I've modified the Henrik Bengtsson code in the following function sys_which(), which should be a more robust and more similar version of Sys.which():
## check if unix
is_unix <- function() grepl("unix", .Platform$OS.type, ignore.case = TRUE)
## robust version of Sys.which
sys_which <- function(x) {
if (is_unix()) {
return(Sys.which(x))
}
sys_win <- function(x) {
if (grepl("\\S", path <- Sys.which(x))) {
return(path)
}
path <- tryCatch(
suppressWarnings(system(sprintf("where %s", x), intern = TRUE)[1]),
warning = function(w) "",
error = function(e) "")
if (!grepl("\\S", path)) {
return(`names<-`("", x))
}
`names<-`(path, x)
}
vapply(x, sys_win, character(1))
}
This has the following advantages:
It's vectorized–sys_which() can handle a vector (one or more input values) e.g., sys_which(c("python", "python3"))
It's more error resistant–use of tryCatch(...) ensures any inputs that result in an error from the system call get passed on to the normal Sys.which() function.
Example:
> sys_which(c("python", "python2.7", "python3", "asdf"))
#> python python2.7 python3 asdf
#> "/usr/bin/python" "/usr/bin/python2.7" "/usr/local/bin/python3" ""