Possible package.skeleton issue affecting Rcpp, RcppArmadillo, RStudio (!!), ...

[eddelbuettel]

So I just did the live webinar on Rcpp and got to show live how package generation now fails (from RStudio) for both Rcpp and RcppArmadillo 😢

It looks the NAMESPACE file now gets an 'echo' from a temp function we create but which is no longer there when the package is finished. And misses an actual exportPatter().

So a simple first fix for RcppArmadillo could be (done and tested)

modified   R/RcppArmadillo.package.skeleton.R
@@ -78,6 +78,8 @@ RcppArmadillo.package.skeleton <- function(name="anRpackage", list=character(),
     ## add a useDynLib to NAMESPACE,
     NAMESPACE <- file.path( root, "NAMESPACE")
     lines <- readLines( NAMESPACE )
+    lines <- lines[!grepl("^export.*fake", lines)]
+    lines <- c(lines, "exportPattern(\"^[[:alpha:]]+\")")
     if (! grepl("useDynLib", lines)) {
         lines <- c(sprintf("useDynLib(%s, .registration=TRUE)", name),
                    "importFrom(Rcpp, evalCpp)",        ## ensures Rcpp instantiation

do not print the fake one but add the pattern. Is my fear justified that the RStudio generator may need this too? Paging @kevinushey ....

[eddelbuettel]

I just pushed a simpler / better fix in a new branch. In essence we seem to need to keep a fake symbol around, and already cleaned up after it at the end. Now, it seems, R changed and somehow that symbol ends up in the NAMESPACE. So ... we clean that too.

That, plus ensuring an exportPattern(...) is set may be all we need here.

@kevinushey Can you remind how it works from RStudio when we create a package? Does it call the Rcpp function?

[kevinushey]

Hmm, it looks like the behavior in package.skeleton() has actually changed in R 4.0.0. Before, it would insert an export pattern; now, it just exports any objects in the global environment when package.skeleton() is called. For example, I see:

$ R --vanilla --slave -e "x <- 1; package.skeleton()" && cat anRpackage/NAMESPACE
Creating directories ...
Creating DESCRIPTION ...
Creating NAMESPACE ...
Creating Read-and-delete-me ...
Saving functions and data ...
Making help files ...
Done.
Further steps are described in './anRpackage/Read-and-delete-me'.
export("x")

Compare with R 3.6:

kevinushey@Kevins-MBP:~/scratch/opkasda
$ R --vanilla --slave -e "x <- 1; package.skeleton()" && cat anRpackage/NAMESPACE
Creating directories ...
Creating DESCRIPTION ...
Creating NAMESPACE ...
Creating Read-and-delete-me ...
Saving functions and data ...
Making help files ...
Done.
Further steps are described in './anRpackage/Read-and-delete-me'.
exportPattern("^[[:alpha:]]+")

So this might warrant a closer look at what package.skeleton() is doing.

[kevinushey]

Looks like this was changed here: wch/r-source@36b27d9#diff-a1b94fcea8b8818d4371aabf04dc2b3c

[eddelbuettel]

Yes, and for the narrow case of an empty package I now have it fixed by

• removing the faux global symbol
• adding the now missing exportPattern()

Question is what, if anything, to do with the more complicated usage patterns the skeleton helpers support "in theory" and which (as far as I can tell) nobody uses...

[eddelbuettel]

Good catch on the commit to R. We should probably stick our heads together, take another look on the weekend or Monday, or report to them. Looks like a bug, doesn't it?

[eddelbuettel]

With @dmurdoch kindly waving the cluebat at me we can assume the beahvior will stay so I think the simple PR here can be merged too.