I was getting this error when running devtools::document but had no idea how to troubleshoot. The file that popped up on my installed package when I entered ?MyPackage-package did not match the text in MyPackage-package.R at all. I initially suspected it might have been from adding the awesome citation functionality from RDpack, but this was not the culprit. How did I go about ultimately fixing the problem?
The error resulted from incorrect formatting in my PackageName-package.R file.
I had heavily edited the file created by usethis::use_package_doc(), and added all of my roxygen comments Below the default content added by usethis. After looking at the documentation for merTools, I saw that it was ok to have the stuff I understand to be important for roxygen2 to make the .Rd files after and not before all the other roxygen comments.
After moving the stuff created by usethis::use_package_doc() (and not just the NULL line; that was already at the end) to the bottom of the .R file, everything seemed to render fine and this error disappeared.
Related
This issue is really strange, I want to read a csv file and after getting rid of all unnecessary parts my entire code boils down to this two-liner:
library(tidyverse)
read_csv('data1.csv')
If I knit the Rmd file, it works and a new webpage opens as usual:
However, if I run it either by (1) clicking the green play button; or (2) clicking Run -> Run All button:
Then it just doesn't work (In case you are wondering whether or not there is a third line of code, I make the scope of the screenshot larger). The code is so short that I have no idea what could possibly be wrong.
Following the comment from #user12728748, I changed
read_csv('data1.csv')
to
readr::read_csv('data1.csv')
and it works! But this is still odd since my understanding is that suppose there aren't namespace conflicts prepending namespace is not needed.
Loading readr explicitly, regardless of the order, does not work since it is loaded by tidyverse already:
I am trying to knit together 3 files using this example: http://rmarkdown.rstudio.com/rmarkdown_websites.html
My files all share the same directory, which has been set in the RStudio build options. I literally copied the YML from the examples with my own file names. Even if I copy the examples directly, I get the same error.
I even ran the site_generator function from the RMarkdown Github: https://github.com/rstudio/rmarkdown/blob/master/R/render_site.R#L157
I noticed there are options for custom generators, which I do not want. All I would like to do is be able to knit together several markdown files into a single webpage and then create a navbar with tabs for each page/section.
I got the same error when attempting to build with an incorrectly named YAML config file. Specifically, the RStudio build option for a website requires that the config file be called _site.yml.
Verify that this file exists and that you're using the extension .yml rather than .yaml (even though the latter is preferred).
What helped for me was putting the line site: bookdown::bookdown_site back to index.Rmd.
lord, my issue was that i didn't set my working directly to where my _site.yml file and index.Rmd files are stored - the little things!
I fixed this error using this steps.
1-) RStudio-Tools-InstallPackages
2-) Install From should be CRAN Repository.
3-) write this command --> install.packages("install.packages("rmarkdown")")
4-) Click Install
And problem has gone... And this is output.
This error also appears when there is a format issue in the yaml section of index.Rmd.
In my case, I encountered the error when the opening "---" in index.Rmd had a couple of white spaces " ---".
If you are having this problem, I would recommend knitting index.Rmd by itself (not building the book) before trying anything more drastic.
When I try to use roxygen2::roxygenize() in RStudio, I get an error message. The message I am coming across is this:
Warning message:
trainModel.Rd not generated by roxygen2. Skipped.
I have tried so much to fix this, but it just won't get fixed unless I remove all of the #' comments out (which would remove the purpose of using roxygen2 in the first place). I even took out everything except for the parts describing the title, description, and details and the error still persists (which makes me imagine that the error is in one of those three parts. But how?). My other document's Rd file gets generated just fine, but this one does not. Can somebody please help?
Try deleting the current Rd file.
I replicated this warning by creating file with your function, roxygenizing the code, and then removing the lines from the resulting Rd file
% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/trainmode.R
It looks like roxygen2 doesn't want to overwrite files it didn't create. If you delete the current trainmode.Rd file, roxygen2 will generate a new .Rd file the next time roxygenize your code.
From what I can gather there is a well documented issue with uploading Rpubs to RStudio. The solution is to create a .Rprofile and with an additional line:
options(rpubs.upload.method = "internal")
and then put the .Rprofile file in your working directory, and restart the program. My issue is that when I attempt this and start up RStudio I am presented with the error:
Error in assign(".popath", popath, .BaseNamespaceEnv) :
cannot change value of locked binding for '.popath'
Can anyone suggest what I may be doing wrong? What have I missed?
The solution is provided by a careful rereading of http://rstudio-pubs-static.s3.amazonaws.com/25030_8e9c9ffc3b3c423d9381d81543423502.html
"Put in options(rpubs.upload.method = “internal”) and no other text at all". Meaning that this line of code is the only code present in the .Rprofile file.
Previously I had been adding the line to a copy of the rest of the Rprofile text. The unnecessary code was the culprit.
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