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.
Related
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.
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.
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.
I am working in team, we mainly use R, I am quite used to use R project in Rstudio, which I like because when I open them I have all my scripts and everything at the right place. However when another member of the team opens one of my project it loads the values and data but does not open the R script (one can see that by physically clicking on the project through the windows explorer rather than using the menu at the top right in R). I guess something can be done in the .Rprofile but I did not find any command to open physically a script, I tried
file.edit("./Main.R")
but it did not open anything. It just got me the message :
Error: could not find function "file.edit"
As always,
Thanks for your help !
**EDIT
I tried to use
file.show
file.edit
shell.exec(file.path(getwd()), "Main.R"))
in the .Rprofile. Nothing worked.
Romain
You can use the following code in the .Rprofile file.
setHook("rstudio.sessionInit", function(newSession) {
if (newSession)
rstudioapi::navigateToFile('<file name>', line = -1L, column = -1L)
}, action = "append")
The rstudioapi library has the function navigateToFile to open a file in Rstudio. The problem is that the code in the .Rprofile runs before Rstudio initialization. To deal with this problem you can use the setHook function (from base package) to make the code execute after the Rstudio initialization.
file.edit requires the utils package
library(utils)
file.edit("Master.R")
However, if it opens in Notepad rather than RStudio you have the same problem as me. I've tried editing the editor= in all possible places: .RProfile, RProfile, RProfile.sites, with and without .First() function statements and calls. However, RStudio does not load the .R file in RStudio if told to. It may be linked to the .RData file being loaded after .RProfile. Bug? Or at least a feature RStudio should incorporate in their RProject file specification.
I have a global ~/.Rprofile file and another .Rprofile file located in my project's current working directory and both of the have the following contents:
.First() <- function() {
options(rstudio.markdownToHTML =
function(inputFile, outputFile) {
system(paste("pandoc", shQuote(inputFile), "-s --webtex -o", shQuote(outputFile)))
}
)
}
Unfortunately, when I open the RStudio app neither of them appear to be working. The aim of what I'm trying to do is to make the "Knit HTML" button render the Markdown file, which has inline LaTeX, process through Pandoc using webtex as the LaTeX renderer.
Does anyone know how I check whether my .Rprofile files are loading at startup?
Thanks for any help!
POST ANSWER EDIT (after Josh's answer):
For clarity, my working project's .Rprofile file (which works) now reads as such:
options(rstudio.markdownHTML =
function(inputFile, outputFile) {
system(paste("pandoc", shQuote(inputFie), "-s --webtex -o", shQuote(outputFile)))
}
)
\\ you will need to end with a blank carriage return underneath
The R docs should help to see how to deal with .Rprofiles. Execute the following at the console:
> ?Startup
The relevant portion of this indicates that you need to put your project .Rprofile in the initial working directory that will be loaded when starting the project. Thus if your project is ~/foo/foobar.Rproj, then you should have your profile be ~/foo/.Rprofile and make sure that when starting up, the initial working directory is ~/foo/. You can see this in the title bar at the top of the console pane in RStudio.
Also to confirm that the correct .Rprofile is actually being loaded, I would personally put in a test to see which (if any) profile is being picked up. For example, include:
print("This is the Rprofile inside the foo project!")
Here is another example about getting this to work:
http://support.rstudio.org/help/discussions/suggestions/1095-different-rprofile-for-a-project#comment_15690293
Finally, if the correct .Rprofile is being loaded inside the project, then there must be something wrong with your code. Looks like you got this from our docs though, so if you get the profile loaded, and continue to have problems, please let us know. You can post a new discussion on our support thread.
Josh
Product Manager - RStudio