for some reason pkgdown is failing to parse one of the .Rd files that I have in my package. I found it fails when I add examples to the roxygen2 documentation using either the #examples tag or the #example inst/example/add.R alternative. I minimized my function to two arguments in order to make it more "reproducible" and still getting the same error. Please find bellow the error message, the .Rd file generated using that devtools::document() and the roxygen2 documentation of the function. As you can see I am using a very simple example that should run with no problems... One more thing to say is that when I run devtools::check() all my examples pass, so I don't understand why pkgdown is failing.
Thank you so much for your help.
Best,
Error message
Reading 'man/merge.Rd'
Error : Failed to parse Rd in merge.Rd
i unused argument (output_handler = evaluate::new_output_handler(value = pkgdown_print))
Error: callr subprocess failed: Failed to parse Rd in merge.Rd
i unused argument (output_handler = evaluate::new_output_handler(value = pkgdown_print))
.Rd file
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/merge.R
\name{merge}
\alias{merge}
\title{Merge two tables}
\usage{
merge(x, y)
}
\arguments{
\item{x}{data frame: referred to \emph{left} in R terminology, or \emph{master} in
Stata terminology.}
\item{y}{data frame: referred to \emph{right} in R terminology, or \emph{using} in
Stata terminology.}
}
\value{
a data.table joining x and y.
}
\description{
This is the main and, basically, the only function in joyn.
}
\examples{
x <- c(1, 2)
}
roxygen2 documentation
#' Merge two tables
#'
#' This is the main and, basically, the only function in joyn.
#'
#' #param x data frame: referred to *left* in R terminology, or *master* in
#' Stata terminology.
#' #param y data frame: referred to *right* in R terminology, or *using* in
#' Stata terminology.
#' #return a data.table joining x and y.
#' #export
#' #import data.table
#'
#' #examples
#' x <- c(1, 2)
This error comes from downlit::evaluate_and_highlight (sad it's not reported in the output), and can be fixed by installing the development version of downlit:
library(devtools)
install_github('r-lib/downlit')
It make sense only if you use the git version also from pkgdown, the stable pkgdown (version 1.6.1) runs just fine with the stable downlit. Of course development version of any package can break at any time, but until it doesn't, it's just alright.
Related
When developing packages, I often have R scripts stored in the inst directory that produce data objects then included in the package, i.e. stored as someObj.rda in the data directory.
These objects, in turn, have R scripts with roxygen2 headers for documentation (e.g. someObj.R).
Ideally, I would like to include a line in the roxygen2 header that sources and formats the script as code, OUTSIDE of examples. Yes, I could copy the lines in, but in the DRY principle, it would be nice to have the documentation include the code automatically.
I have tried the following with no success:
rdScript <- function(x) {
lns <- readLines(x)
lns <- sprintf("#' \\code{%s}", lns)
cat(lns, sep = "\n")
}
#' #name someObj
#' #title Some R Bbject
#' #description Some R Object
#' #details
#' Data created with the following script:
#' #eval rdScript("inst/createCrimeData.R")
#'
NULL
And this:
rdScript <- function(x) {
lns <- readLines(x)
lns <- sprintf("\\code{%s}", lns)
lns
}
#' #name someObj
#' #title Some R Bbject
#' #description Some R Object
#' #details
#' Data created with the following script:
#' #eval rdScript("inst/createCrimeData.R")
#'
NULL
Edit in response to arguments against placing these scripts in the inst
While this was not the intention of this question, I would like to make the argument for inst being the ideal place for these scripts. This situation comes up for me personally when producing not general-use R packages, but R packages to accompany manuscripts and reproduce analyses. R packages provide an ideal format for disseminating fully-reproducible analyses. However, often analyses include large datasets that are not needed in entirety. By including a script in inst, users can choose (easily) to reproduce the data included in the package BUT are not required recreate the input data for the analysis. It does not make sense to obscure the scripts away.
First, I would agree with Hong Ooi and say that in general you shouldn't put it in inst/; that is copied into the user's installation. I follow the advice in Hadley Wickham's R Packages and put them in a folder called data-raw/ (which you then add to .Rbuildignore). However, for the use case you further describe in the edits to your question, I can see why you would want to put the script in inst/ to distribute to your users.
