Two Environment Variables for More Robust R Code

The good, the bad, and the ugly of R's typing system and how environment variables can remedy the situation.

Two Environment Variables for More Robust R Code

I was recently contacted because my Bioconductor package openPrimeR was failing the automated package tests. The reason for this is that the Bioconductor team had decided to set a new environment variable when testing the packages, which is called _R_CHECK_LENGTH_1_LOGIC2_. I then looked into this environment variable a bit more and found that there is also _R_CHECK_LENGTH_1_CONDITION_. Because I really like the idea behind these environment variables, I’d like to share what you can do with them:

  1. Prevent non-scalar conditions using _R_CHECK_LENGTH_1_CONDITION_
  2. Ensure that logical operators && and || are applied only to scalars: _R_CHECK_LENGTH_1_LOGIC2_

To understand the motivation for the environment variable _R_CHECK_LENGTH_1_CONDITION_, let’s take a look at conditionals in R.

Conditionals

In R, conditionals have the following form:

if (<condition>) {
    <statements>
}

Only if <condition> evaluates to TRUE will the <statements> be executed. For example:

if (TRUE) {
    print("yay")
}
## [1] "yay"

Since R is heavily focused on vectorized operations, R users will often use non-scalar expressions in the <condition> block. However, every <condition> is automatically coerced to a scalar value. Unfortunately, the coercion of conditions with length greater than 1 is a valid operation in R that results only in a warning. This means that we can write something like this:

cond <- c(TRUE, FALSE, FALSE)
if (cond) {
    print("First entry was True, so we're fine ...")
}
## Warning in if (cond) {: the condition has length > 1 and only the first element
## will be used
## [1] "First entry was True, so we're fine ..."

Note that, when the developer’s intention was anything else than merely checking the first entry of the condition, then something is probably wrong with the program. Even if this was the developer’s intention, he should have explicitly used cond[1] in the condition rather than abusing a “language feature” that is more destructive than helpful.

What can we do to forbid non-scalar conditions? This is where _R_CHECK_LENGTH_1_CONDITION_ comes to the rescue. When activated, the evaluation of non-scalar conditions will cause an error rather than a warning. Let’s see this in action on the previous code snippet:

# prevent length 1 condition
Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = "TRUE")
cond <- c(TRUE, FALSE, FALSE)
if (cond) {
    print("First entry was True, so we're fine ...")
}

This gives us the output:

Error in if (cond) { : the condition has length > 1

So, by using _R_CHECK_LENGTH_1_CONDITION_, we can find any potential problem in our code relating to non-scalar conditions.

Next, let’s quickly recapitulate logical operators in order to learn how _R_CHECK_LENGTH_1_LOGIC2_ can help us.

Logical Operators && and ||

In R, there are two types of operators for logical conjunctions (AND, &&, &) and disjunctions (OR, ||, |). Let’s consider conjunctions as an example. Operator && evaluates only the first element of each vector, thereby producing a scalar value. Operator &, on the other hand, evaluates each vector element, thereby (potentially) producing a vector.

Unfortunately, && can be also be applied to vectors and not only scalars, which can lead to problems. For example, let’s consider that a developer wants to check whether the element-wise conjunction of two vectors evaluates to TRUE. He ends up with the following code:

x <- c(TRUE, FALSE)
y <- c(TRUE, TRUE)
if (x && y) {
    print("Pairwise conjunction was TRUE") # CAUTION: this is a false claim
}
## [1] "Pairwise conjunction was TRUE"

However, the result is wrong because && checks only the first elements of x and y, respectively. In fact, what the developer had intended to do was to write the following code, which yields the correct result:

if (all(x & y)) {
    print("Conjunction of all values was TRUE")
} else {
    print("Conjunction of all values was FALSE")
}
## [1] "Conjunction of all values was FALSE"

To prevent unintended results due to the application of operator && on non-scalar values, we can activate the environment setting _R_CHECK_LENGTH_1_LOGIC2_. Let’s see how it works in practice with our example from earlier:

Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_" = "TRUE")
if (x && y) {
    print("Pairwise conjunction was TRUE") # CAUTION: this is a false claim
}

The output is:

Error in x && y : 'length(x) = 2 > 1' in coercion to 'logical(1)'

So, by setting _R_CHECK_LENGTH_1_LOGIC2_, we are protected from mistakenly applying && on non-scalar values.

More Configuration Options for Environment Settings

Besides activating environment settings using TRUE, we can also define further behavior. For example:

  • Print stack trace and throw error: Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_" = "verbose")
  • Abort the R session: Sys.setenv("_R_CHECK_LENGTH_1_LOGIC2_" = "abort")

It can also be useful to set these environment variables on the command-line. For example, before running R CMD check on a package, we could activate _R_CHECK_LENGTH_1_LOGIC2_ in the following way:

export _R_CHECK_LENGTH_1_LOGIC2_=TRUE

Conclusion

Using environment variables such as _R_CHECK_LENGTH_1_CONDITION_ and _R_CHECK_LENGTH_1_LOGIC2_, we can write more robust R code by spotting potential errors earlier. This is why I would advise everyone to activate these variables during development. Another benefit is that we can also spot potential errors in libraries that we are using. By reporting/fixing these findings, we can improve the overall quality of R software.

If you like the idea of always using these environment settings by default, you can insert the following lines into the .Renviron file in your home folder:

_R_CHECK_LENGTH_1_LOGIC2_=TRUE
_R_CHECK_LENGTH_1_CONDITION_=TRUE

And now, happy coding!

Author: Matthias Döring

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