Cross posted from: https://community.rstudio.com/t/link-to-r6-method-from-separate-package-in-help-pages-and-pkgdown/134702
I'm currently writing an R package and would like to link to the help page for an R6 method in a separate package. The page I want to link to is here: https://mc-stan.org/cmdstanr/reference/model-method-sample.html, and there is an .Rd file for the method as well (https://github.com/stan-dev/cmdstanr/blob/master/man/model-method-sample.Rd). Finally, I can also access the help page from R directly with ?cmdstanr::`model-method-sample`.
However, when I try to add a link to my own help page using the normal link to another package syntax described here, [cmdstanr::`model-method-sample`], I get this error:
Warning: Link to unknown topic: cmdstanr::`model-method-sample`
I feel like there must be some way to link to this help page, given that it definitely exists and has an .Rd page, but I haven't found a solution yet. Has anyone else run into this problem or know the solution?
I think you (or Roxygen) are using the wrong syntax for the link. According to Writing R Extensions, the Rd syntax should be:
\link[cmdstanr]{model-method-sample}
I'm not sure how to generate this from Roxygen, but it appears to work as-is if I put it in Roxygen comments.
If you want the link with different text, the syntax is
\link[cmdstanr:model-method-sample]{link text}
Related
So, I'd like to reference one of my package vignettes inside the roxygen2 comments of a function but I'm having a hard time understanding how to do it.
More generally, how do we reference documents inside /inst/doc? E.g. I'd like to reference /inst/doc/mypdf.pdf inside the roxygen2 comments for myFunc. What would that look like? Is it even possible?
I just tell people to run the code that opens the vignette:
#' For more details see the help vignette:
#' \code{vignette("help", package = "mypkg")}
I know this is 4 years old...and hadley provided the answer...but I'd like to offer another option:
\href{../doc/help.html}{\code{vignette("help", package = "mypkg")}}
This gives a direct link to opening the vignette, and provides the code to show the user how to open it on their own.
As already mentioned I'm using the Atom text editor.
I'm currently working on a project written in c++. Of course it is desirable to jump to the definition of a function (in another project file), or other uses of this function (within the project). As far as I know this can be achieved with the packages I'll mention below. I want the package to display me the definition along with the path to the corresponding file which holds the definition and ideally the line where it occurs.
I'll welcome any comments and suggestions on how to solve the below mentioned problem(s) I have with (one of) the packages. Moreover I'm also thankful about pointers to possible solutions or posts concerning my problem(s), or how I can achieve this with another package.
Here is what I found / tried / did so far.
goto
Currently I'm using this package, although it is rather slow and does not show the arguments of the function as e.g. atom-ctags does, but it's the only package which displays me the files I need to see.
It shows me where the function is defined as well as where it is also used. However it does not show me the path to the file corresponding file it refers to.
atom-ctags
I also tried this package, building the tags is quite fast and moreover it show me the path to the file. But this package only lists the .cc files and not the .h files. It appears to me as if it only shows me the other uses but not the definition, which is obviously a problem.
I also tried generating the ctags myself and changing the command options in the settings of the package, unfortunately without any success.
Atoms built-in symbols-view
In order to get this to work, one needs to generate the symbols. This can be, for example, achieved with the symbol-gen package. However, it shows me some of the definitions, but also no .h files. Moreover, jumping to the definition results in a Selected file does not exist., therefore it is not usable at all.
goto-definition
Just for completeness, there is also this package. It does not work for me, since c++ is not supported but maybe others will find it useful.
symbols-plus
Again, for completeness, this should be a replacement for the atom built-in, but when disabling the build-in it does not show me any jump functionality nor is a short cut mentioned.
So, basically, nothing really works well. I have tried Symbol Tree View but it but barely works.
It is my first experience in writing an R-package. I used roxygen2 by following the instructions given in this link http://kbroman.org/pkg_primer/
Everythig is working fine except few things.. there could be a simpler solution to solve the issues, but I am not finding clues what I am doing wrong. I hope someone here in this blog can give a solution to solve my issues.
First issue is about {\code\link{function-name}} in roxygen2:
In .R script I inlcuded this line:
#' #seealso \code{\link{s2a}}
After documenting (generating .Rd files) there is no hyperlink to s2a ,
in documentation s2a shows like a normal text not like hyperlink..
export(s2a) is listed out in NAMESPACE.
Is there any other place i need to modify ?
Second issue is about data():
I saved the dataset in .Rdata format and placed in the data/ in package directory. I also created the .R script in R/ as like following steps here http://kbroman.org/pkg_primer/pages/data.html
In DESCRIPTION file LazyData: true .
but when I type data(shh) in R console gives a warning message
data(shh)
Warning message:
In data(shh) : data set ‘shh’ not found
Any ideas is of great help:)
It's been a while since you asked this, but I was having the exact same problem with hyperlinks in documentation not appearing correctly, so for anyone who might be having a similar problem: Are you possibly viewing the development documentation? The links don't seem to work there. (You'll know this is the case if you see Using development documentation for your_function_name in your console output when you run ?your_function_name.)
The links should appear in the non-development documentation. To generate this you can try building and reloading your package, for instance by following the steps here: http://r-pkgs.had.co.nz/man.html#man-workflow-2
I am working to document a visualization function in a package of mine. For this purpose I would like to have an image embedded through the Rd-file 'funcname.Rd' that could explain various parameters utilized in the function, and which would pop up if user goes to read the package manual PDF or writes '?funcname' in R. Something in the lines of:
'Writing R extensions'-document doesn't seem to address this issue, and the only references I could find were this blog post and this R-devel discussion. The former has a broken link to a package called 'base64' and the latter only addresses various alternatives like including the images in R package vignettes instead. It would be great if this could be CRAN-compatible.
Any advice on how to approach this issue would be appreciated, thanks!
Untested, but look at the R source on GitHub, it would appear they add an image to ?par documentation file in the following manner:
\item{\code{mai}}{A numerical vector of the form \code{c(bottom,
left, top, right)} which gives the margin size specified in
inches.\cr
\if{html}{\figure{mai.png}{options: width="35\%" alt="Figure: mai.png"}}
\if{latex}{\figure{mai.pdf}{options: width=7cm}}
}
The figure appears to be saved in /man/figures.
For more details see the Writing R Extensions section on the topic.
The help page of the news() R function says:
it is attempted to read its news in structured form from files
‘inst/NEWS.Rd’, ‘NEWS’ or ‘inst/NEWS’ (in that order).
Doing so and installing the package, we get (under windows) a link to the NEWS file at the top of the html page open by the command help(package=packagename). For an example, assuming you have installed party, you can try
help(package="party")
This works however only with files named NEWS. When we provide instead a NEWS.Rd file, there is no link to the news. Try
help(package="survival")
Is there a way to get this link when we provide a NEWS.Rd file?
Thanks for your help.
The problem has been solved since R 3.0.0.
It seems, however, that a series of the Rd formatting code such as \code{} for example are ignored when rendering the NEWS.Rd in html.