But, on to the problem at hand. You can do this by instead using #evalRd and adding the \details{} part in rdScript(). I set up a dummy package foo with the file inst/bar.R with the following code in it:
a <- 5
b <- 8
Then I made R/baz.R with
rdScript <- function(filename, prepend = "") {
lns <- readLines(filename)
lns <- paste(sprintf("\\code{%s}", lns), collapse = "\n\n")
return(paste("\\details{", prepend, "\n", lns, "}", sep = "\n"))
}
#' #name someObj
#' #title Some R Object
#' #description Some R Object
#'
#' #evalRd rdScript("inst/bar.R", "Data was created with the following script:")
NULL
After document()ing, I get the following in man/someObj.Rd:
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/baz.R
\name{someObj}
\alias{someObj}
\title{Some R Object}
\description{
Some R Object
}
\details{
Data was created with the following script:
\code{a <- 5}
\code{b <- 8}
}
which renders in RStudio's help viewer as
I've written a package (myHelpers) that had been using the following function:
#' Negate the \code{\%in\%} function.
#'
#' Use this for the OPPOSITE of \code{\%in\%}.
#'
#' #export
"%not in%" <- function(x, y) !x %in% y
In the past (last year) this worked fine with my package. But now (and I don't know why) with the following:
library(myHelpers)
df1 <- c(1,2,3,4,5)
df2 <- c(4,5)
df1 %not in% df2
Produced the following error:
Error in df1 %not in% df2 : could not find function "%not in%"
I don't know if something's changed when I build the package using roxygen2, but this is frustrating.
When I simple add this to my global environment in my session, everything is fine.
Any idea on how to get this function (with the SPECIAL characters of %) exported and seen with my myHelpers package would be appreciated.
Thanks,
Michael
EDIT 9-13-19 14:07 PST
I'm using RStudio and my shortcut to build the documentation (and the Namespace presumable) with Command+Shift+D. I'm assuming the documentation gets written as it's in the MAN folder for the package. BUT, I get this error in the Build pane:
Warning message:
roxygen2 requires Encoding: UTF-8
AND, when I look in the Namespace file, my function is missing (even tough I'm telling roxygen to export it (with the #export).
Looking for the fix...
EDIT 9-13-19 14:14 PST
FIXED
Added:
Encoding: UTF-8
To Description file...and I had an error that I didn't see. I was using:
#keyword export
Because I had been using #keyword internal for a bit with the function....Now, I changed it to the CORRECT:
#export
And I'm off and running. Thanks for helping with overtired academic discover his mistake.
I have one package "testing" with a data object "test_data" saved in data folder under file name "test_data.RData".
testing contains one function hello() that uses this data object
#' hello
#'
#' #return Prints hello "your_name"
#' #export
#'
#' #examples
#' hello()
hello <- function(your_name = "") {
print(paste("test_data has", nrow(test_data), "rows"))
print(sprintf("Hello %s!", your_name))
}
the following code works fine:
require(testing)
testing::hello()
[1] "test_data has 32 rows"
[1] "Hello !"
but this fails:
testing::hello()
Error in nrow(test_data) : object 'test_data' not found
Actually I do not use it directly but in another package testingtop that imports this function:
#' Title
#'
#' #export
#' #importFrom testing hello
hello2 <- function(){
hello()
}
I have testing in the Imports section of DESCRIPTION and this fails.
require(testingtop)
testingtop::hello2()
Error in nrow(test_data) : object 'test_data' not found
If I put it in Depends it works if I load the package with library()
otherwise it still fails:
> library(testingtop)
Loading required package: testing
> testingtop::hello2()
[1] "test_data has 32 rows"
[1] "Hello !"
Restarting R session...
> testingtop::hello2()
Error in nrow(test_data) : object 'test_data' not found
if it was a function instead of a data object Imports would be fine, why is it different with a data object and I need to load the imported package? Did I miss something? And is it related to LazyData and LazyLoad ?
