R packages: "Error: object 'compute' not found whilst loading namespace .."

Question

My directory structure is as follows:

c:/Users/bob/MyPackageName
c:/Users/bob/MyPackageName/R
c:/Users/bob/MyPackageName/tests
c:/Users/bob/MyPackageName/tests/testthat

My development session normally consists of starting an R session in the package root (c:/Users/bob/MyPackageName), and running

devtools::load_all()
devtools::test()

followed by alternating the addition of little bits in MyPackageName/tests/testthat/mytest.R and in MyPackageName/R/mycode.R.

When starting a session returns

Loading MyPackageName
Error: object 'compute' not found whilst loading namespace 'MyPackageName'

I try:

1. Calling an explicit devtools::load_all("c:/Users/bob/MyPackageName")
2. Searching for an errant instance of compute (package required, function name, anything..). But all is good.
3. Clearing some caches, rm(list=ls()).
4. Calling a localized devtools::load_all() from a session in c:/Users/bob/MyPackageName/tests/testthat and another in c:/Users/bob/MyPackageName/tests/testthat.
5. Regenerating the documentation through devtools::document(), lest some corruption in those has gone awry.
6. Delete MyPackageName/.RData and MyPackageName/.Rhistory.

But nothing. I still get Error: object 'compute' not found whilst loading namespace 'MyPackageName'

What else can I try? For example, what is the pre-Devtools method of "loading all"? What is "object 'compute'"?

When I start an R session outside of the package directory, all is well. Hence my R setup is fine; this question is in the context of writing an R package.

Answer 1

This may be a work-around. Perhaps you can give it a try.

I have encountered similar error Error: object 'compute' not found whilst ... when I rebuilt a package (R version 3.5.0, roxygen2 version 3.5.0).

I wound up with manually removing the first row S3method(compute,...) in NAMESPACE to get the package rebuilt.

Answer 2

It's hard to tell without seeing the function names but this could be an issue since ROxygen >3 now uses @export for both S3 objects and functions. Therefore, if you have a function using dots e.g. compute.something.cool() and you use ROxygen's #' @export, it might be inferring that it is a S3 object rather than a function.

This is described in more detail here but in short explicitly name your function with the export call:

#' @export compute.something.cool

This approach will mean you can still use devtools::document() to keep your NAMESPACE updated without having to manually do it. A note, that Bioconductor do not permit packages to use dot naming conventions, probably for this very reason so it might be worth avoiding this in the future.