Is there any way I can include links between package vignettes in R? I know I can link between section, for example
# Section 1 {#section1}
My first section
# Section 2
A link to [Section 1](#section1)
But is there any way I can get a clickable link that will launch the HTML doucment of another vignette? Or is it just easier to give the code to launch it?
```r
vignette("my vignette", package = "myPackage")
```
Note I have generated all of my vignettes using Rmarkdown and knitr.
Yes, this is simple. Vignettes are all stored in the same directory, so you simply refer to the appropriate file name. The drat package vignettes have several examples of this. Here is a link from one vignette to the other:
This vignette deals with the first case: How to use
[drat](http://dirk.eddelbuettel.com/code/drat.html) as a package author. A
[companion vignette for package users](DratForPackageUsers.html) is available as well.
This will work on CRAN and on a user's machine.
You should also be able to link from vignettes to documentation, and vice versa, on a user's machine, knowing that vignettes are stored in library/PKGNAME/doc/ and documentation is stored in: library/PKGNAME/html/.
Related
I want to cite another package (the whole package, not just a function from it) in the documentation of some functions I'm developing. I am using Roxygen2 comments to document my package functions.
I cannot find a way to create a link to a whole third-party package using Roxygen2. To link to a package function, one would write [pkg::fun()] but I don't know how to create a link to the package itself.
Some packages expose a general man page, and it's possible to link to it via e.g. [pkg::pkg].
But many packages don't have this and there's just a general package vignette with the list of functions and a link to the description:
Such page can be reached by clicking on a package name in the packages tab in RStudio.
How can I link to it from a function documentation made in Roxygen2 markdown.?
You cannot link to the page that comes up when you click on the name of a package in RStudio's Packages pane. RStudio invisibly calls help(package = "<name>"), which renders the package's index.
From the R-exts manual:
The markup \link{foo} (usually in the combination \code{\link{foo}}) produces a hyperlink to the help for foo. Here foo is a topic, that is the argument of \alias markup in another Rd file (possibly in another package).
Hence \link and the equivalent Markdown markup supported by roxygen2 can only link to topics. A package index is not a topic in this sense because there is no corresponding Rd file.
It might be best just to remind users that they can use help to access the index of the package to which you are referring.
I recently released a vignette with version 1.1 of my R package. The Rmd for the vignette can be found here. When I create the vignette locally, I see author information and the table of contents at the top of the vignette, as expected. However, when I submitted this package to CRAN and the vignette was created there, I no longer see the table of contents or author information. Does anyone know why this may be happening?
Thanks.
I glanced at your DESCRIPTION here and noticed that the VignetteBuilder field does not contain rmarkdown. Since you are using knitr::rmarkdown as an engine, I suspect that you need:
VignetteBuilder: knitr, rmarkdown
Here is a relevant paragraph from the R-exts manual:
The VignetteBuilder field names (in a comma-separated list) packages that provide an engine for building vignettes. These may include the current package, or ones listed in Depends, Suggests or Imports. The utils package is always implicitly appended. See Non-Sweave vignettes for details. Note that if, for example, a vignette has engine knitr::rmarkdown, then knitr provides the engine but both knitr and rmarkdown are needed for using it, so both these packages need to be in the VignetteBuilder field and at least suggested (as rmarkdown is only suggested by knitr, and hence not available automatically along with it). Many packages using knitr also need the package formatR which it suggests and so the user package needs to do so too and include this in VignetteBuilder.
This is not a guaranteed fix, but it is maybe a first step.
I'm developing an R package, and I'm trying to make a link from the manual of the package to its vignette (a pdf). I've make this in the R function code, and it works:
\link[=../doc/package.pdf]{package's User Manual}
The problem is that the devtools::check() complains with a warning, which also causes a delay in the process of revision when uploading to CRAN...
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'package.Rd':
'../doc/package.pdf'
Is there a better way of linking from man to vignette? or it is not correct to do so? As the pdf can contain more graphical information, it seems desirable to be able to link to it.
If you use pkgdown to make a website out of your package, then you can directly link to the url of the specific vignette.
Or you can just write
Run \code{vignette("NAME_OF_YOUR_VIGNETTE", package = "NAME_OF_YOUR_PACKAGE")} to see the corresponding vignette.
