xfun | Miscellaneous R functions | Development Tools library

tl;dr somewhere deep in the guts of the cli package (called to generate the pretty-printed output about column types), the code is generating a random string to use as a label.

A major clue is that

I want to suggest a different method for getting where you want.

As discussed in the comments, not all R packages have public GitHub repos.

Here is a version of some code from an answer to another question by Dirk Eddelbuettel that retrieves information from CRAN's database, including the package name and the URL field. If a package has a public GH repo, it is very likely that the authors have included that information in the URL field: there may be a few packages where the GH repo information is guessable (i.e. the GH user name is the same as (e.g.) the identifier in the maintainer's e-mail address; the GH repo name is the same as the package name), but it seems like a lot of work to do all that guessing (and accessing GitHub to see if the guess was correct) for a relatively low return.

You need to tell R where to find ghostscript. For Windows, download ghostscript from http://ghostscript.com/download/gsdnld.html After installing ghostscript, we still need to tell R where to find ghostscript. To do so, it is necessary to set adapt your system’s Path variable: Go to Control Panel → System and Security → System → Advanced System Settings → computer name, domain and workgroup settings → Advanced → Environment Variables Find the Path variable within System Variables, select it and click on edit. Add C:\Program Files\gs\gs9.23\bin (or the directory where you installed ghostscript to) to the Path variable. In Windows 10, you can do this by clicking on New and entering the path. In other Windows versions, just append the path to the variable value, seperated by a semicolon. Restart R For MacOS, download and install the Ghostscript 9.23 package from http://pages.uoregon.edu/koch/ Restart R

I found the solution from this website https://rnbeads.org/data/installing_rnbeads.html

The timezone offset is causing the issue I think. Try

A combination of reinstalling R Studio after uninstalling MikTex, and finally installing the R package tinytex worked.

I think @samcarter_is_at_topanswers.xyz was right that "the problem was an outdated latex version. utf8 became the default encoding some time ago, but if your tex version was older then such special characters would cause problems. "

Lessons learned:

1. The tinytex package is all you need for R Markdown. You can even open tex files in R Studio to edit and compile them to pdf. See how to install it here.

2. Update MikTex frequently. I assumed that it automatically updated when needed, but that seems not to be true. Windows > MikTex > Update. It's that simple. Remembering to do it is another thing if you decide to use it.

3. Being able to check that the environment paths are all there and are pointing to the right directory didn't help in this case, but it was good to learn. This link was helpful.

This is tricky, and the answer below doesn't solve this 100%. Now there are a number of different ways assertr lets you handle errors/stops, just see ?error_stop (which is the default).

You need to not only filter out rows that fail, but also collect them (all) for later inspection.

Below I wrote my own error handler. It fetches those rows that fail, filter them away, and stores them in the global environment under the varibale my.failed.rows.

In case others also run into this issue in the future, I am posting the solution that was suggested to me by https://answers.launchpad.net/ubuntu. Here is the link to the question I posted: https://answers.launchpad.net/ubuntu/+question/696623.

The issue turned out to be that R was using gcc-9 rather than gcc-10 to compile packages. The older version of gcc was throwing an error. Here are the steps I took to solve the problem:

1. Install gcc-10, which was not available on my system: sudo apt install gcc-10.
2. Edit the CC= pointer in the /usr/lib/R/etc/Makeconf file to gcc-10: open Terminal, type sudo nano /usr/lib/R/etc/Makeconf and replace the current CC= to CC=gcc-10. Save the file.
3. Restart R and run the install.packages() command for those packages that were not compiling correctly.

EDIT: Please see the comments below for a discussion. The above steps resolve the issue, but are not recommended. The issue was related to R not using the system package manager to install packages when the call install.packages() was used in R.

Installing the package bspm solved the issue for me. This package and its utility is discussed here for those who are curious.

To use install.packages() within R, bspm can be used in two ways:

1. bspm::enable() within R and then install.packages()
2. As written in its documentation: To enable bspm system-wide by default, include the following: suppressMessages(bspm::enable()) into the Rprofile.site file.

Thanks very much to Dirk for his guidance.

I did got a similar error while troubleshooting.

This was resolved by individually running each command/chunk until it completes, I did have intermittent execution issues, sometimes I got errors, sometimes it ran successfully, I just reran it until it completed.

To better help me understand, What does your YAML look like? And how exactly are you building the book? is it a gitbook?

The way I found a solution was with a little bit of bookdown understanding. I had 2 files, the index.Rmd and the 01-covid19.Rmd the index.Rmd is empty and only has YAML for the book. in the 01-covid19.Rmd I pasted your code

index.Rmd

Is 6.R actually the content of 1.R?

I think you are seeing 1.R renamed to 2.R and over-writing 2.R in the process. The new 2.R to 3.R etc.