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.
Related
So to get to the point: I need to use an R package called machuruku. To get familiar with the package I used the dataset provided in the original paper (https://academic.oup.com/sysbio/article/70/5/1033/6171196). While trying to run the code for the simulation I get an error message saying that the command "machu.simulation" doesn't exist. Any of you have any idea why that's happening? Am I missing a package?
I downloaded the dataset zip file, dove into the second nested zip file Guillory_and_Brown_simulation-validation.zip, then into its file code_simulation-validation.R, and noticed that this source file uses machu.simulation several times before defining the function starting in line 519.
Suggestions:
Grab lines 519 through the end, save into a different file, source that new file, then try to run the code in the beginning of the file again.
Complain (not quietly?) to the authors, the fact that they think this is reproducible means they might have missed something else, too.
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 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.
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 just starting to explore the rmarkdown package. I don't use Rstudio. I use the default R environment. What I did was as follows.
I created a new R document.
Started typing few lines in rmarkdown format.
Saved the file with Rmd extension.
I saved the file in the working directory.
I installed the pandoc using the pkg file.
I installed 'rmarkdown' package. Loaded the package.
Used the following command to render the Rmd file.
rmarkdown::render("Untitled.Rmd")
I get the following error.
Error in tools::file_path_as_absolute(input) : file 'Untitled.Rmd'
does not exist
I tried all the possible ways such as giving the exact path instead of filename etc. But nothing worked out. I googled the error message and found that none had similar error. Can someone help me with this. What I am missing. What the error message mean?
Most of the time the error file not found is either a type error or a real missing file (as in your case, the real one is named in another way).
In order to discard those possibilities:
Copy the fullpath from your filebrowser.
Make sure the file exists, inside R you could type:
file.exists("/fullpath/to/file")
If that return TRUE and the error persists, then you suspect another thing is going on.