I'm writing a vignette for one of my packages.
In this vignette, I would like to demonstrate how this package can interact with other packages that are not being imported by the NAMESPACE or by the Imports section of the DESCRIPTION file.
So, I'm putting a require call to use these external packages in my vignette, but of course I got the following NOTE when I try to R CMD check the package:
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ call not declared from: ‘RColorBrewer’
Is there any way around this, or should I either import these external packages or "fake" the vignette using eval=FALSE?
Put it in Suggests: of your DESCRIPTION file.
From p. 6 of the R extensions manual:
The ‘Suggests’ field uses the same syntax as ‘Depends’ and lists
packages that are not necessarily needed. This includes packages used
only in examples, tests or vignettes (see Section 1.4 [Writing package
vignettes], page 26), and packages loaded in the body of functions.
E.g., suppose an example from package foo uses a dataset from package
bar. Then it is not necessary to have bar use foo unless one wants to
execute all the examples/tests/vignettes: it is useful to have bar,
but not necessary. Version requirements can be specified, and will be
used by R CMD check.
In addition if the vignette properly depends on that package, there should be a
% \VignetteDepends{...}
statement in the vignette itself: Sweave, Part II: Package Vignettes, R News 3/2 (Oct. 2003), 21 - 24.
However, your case possibly is a bit different:
I use if (require ("pkgxy")) without % \\VignetteDepends{pkgxy} (Suggests: pkgxy in the DESCRIPTION is needed anyways) for some things I want to show but where I don't want to force the user to have all the suggested pacakges installed. I put a box at the beginning of the vignette where I report which of those packages are available and if a package is not available when the vignette is built, an "pkgxy is needed to do this" text is put into the vignette.
The "introduction" vignette of package hyperSpec is an example (to find out how it actually works, you need not only the .Rnw but also some more definitions).
Can I include some PDF in the pkg/doc folder so that the vignette function works, but no corresponding Rnw, Rtex, etc exists?
I am thinking of slides or documents containing markdown text weaved with R chunks, which have a different build process and hence different file extensions.
The writing R extensions guide suggests that it should be possible to include documents which can not be build at installation time, but the vignette function seems to look for files with special extensions (Rnw, Rtex, etc) and also for a file called vignette.rds.
Any hints are appreciated.
I asked about this several years ago, and while Fritz Leisch is amenable to the idea, he hasn't had the time to implement it.
(Cross-posted from a response I just left on R-help:)
As a workaround, you could include your own xvignette function in your package: see below.
It won't show you indices, but it will pick up any appropriately named file that you include in the inst/doc directory of your
package ...
xvignette <- function(vname,pkg,ext="pdf") {
vname <- paste(vname,ext,sep=".")
fn <- system.file("doc",vname,package=pkg)
if (nchar(fn)==0) stop("file not found")
utils:::print.vignette(list(pdf=fn))
invisible(fn)
}
You'll have to somehow alert your package users to the fact that this alternative documentation exists -- perhaps in the help file for the package itself.
You might fill in the default value of pkg above with your package name to make it easier on the user: I thought about using some variant of getPackageName(environment(xvignette)) to do it automatically, but that seems too complicated ...
Brian Ripley also mentioned in his response to the question that:
At present vignette() means Sweave documents, as only they have
metadata like titles. This is planned to be changed soon.
... but I don't know what "soon" means (it will be about 6 months until 2.14.0 comes out, I think)
edit: http://article.gmane.org/gmane.comp.lang.r.devel/28449 details another workaround (creating a dummy vignette that incorporates the existing PDF file)
edit 2: And
here's what Yihui Xie has to say about including knitr-based vignettes in packages (essentially another "dummy vignette" strategy)
vignette about non-Sweave vignettes from the R.rsp package
This is supported natively as of R 3.0.0, see http://yihui.name/knitr/demo/vignette/.
Instructions to use knitr as vignette engine boil down to:
add %\VignetteEngine{knitr::knitr} to the Rnw source document (note you still need %\VignetteIndexEntry{} as before)
specify VignetteBuilder: knitr in the package DESCRIPTION file
add Suggests: knitr in DESCRIPTION if knitr is needed only for vignettes
See also the official R documentation on that topic.