Re: [Rd] Possibly broken system2 env-option
Studying Professor Dalgaard's code a bit, here is a little hack that
returns the desired result on Unix-alikes:
From
>* system2("echo", env = c("VAR='Hello World'"), args = c("$VAR"))*
to
>* system2("echo", env = c("VAR='Hello World';"), args = c("$VAR"))*
Hello World
That is, adding the semi-colon effectively transforms
pd$ VAR="foo" echo $VAR
to
pd$ VAR="foo"; echo $VAR
Maybe this doesn't apply to more complicated situations,though.
luke
[[alternative HTML version deleted]]
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Possibly broken system2 env-option
Okay, thanks for clarification.
On 3/19/19 10:51 AM, peter dalgaard wrote:
> You are using it wrong. It wants strings of the form "name=value", not a
> character vector with names as labels. So this is closer to the mark:
>
>> system2("echo", env = c("VAR='Hello World'"), args = c("$VAR"))
>
>>
>
> However, as you see it doesn't work as intended. The problem is that the
> $-substitution refers to the environment of the shell executing the command.
> I.e. this does not work from a terminal command line either:
>
> pd$ VAR="foo" echo $VAR
>
> pd$
>
> Or even
>
> pd$ VAR="bar"
> pd$ VAR="foo" echo $VAR
> bar
>
> What you need is something like (NB: single quotes!)
>
> pd$ VAR="foo" sh -c 'echo $VAR'
> foo
>
> So:
>
>> system2("sh", env = c("VAR='Hello World'"), args = c("-c 'echo $VAR'"))
> Hello World
>
> -pd
>
>> On 18 Mar 2019, at 17:28 , Henning Bredel wrote:
>>
>> Hey all,
>>
>> what is wrong with this command:
>>
>> system2("echo", env = c(VAR = "Hello World"), args = c("$VAR"))
>>
>> I am a bit confused, as help("system2") writes about the env option:
>>
>>> character vector of name=value strings to set environment variables.
>>
>> Is this option buggy, or am I using it just wrong?
>>
>> Thanks for your help
>>
>> Henning
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Possibly broken system2 env-option
Right. I suppose, one thing you can do is setting the env var in the
current process, call system2() and then unset/restore the env var.
This is unlikely to cause problems, unless your R process is
multi-threaded, and the env var causes troubles in the other threads.
The withr package makes setting the temporary env var convenient, but
it is easy to write your own with_envvar() function:
withr::with_envvar(
c(VAR = "Hello world"),
system2("sh", "-c 'echo $VAR'"))
This seems to be portable, at least it works on macOS and Windows.
G.
On Tue, Mar 19, 2019 at 10:44 AM peter dalgaard wrote:
>
> On Windows, ‘env’ is only supported for commands such as ‘R’ and
> ‘make’ which accept environment variables on their command line.
>
> So I suppose that would be tricky.
>
> The basic issue is that on Unix-alikes, system2 constructs a command like
>
> FOO=bar cmd args
>
> and passes that to sh via system(). On windoes, system() does not call sh, so
> system2() does (effectively)
>
> cmd FOO=bar args
>
> and hopes that cmd knows what to do with the env setting.
>
> -pd
>
> > On 19 Mar 2019, at 11:09 , Gábor Csárdi wrote:
> >
> > On Tue, Mar 19, 2019 at 9:59 AM peter dalgaard wrote:
> > [...]
> >> What you need is something like (NB: single quotes!)
> >>> system2("sh", env = c("VAR='Hello World'"), args = c("-c 'echo $VAR'"))
> >> Hello World
> >
> > Just out of curiosity, do you think it is possible to make this
> > portable, assuming sh is available? On Windows it gives
> >
> >> system2("sh", env = c("VAR='Hello World'"), args = c("-c 'echo $VAR'"))
> > /rtools34/bin/sh: VAR=Hello World: No such file or directory
> > Warning message:
> > running command '"sh" VAR='Hello World' -c 'echo $VAR'' had status 127
> >
> > G.
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk Priv: pda...@gmail.com
>
>
>
>
>
>
>
>
>
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Possibly broken system2 env-option
On Windows, ‘env’ is only supported for commands such as ‘R’ and
‘make’ which accept environment variables on their command line.
So I suppose that would be tricky.
The basic issue is that on Unix-alikes, system2 constructs a command like
FOO=bar cmd args
and passes that to sh via system(). On windoes, system() does not call sh, so
system2() does (effectively)
cmd FOO=bar args
and hopes that cmd knows what to do with the env setting.
