通过 R 中的 system2() 对终端提示响应是

Question

tl;dr : How can I invoke the system command y | conda create --name gee_interface y | conda create --name gee_interface from an R console, eg via system2()? I'm comfortable enough with system2('conda', c('create', '--name', 'gee_interface')) , but I don't know how to handle piping in the 'y' via system2() .

Details I am trying to use an R console to run the bash command conda create --name gee_interface (OSX Mojave with Anaconda installed).

In terminal, that command executes just fine, but prompts me to answer with Proceed ([y]/n)? (I answer 'y' and everything works smoothly).

In R, I run

Sys.setenv(PATH = paste(c("/Applications/anaconda3/bin", Sys.getenv("PATH")), collapse = .Platform$path.sep)) # ensures that system2() finds conda

system2('conda', c('create', '--name', 'gee_interface')) # This is the key line for the purposes of this question

When running the second line [ie system2('conda', c('create', '--name', 'gee_interface')) ], the process never finishes, but quickly falls to zero CPU usage. Presumably the system is waiting for my response to the prompt, but I don't know how to provide it. How does one do this via an R script? Note also that in my particular case, the number of times that I need to respond 'y' is variable, depending on whether an environment of the name gee_interface already exists or not.

Answer 1

The fix to your first problem is to tell conda not to ask for confirmation using -y :

system2('conda', c('create', '--name', 'gee_interface', '-y'))

As to the second part (variable times that your input is required), I'm guessing it's to overwrite the environment if it exists? In that case, you could check for its existence first with conda info --envs , and run conda remove --name gee_interface --all if necessary before creating it.

See:

https://docs.conda.io/projects/conda/en/latest/commands/create.html

https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#removing-an-environment

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You could also try your system2 call, with the argument input = "y" , but that doesn't fix your second problem of needing to affirm multiple times.

See: Invoke a system command and pipe a variable as an argument