Error in loadNamespace(Name) : There is No Package Called 'here' | Credibly Curious

[utterances-bot]

Error in loadNamespace(Name) : There is No Package Called 'here' | Credibly Curious

https://www.njtierney.com/post/2020/05/29/there-is-no-pkg/

[m-hefnawy]

Thanks to you for this post.

[njtierney]

No worries!

[leahymr]

Nick, I'm getting this error when attempting to knit an RMarkdown file. If I run library ("papaja") in the console, the library is loaded. But the same command in the .Rmd file causes Error in loadNamespace(name) : there is no package called ‘papaja’. Do you have suggestions on how to debug this?

[leahymr]

I can add that I am able to execute render("file.Rmd") from the RStudio command line, so all the components are there, just knitr can't find papaja. I compared .libPaths() from the RStudio command line and from a code block within the .Rmd file, and they give the same set of paths, in the same order.

I am running Mac OS 14.6 with R 4.0.4 and RStudio 1.4.1106.

[njtierney]

Hi @leahymr - that sounds a bit tricky, do you have an example I could look at on github, or elsewhere? Happy to take a look and see if I can help.

[leahymr]

@njtierney , I have posted my code at github.com:leahymr/papaja-problems.git.
Two .Rmd files: Simple.Rmd is trivial, Default.Rmd is a minimized version of the default papaja .Rmd file.

Since I can render("Default.Rmd") but knitting Default.Rmd fails, it must be a difference in the knit environment.
I generated what I know to generate and put them in the Render and RMarkdown files.

Are there some other commands that I should try to find differences?

Oh, I have the following commands in my .Rprofile file:
.libPaths("/usr/local/lib/R/site-library")
.First <- function() {
trace(base:::loadNamespace, quote({
if (package == "papaja")
utils::str(sys.calls())
}), print = FALSE)
utils::sessionInfo()
}

and my .Renviron file:
R_LIBS_USER="/Users/leahym/Library/R/4.0/library"

Thanks.

[leahymr]

@njtierney, I found my problem. As soon as I commented out the .libpaths() command in the .Rprofile file, the problem went away.

Having a .libpaths() command caused two problems:

1. I could not knit a papaja document
2. I could not knit an RMarkdown > Shiny > Shiny Document

Perhaps this note will help others who get the Error in loadNamespace(name) and the other explanations don't fit.

[njtierney]

@leahymr I'm so happy to hear you've solved the issue! Thank you for documenting it, and sorry I didn't get back to you sooner.

[leahymr]

For the record, the correct way to do what I was trying to do (add a site directory to the library search path) would be to put the string R_LIBS_SITE="/path/to/site-library" (separate multiple directories with colons) in the file $R_HOME/etc/Renviron.site or the string R_LIBS_USER="/path/to/user-library" in the file $HOME/.Renviron.

My problem was I overwrote the .libPaths() value, causing R to no longer know where the rest of the libraries were installed.

For full details, see
https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/Startup

[SeokLeeUS]

install.packages("here")