-pd
> On 19 Mar 2019, at 11:09 , Gábor Csárdi wrote:
>
> On Tue, Mar 19, 2019 at 9:59 AM peter dalgaard wrote:
> [...]
>> What you need is something like (NB: single quotes!)
>>> system2("sh", env = c("VAR='Hello World'"), args = c("-c 'echo $VAR'"))
>> Hello World
>
> Just out of curiosity, do you think it is possible to make this
> portable, assuming sh is available? On Windows it gives
>
>> system2("sh", env = c("VAR='Hello World'"), args = c("-c 'echo $VAR'"))
> /rtools34/bin/sh: VAR=Hello World: No such file or directory
> Warning message:
> running command '"sh" VAR='Hello World' -c 'echo $VAR'' had status 127
>
> G.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk Priv: pda...@gmail.com
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Possibly broken system2 env-option
On Tue, Mar 19, 2019 at 9:59 AM peter dalgaard wrote:
[...]
> What you need is something like (NB: single quotes!)
> > system2("sh", env = c("VAR='Hello World'"), args = c("-c 'echo $VAR'"))
> Hello World
Just out of curiosity, do you think it is possible to make this
portable, assuming sh is available? On Windows it gives
> system2("sh", env = c("VAR='Hello World'"), args = c("-c 'echo $VAR'"))
/rtools34/bin/sh: VAR=Hello World: No such file or directory
Warning message:
running command '"sh" VAR='Hello World' -c 'echo $VAR'' had status 127
G.
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Possibly broken system2 env-option
You are using it wrong. It wants strings of the form "name=value", not a
character vector with names as labels. So this is closer to the mark:
> system2("echo", env = c("VAR='Hello World'"), args = c("$VAR"))
>
However, as you see it doesn't work as intended. The problem is that the
$-substitution refers to the environment of the shell executing the command.
I.e. this does not work from a terminal command line either:
pd$ VAR="foo" echo $VAR
pd$
Or even
pd$ VAR="bar"
pd$ VAR="foo" echo $VAR
bar
What you need is something like (NB: single quotes!)
pd$ VAR="foo" sh -c 'echo $VAR'
foo
So:
> system2("sh", env = c("VAR='Hello World'"), args = c("-c 'echo $VAR'"))
Hello World
-pd
> On 18 Mar 2019, at 17:28 , Henning Bredel wrote:
>
> Hey all,
>
> what is wrong with this command:
>
> system2("echo", env = c(VAR = "Hello World"), args = c("$VAR"))
>
> I am a bit confused, as help("system2") writes about the env option:
>
>> character vector of name=value strings to set environment variables.
>
> Is this option buggy, or am I using it just wrong?
>
> Thanks for your help
>
> Henning
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk Priv: pda...@gmail.com
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Possibly broken system2 env-option
Probably not broken, just hard to get the quoting right? Or it does
not work with echo?
It is surely hard to get it right, I have been trying for 15 minutes.I
am pretty sure that the correct form is env = "VAR='Hello-World'" but
spaces and other special characters might cause trouble. E.g. this
works, but only without spaces (px is an internal tool for testing,
that can get an env var, and it is portable):
❯ px <- processx:::get_tool("px")
❯ system2(px, c("getenv", "VAR"), env = "VAR=foo")
foo
❯ system2(px, c("getenv", "VAR"), env = c(VAR="Hello World"))
sh: Hello: command not found
Warning message:
In system2(px, c("getenv", "VAR"), env = c(VAR = "Hello World")) :
error in running command
Somebody with more system2() experience can probably fix this, but
here is an alternative, using the processx package:
❯ processx::run(px, c("getenv", "VAR"), env = c(Sys.getenv(), VAR =
"Hello World"))
$status
[1] 0
$stdout
[1] "Hello World\n"
$stderr
[1] ""
$timeout
[1] FALSE
For processx, you don't need to quote anything (i.e. command,
arguments or env vars), because it does not
use an intermediate shell.
Disclaimer: I am an author of processx.
Gabor
On Tue, Mar 19, 2019 at 9:28 AM Henning Bredel wrote:
>
> Hey all,
>
> what is wrong with this command:
>
> system2("echo", env = c(VAR = "Hello World"), args = c("$VAR"))
>
> I am a bit confused, as help("system2") writes about the env option:
>
> > character vector of name=value strings to set environment variables.
>
> Is this option buggy, or am I using it just wrong?
>
> Thanks for your help
>
> Henning
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
