Error: could not find function "str2expression"

[jimmygillan]

Hi! Excited to make use of this tool, but running into some basic issues.

Cobalt version 4.2.0 MatchIt version 3.0.2 R version 3.5.3 (2019-03-11) OS linux-gnu

The following code generates the following errror: Error: could not find function "str2expression"

xdata <- data.frame(treat = 1 * (runif(100) <= 0.5),
                    x1 = rnorm(100, 2, 4),
                    x2 = rnorm(100, 5, 2))
matching <- MatchIt::matchit(treat ~ x1 + x2, data = xdata, distance = "mahalanobis", replace = TRUE)
cobalt::bal.plot(matching)

Let me know if I can clarify anything.

Thanks.

[ngreifer]

Hi Jimmy,

This is because you are using an old version of R. You can either update R to a new version or update the backports package. Let me know if either of these fixes fails to solve the problem.

Noah

[kthohr]

Just a suggestion, but if you are relying on functionality introduced in R 3.6, consider incrementing the minimum version of R in your package description file. This will make it easier for users (and admins) to track their R version dependencies.

[ngreifer]

@kthohr I import the backports package, which contains all functions from previous R versions. Normally, importing it is sufficient and this problem doesn't occur. There was a bug in backports that caused the package to fail, propagating to my package. So the problem isn't that users need a higher R version, it's that a package I depended on failed and I didn't catch the bug until I got a few complaints like the one above. As soon as I noticed, I contacted the backports developer and they fixed the bug. cobalt still only requires R 3.3.0. Updating R is just one immediate solution to the problem (and is recommended in general).

[kthohr]

@ngreifer My understanding is that str2expression was a new addition with R 3.6, and is not included in the backports package.

[ngreifer]

@kthohr The backports package contains all the new functions that have been added in recent R versions, including str2expression. Its purpose is to allow package authors to depend on early versions of R while still taking advantage of the functions released in recent versions of R. By importing backports in my R package, I can allow users not to update R while still being able to use the new R functions in my code.

If you look at the documentation for backports, you won't see str2expression or any recently added functions. backports has a special function for use in R packages that imports all the new functions. Users should not have to use backports, or generally even know it exists. This time, due to a bug in it, it was unable to do its job with my package.

[kthohr]

The backports package does not provide all of the new functions that have been added to R since version 3.0.0; and, to my eyes, the backports package description does not claim this level of coverage. I am looking at the source code for backports and it does not include str2expresssion.

I just tested this on a fresh installation of R 3.5.3. I suggest trying this for yourself.

[ngreifer]

@kthohr Wow, you're absolutely right! I'm honestly shocked to find this. I really had assumed they had implemented every new function, but it seems they have forgotten a few. I'm going to manually add str2expression to my package's environment so that old versions of R along with the newest version of backports should work correctly.

Onbackports's README, step 3 is to set the R version in DEPENDS to >=3.0.0, which I took to mean that using backports was sufficient for adding support for all R versions after 3.0.0. Clearly I was wrong.

Thank you so much for looking into this in-depth even as I was inappropriately adamant that I was right. I'm sorry that I was short with you. I'm going to update cobalt shortly.

[kthohr]

No worries. Glad there's an easy fix.

The omission of str2expression (as well as str2lang) from backports is likely due to the somewhat more complicated implementation of these functions in base R; a strict backport would likely require copying chunks of the base C code (do_str2lang, for sure, and probably more).

[ngreifer]

That makes sense. I included the following line in the cobalt source:

 if (getRversion() < 3.6) str2expression <- function(text) parse(text=text, keep.source=FALSE)

Do you think that will be sufficient?

[kthohr]

Looks good to me, and matches the R-level implementation noted in the base R code.