"Could Not Find Function" in Roxygen Examples During Cmd Check

Could not find function in Roxygen examples during CMD check

My guess is that you need to #' @export the function in the Roxygen comment, otherwise the function is not exported to the namespace of the package and it cannot be found.

could not find function when running examples in package check

You should also have :

importFrom(dplyr,inner_join)

in NAMESPACE

you can get Roxygen to create this in NAMESPACE by having :

#' @ImportFrom dplyr inner_join
NULL

in one of your package's R scripts

Could not find function %% during CMD check

Add this to the script that contains the function(unless you imported the entire dplyr).

@importFrom magrittr "%>%"

If you intend to use dplyr functions maybe explicitly call them like:

dplyr::group_by
dplyr::filter_at

CRAN checks errors on roxygen @examples: base::assign and missing reshape2

As @stefan suggested in the comments, I had to add reshape2 into the Suggested packages in the description file. I added using:

usethis::usepackage("reshape2", "Suggests")

Followed by regenerating the docs:

devtools:document()

Package is on its way to CRAN!

R CMD check gives warning when using @includeRmd for examples using Roxygene

Your usage of the @includeRmd tag does not appear to be supported. You can use it to generate a Description or (sub)sections of Details, but not Examples. The documentation states:

It is currently not possible to document function arguments, return values, etc. in external Rmd documents.

That isn't too surprising, for a couple of reasons:

• R CMD check expects the \examples{} block to contain verbatim R code, not Markdown, so injecting Markdown into the block without preprocessing is doomed to fail. Due to the chunk header and footer, the following is not valid R code:

  ```{r adder_examples}
  adder(3, 5, 6)
  ```
  

  That said, roxygen2 seems to do some preprocessing, since the above generates the following \examples{} block:

  \examples{
  \if{html}{\out{<div class="sourceCode r">}}\preformatted{adder(3, 5, 6)
  }\if{html}{\out{</div>}}\preformatted{## [1] 14
  }
  

  The injected text would be valid inside of \description{} or \details{}, but isn't valid inside of \examples{} as it is not verbatim R code.

• As exceptions to the "verbatim" rule, the \examples{} block permits the \dontrun, \dontshow, and \donttest macros. They are handled exceptionally by R CMD check, but not by the knitr vignette engine. You'd get a build failure if you tried to insert this chunk into a vignette:

  ```{r adder_examples}
  adder(3, 5, 6)
  \dontrun{
  adder(3, 5, "6")
  }
  ```
  

  With chunk option eval = 1L, the parser still throws an error. (eval = FALSE seems OK, but then the first line isn't evaluated.) Hence, even if @includeRmd could be used to generate a valid \examples{} block, you wouldn't necessarily be able to share the code with a vignette.

If you really want to externalize your Examples, then you can try doing it the old-fashioned way, i.e., with a shell script and sed, using @examples as a marker for text insertion (some examples here). I doubt the complexity is worth it, but you can be the judge...

---

Update: I've just tried to hack things a bit with my own minimal package...

pkgname <- "foo"
usethis::create_package(pkgname, rstudio = FALSE, open = FALSE)
setwd(pkgname)
usethis::use_directory(file.path("inst", "examples"))
text <- "
#' @title A title
#' @description A description.
#' @param a,b Arguments.
#' @includeRmd inst/examples/add.Rmd examples
#' @export
add <- function(a, b) a + b
"
cat(text, file = file.path("R", "add.R"))
text <- "
add(1, 1)
"
cat(text, file = file.path("inst", "examples", "add.Rmd"))
roxygen2::roxygenize(".")
writeLines(readLines(file.path("man", "add.Rd")))

\examples{
add(1, 1)
}

So it seemed like deleting the chunk header and footer might allow roxygen2 to generate a sensible \examples{} block. But I was wrong:

text <- "
add(1, 1)
add(2, 2)
"
cat(text, file = file.path("inst", "examples", "add.Rmd"))
roxygen2::roxygenize(".")
x <- readLines(file.path("man", "add.Rd"))
writeLines(tail(x, -(grep("^\\\\examples", x) - 1L)))

\examples{
add(1, 1) add(2, 2)
}

The generated text is invalid R code when the example spans two or more lines, because Markdown treats newlines like spaces.

### ** Examples ... Error: could not find function building packages in R

The following achieves what you want, I believe:

lad <- function(y, x, data) {
  dat <- setNames(read.csv(data)[, c(x, y)], c('x', 'y'))
  sum.abs.dev <- function(beta, data) {
    with(data, sum(abs(y - beta[1] - beta[2] * x)))
  }
  fit <- lm(y ~ x, dat)
  optim(par=coef(fit), sum.abs.dev, data=dat)$par
}

lad(y = "farm", x = "land", data="FarmLandArea.csv")

#  (Intercept)            x 
# -605.2293682    0.3642028 

r: errors creating package with devtools & roxygen2

Best answer I've found is in this blog post: Hilary Parker R-Package Blog Post

The steps I follow to document and install are as follows:

1. Within the project that contains my package, open a new R Script and run setwd('..')
2. Run devtools::document()
3. Run devtools::install()

This works for me when initially installing my package and also updating it.

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