Probably a duplicate of this question
SO I think I've found the solution from the doc of the data function ?data
Use of data within a function without an envir argument has the almost always undesirable side-effect of putting an object in the user's workspace (and indeed, of replacing any object of that name already there). It would almost always be better to put the object in the current evaluation environment by data(..., envir = environment()). However, two alternatives are usually preferable, both described in the ‘Writing R Extensions’ manual.
For sets of data, set up a package to use lazy-loading of data.
For objects which are system data, for example lookup tables used in calculations within the function, use a file ‘R/sysdata.rda’ in the package sources or create the objects by R code at package installation time.
A sometimes important distinction is that the second approach places objects in the namespace but the first does not. So if it is important that the function sees mytable as an object from the package, it is system data and the second approach should be used.
Putting the data in the internal data file made my function hello2() see it
> testingtop::hello2()
[1] "test_data has 32 rows"
[1] "Hello !"
To supplement Benoit's answer. I had essentially this problem, but when using my package data as a default for a function parameter. In that case there's a third solution in the ?data help file: "In the unusual case that a package uses a lazy-loaded dataset as a default argument to a function, that needs to be specified by ::, e.g., survival::survexp.us."
This third approach solved it for me. (But I found it thanks to Benoit's link.)
I am writing an R package and create documentation using roxygen2. I build the package and the documentation using the button Build & Reload in RStudio. According to RStudio's output, it uses devtools::document(roclets=c('rd', 'namespace')) to compile the documentation.
I want to use the #family tag to link together a number of functions in the documentation and this is where my problem occurs. This line
#' #family functions returning some object
is converted in the .Rd file to the following
\seealso{
Other functions.returning.some.object: \code{\link{test2}}
}
I don't want the dots between the words. I have an older package, where this does not happen, even if I recompile the documentation in the exact same setting as I compile the new package. I can see no fundamental difference between this older package and my new attempt.
I have written a very simple test package, where the problem also occurs. It contains a single R file (testpackage.R):
#' Test function 1
#'
#' #param x a number
#'
#' #family functions returning some object
#' #family aggregate functions
#'
#' #export
test1 <- function(x) {
x*x
}
#' Test function 2
#'
#' #param x a number
#'
#' #family functions returning some object
#' #family aggregate functions
#'
#' #export
test2 <- function(x) {
x*x*x
}
The DESCRIPTION file is
Package: testpackage
Type: Package
Title: Package for testing purposes
Version: 1.0
Date: 2015-05-21
Author: Me
Maintainer: Me <me#somewhere.com>
Description: Package for testing purposes
License: GPL-3
NAMESPACE is generated by roxygen. For the documentation test1.Rd, I get:
% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/testpackage.R
\name{test1}
\alias{test1}
\title{Test function 1}
\usage{
test1(x)
}
\arguments{
\item{x}{a number}
}
\description{
Test function 1
}
\seealso{
Other aggregate.functions: \code{\link{test2}}
Other functions.returning.some.object: \code{\link{test2}}
}
with the unwanted dots in the \seealso section. Clearly, the number of words in the #family tag seems not to matter. I have tried enclosing the text in quotation marks, various kinds of brackets, etc. with no positive effect. Of course, I could edit the Rd files, but this would miss the point of using roxygen2.
R CMD check runs without warnings or errors on testpackage.
Why do these dots appear? And how can I get rid of them?
This is a bug in roxygen2 -- I've logged an issue here. It effectively results from the use of unstack(), which performs some unwanted conversions.
I upgraded to Roxygen 5.0.0 (which is now the CRAN version) and found that the problem went away.
I am new to roxygen and am struggling to see how to be able to use it to quickly create a new/custom package.
I.e. I would like to know the minimum requirements are to make a package called package1 using devtools, roxygen2/3 so that I can run the commands
require(package1)
fun1(20)
fun2(20)
to generate 2000 and 4000 random normals respectively
So lets take the simplest example.
