[FIXED] How to key in "Yes" or "No" in Jupyter notebook

Issue

I already referred this post and this post. But it doesn't solve my problem. Please don't mark it as duplicate

I am trying to run the below piece of code in Jupyter Notebook with R kernel.

model_predictors <- buildModel(flag, fv_full_data, outcomeName, folder)

I get an error message like below

Model about to be built   # this is log message and not error

1 package is needed for this model and is not installed. (randomForest). Would you like to try to install it now?    # here I see that it asks for a question but without my input it selects `No`
Error: Required package is missing
Traceback:

1. buildModel(flag, fv_full_data, outcomeName, folder)
2. train(x = trainDF[, predictorsNames], y = factor(trainLabels), 
 .     method = "rf", metric = "Fscore", trControl = objControl, 
 .     tuneGrid = rf_grid, preProcess = c("center", "scale"))
3. train.default(x = trainDF[, predictorsNames], y = factor(trainLabels), 
 .     method = "rf", metric = "Fscore", trControl = objControl, 
 .     tuneGrid = rf_grid, preProcess = c("center", "scale"))
4. checkInstall(models$library)
5. stop("Required package is missing", call. = FALSE)

How can I avoid this error and prevent jupyter selecting No as default for dynamic prompts?

Solution

In your example, you actually never reach the part of code that handles input. These inputs only occur for interactive sessions - which Jupyter is not. You can check with

interactive()
#> FALSE

menu(c("yes", "no"))
#> Error in menu(c("yes", "no")): menu() cannot be used non-interactively
#> Traceback:
#> 
#> 1. menu(c("yes", "no"))
#> 2. stop("menu() cannot be used non-interactively")

caret::checkInstall prints out the message "Would you like to try to install x now?", but it will only accept input for interactive sessions.

Here is the code for caret::checkInstall with my comments.

function (pkg) 
{
    good <- rep(TRUE, length(pkg))
    for (i in seq(along = pkg)) {
        tested <- try(find.package(pkg[i]), silent = TRUE)
        if (inherits(tested, "try-error")) 
            good[i] <- FALSE
    }
    if (any(!good)) {
        pkList <- paste(pkg[!good], collapse = ", ")
        msg <- paste(sum(!good), ifelse(sum(!good) > 1, " packages are", 
            " package is"), " needed for this model and", 
            ifelse(sum(!good) > 1, " are", " is"), 
            " not installed. (", pkList, "). Would you like to try to install", 
            ifelse(sum(!good) > 1, " them", " it"), 
            " now?", sep = "")
        cat(msg) # Print the message
        if (interactive()) { # In Jupyter, `interactive()` is `FALSE`.
            bioc <- c("affy", "logicFS", "gpls", 
                "vbmp")
            installChoice <- menu(c("yes", "no")) # This is where it gets input
            if (installChoice == 1) {
                hasBioc <- any(pkg[!good] %in% bioc)
                if (!hasBioc) {
                  install.packages(pkg[!good])
                }
                else {
                  inst <- pkg[!good]
                  instC <- inst[!(inst %in% bioc)]
                  instB <- inst[inst %in% bioc]
                  if (length(instC) > 0) 
                    install.packages(instC)
                  biocLite <- NULL
                  source("http://bioconductor.org/biocLite.R")
                  biocLite(instB)
                }
            }
            else stop("Required package is missing", call. = FALSE)
        }
        else stop("Required package is missing", call. = FALSE) # Because `interactive()` is `FALSE`, this `stop` is called
    }
}

For your situation, install.packages("randomForest") is the best option.

If you were in RStudio, you could use the rstudioapi like this

f <- function() {
  rstudioapi::sendToConsole("1")
  menu(c("yes", "no"))
}
f()
#> 1: yes
#> 2: no
#> 
#> Selection: 1
#> [1] 1

Answered By - Paul