Each entry lists the error message, the usual cause, and the fix that works most of the time.
Error:
there is no package called 'xyz'
Cause: the package is not installed in the library R is looking in.
Fix: install.packages("xyz"). If you are using renv, run
renv::restore() instead to keep the lock file authoritative.
Error:
could not find function "ggplot"
Cause: package is installed but not loaded.
Fix: library(ggplot2) (or library(tidyverse)).
Error:
non-finite value supplied by optim
Cause: the model failed to converge, often because of extreme starting values, perfect separation (logistic regression), or a misspecified formula.
Fix: rescale predictors, use sensible starting values, or for logistic regression check for zero cells in the outcome-by-predictor table.
Error:
contrasts can be applied only to factors with 2 or more levels
Cause: a factor predictor has been filtered down to a single level.
Fix: check table(your_data$predictor) and restore levels, or drop
that predictor from the model.
Error:
Error in UseMethod("predict") : no applicable method for 'predict' applied to an object of class "c('list')"
Cause: you passed the wrong object to predict(). Usually a list
instead of the fitted model.
Fix: check the object with class() and pass the model object itself,
e.g. predict(fit, newdata = nd).
Error:
Loading required package: foo — there is no package called 'foo'
Cause: an installed package has a dependency that is missing.
Fix: install.packages("foo", dependencies = TRUE).
Error:
quarto: command not found
Cause: Quarto is not on your PATH.
Fix: install from https://quarto.org and restart your terminal.
On macOS, check that /usr/local/bin (or the Homebrew prefix) is in
your PATH.
Error:
Failed to render: your system is missing pandoc
Cause: older versions of R Quarto missed the bundled pandoc.
Fix: upgrade Quarto to the latest release.
Error:
Error running filter shortcodes
Cause: a Quarto extension is missing after cloning.
Fix: run quarto add for the extension, or ignore if the extension is
optional.
Error:
output file: docs/index.html does not exist
Cause: quarto render was interrupted or output-dir changed.
Fix: re-run quarto render from a clean state; if the interruption
wedged .quarto/, delete that cache directory and try again.
Error:
GitHub Pages deployment failed: 404
Cause: Pages is pointing at the wrong branch or path.
Fix: in the repo Settings → Pages, select the gh-pages branch and
the / (root) folder. Our workflow deploys to gh-pages by default.
renv
Error:
renv::restore() failed with: cannot install package 'xyz' from source
Cause: a system library is missing. The error above this line usually names the header file.
Fix: install the matching -dev package on Linux, the corresponding
Homebrew package on macOS, or Rtools on Windows. Common culprits:
libcurl4-openssl-dev for curl
libxml2-dev for XML / xml2
libssl-dev for openssl
libfontconfig1-dev, libfreetype6-dev, libharfbuzz-dev, libfribidi-dev for systemfonts, ragg, textshaping
libgit2-dev for gert
Error:
renv is out of sync with the lockfile
Cause: the project library differs from renv.lock.
Fix: renv::status() to see what, then renv::restore() to synchronise.
Error:
pandoc document conversion failed with error 2
Cause: YAML front matter is malformed — often an unquoted colon in a title.
Fix: quote the offending string. title: "Two:peas in a pod".
Error:
Error in chunkname: object 'xyz' not found
Cause: an earlier chunk was skipped or cached stale.
Fix: clear the knitr cache (knitr::clean_cache()) and re-render;
check chunk evaluation with eval = TRUE.
Error:
fatal: refusing to merge unrelated histories
Cause: you cloned one repo and then tried to pull from a different initialisation.
Fix: only run git pull --allow-unrelated-histories if you are sure
you want to merge.
Error:
Permission denied (publickey)
Cause: your SSH key is not registered with GitHub.
Fix: add your key via Settings → SSH and GPG keys, or switch the
remote to HTTPS: git remote set-url origin https://github.com/....