If I have two functions fun1 and fun2
fun1 <- function(x){
rnorm(100*x)
}
and
fun2 <- function(y){
rnorm(200*y)
}
the params are numeric, the return values are numeric. I'm pretty sure this isn't an S3 method, lets call the titles fun1 and fun2....im not too sure what other info i would need to provide. I can put fun1 and fun2 in separate .R files and add abit of #' but am unsure to include all relevant requirements for roxygen and also am unsure what to include as relevant requiremetns and how to use it to create the rd documentation to go with a package are. I presume the namespace would just have the names fun1 and fun2? and the package description would just be some generic information relating to me...and the function of the package?
any step by step guides would be gladly received.
EDIT: The below is how far I got to start with...
I can get as far as the following to create a pacakge...but cant use roxygen to make the documentation...
package.skeleton(list = c("fun1","fun2"), name = "package1")
and here is where I am not sure if I am missing a bunch of steps or not...
roxygenise("package1")
so when trying to install i get the following error message
system("R CMD INSTALL package1")
* installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
* installing *source* package ‘package1’ ...
** R
** preparing package for lazy loading
** help
Warning: /path.to.package/package1/man/package1-package.Rd:32: All text must be in a section
*** installing help indices
Error in Rd_info(db[[i]]) :
missing/empty \title field in '/path.to.package/package1/man/fun1.Rd'
Rd files must have a non-empty \title.
See chapter 'Writing R documentation' in manual 'Writing R Extensions'.
* removing ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/package1’
I'm surprised #hadley says to not use package.skeleton in his comment. I would use package.skeleton, add roxygen comment blocks, then delete all the files in the "man" directory and run roxygenize. However, since Hadley says "Noooooooooo", here's the minimum you need to be able to build a package that passes R CMD check and exports your functions.
Create directory called "package1". Under that directory, create a file called DESCRIPTION and put this in it (edit it appropriately if you like):
DESCRIPTION
Package: package1
Type: Package
Title: What the package does (short line)
Version: 0.0.1
Date: 2012-11-12
Author: Who wrote it
Maintainer: Who to complain to <yourfault#somewhere.net>
Description: More about what it does (maybe more than one line)
License: GPL
Now create a directory called "R" and add a file for each function (or, you can put both of your functions in the same file if you want). I created 2 files: fun1.R and fun2.R
fun1.R
#' fun1
#' #param x numeric
#' #export
fun1 <- function(x){
rnorm(100*x)
}
fun2.R
#' fun2
#' #param y numeric
#' #export
fun2 <- function(y){
rnorm(200*y)
}
Now you can roxygenize your package
R> library(roxygen2)
Loading required package: digest
R> list.files()
[1] "package1"
R> roxygenize("package1")
Updating collate directive in /home/garrett/tmp/package1/DESCRIPTION
Updating namespace directives
Writing fun1.Rd
Writing fun2.Rd
Since you mentioned devtools in the title of your Q, you could use the build and install functions from devtools
build('package1')
install('package1')
Or you can exit R and use the tools that come with R to build/check/install.
$ R CMD build package1
$ R CMD check package1_0.0.1.tar.gz
$ R CMD INSTALL package1_0.0.1.tar.gz
Now, fire up R again to use your new package.
$ R --vanilla -q
library(package1)
fun1(20)
fun2(20)
But, figuring out the minimum requirements is unlikely to help you (or the users of your package) much. You'd be much better off studying one of the many, many packages that use roxgen2.
Here's a better version of the fun1.R file which still doesn't use all the roxygen tags that it could, but is much better than the bare minimum
Modified fun1.R
#' fun1
#'
#' This is the Description section
#'
#' This is the Details section
#'
#' #param x numeric. this is multiplied by 100 to determine the length of the returned vector
#' #return a numeric vector of random deviates of length \code{100 * x}
#' #author your name
#' #seealso \code{\link{fun2}}
#' #examples
#' fun1(2)
#' length(fun1(20))
#' #export
fun1 <- function(x){
rnorm(100*x)
}
Much later - You could let RoxygenReady prepare your functions with the minimal Roxygen annotation skeleton. It basically brings you from your 2 input functions to GSee's answer, which is the input of Roxygen2.