R system functions always returns error 127

Question

I need to execute an external tool from R and process errors (if any) occurred in that tool. I know 3 functions to do something familiar with my task:

shell, system and system2.

Trying to test those, I see that command

shell("notepad")

opens notepad. As far as I know shell doesn't allow to check errors (there's no interface to look into stderr).

When I call

system("notepad")

or

system2("notepad")

R freezes trying to make those commands.

Calling

system("start notepad")

or

system2("start notepad")

returns warning

Warning message:
running command '"start notepad"' had status 127

The problem boils down to `notepad` not being in the PATH and therefore is not visible to R for executing it. On my machine, I can call `system("java -version")` with no trouble. Strangely, I could not get Notepad to launch from R even after adding it to my PATH. — Tim Biegeleisen, Nov 11 '15 at 08:49
I can also get `system("git version")` to work. There may be an issue with non command line programs in R. Why do you want to launch Notepad from R may I ask? — Tim Biegeleisen, Nov 11 '15 at 08:51
> system("git version") Warning message: running command 'git version' had status 127 — Powerfool, Nov 11 '15 at 08:54
Yes, because `git` is not on your `PATH`. Type `echo %PATH%` from a command prompt and you will see this. — Tim Biegeleisen, Nov 11 '15 at 08:56
Yes, this just worked for me as well. It seems like `system()` cannot launch a new window. So it hangs for Notepad. — Tim Biegeleisen, Nov 11 '15 at 08:59

score 21 · Answer 1 · answered Nov 19 '16 at 16:29

21

Adapting @DavidTseng's answer (sorry for not having enough reputation to upvote it)...

system("cmd.exe", input = "notepad")

worked for me in Windows.

answered Nov 19 '16 at 16:29

Jonas Luz Jr.

321
2
3

This is very useful in several ways - for instance, `system("cmd.exe", input = "tree > Tree.txt /A /F")` will make a file `Tree.txt` containing a directory tree with all folders, subfolders and files. – Dag Hjermann Sep 29 '21 at 09:30

score 5 · Accepted Answer · edited Jan 11 '17 at 03:31

As I mentioned in my comments, the R documentation reveals that in Windows the system() function does not launch a separate shell (if needed). This is why command line commands run with system(), but Notepad, which needs a separate window, does not run:

From the documentation for system():

The most important difference is that on a Unix-alike system launches a shell which then runs command. On Windows the command is run directly – use shell for an interface which runs command via a shell (by default the Windows shell cmd.exe, which has many differences from a POSIX shell).

score 4 · Answer 3 · answered Nov 09 '16 at 12:59

4

system("bash -l", input = "notepad")

answered Nov 09 '16 at 12:59

KST

589
9
15

score 1 · Answer 4 · answered Aug 23 '19 at 13:43

I'm not sure if there's been an update to R that allows this since the question was asked nearly four years ago, but system("\"C:\path\to\exe.exe\" args", intern = T) works for me and WILL bring up a separate child window and works on Windows 10 + R 3.6 + RStudio.

Not using the 'intern = T' was giving me a return code of 127 and did not run the process.

score 1 · Answer 5 · edited Jun 20 '20 at 09:12

1

I had the same issue. there is an additional step in the installation process which i did not do.

refer to to the url

https://cran.r-project.org/bin/windows/Rtools/

Look for "Putting Rtools on the PATH"

writeLines('PATH="${RTOOLS40_HOME}\usr\bin;${PATH}"', con = "~/.Renviron")

edited Jun 20 '20 at 09:12

Community

1
1

answered May 21 '20 at 10:47

Choc_waffles

518
1
4
15

score 0 · Answer 6 · answered Jul 13 '18 at 11:47

0

for windows users wrong: system(path("c:", "program files", "r", "anysoft.EXE")) but works : system(path("c:", shQuote("program files"), "r", "anysoft.EXE"))

answered Jul 13 '18 at 11:47

Никита Завьялов

11

score -3 · Answer 7 · edited Aug 12 '18 at 00:49

-3

You guys are making it so complicated. I solved this problem by referring to this answer. The problem is with the PATH. type Sys.which('') in R, and you will see nothing. So you have to set the path in CMD, and then use Sys.setenv(PATH = '') in R to get this work.

edited Aug 12 '18 at 00:49

ggorlen

44,755
7
76
106

answered Aug 11 '18 at 18:04

Bowen Chen

5
2

R system functions always returns error 127

7 Answers7

refer to to the url

Look for "Putting Rtools on the PATH"

Linked