First things first I just wanted to say I’m a long time reader but first time poster so hopefully I can present my question clearly. I have a fair amount of experience with R (near daily use for about 3 years) but only recently took up Quarto/Markdown (~4 weeks now) and so am still learning the ropes. Onto the issue at hand:

I am working on a Quarto pdf output document, yesterday everything was fine but today when I went to render the document (no changes made*) it threw an error:

compilation failed- error
LaTeX Error: Loading a class or package in a group.

See the LaTeX manual or LaTeX Companion for explanation.
Type H for immediate help.

l.90 …ageloaded{caption}{}{usepackage{caption}}

I have been able to get my document to render now. After some tense (unhelpful) conversation with chatgpt I concluded the problem was related to the loading of the packages in my YAML header-includes section though I can’t understand why.
I was able to just copy the header-includes section from another doc I was working on that was rendering fine and lo and behold my document is fine now; but I want to understand why I got this error so I can avoid it in the future!

*at least no changes made consciously, I have a 2 month old and so am a bit sleep deprived. Anything that would have changed would have to be an errant keystroke nothing substantial and again I’m not sold that I did anything

Here is the offending YAML

---
title: "Teaching Portfolio"
author: "me"
format: 
  pdf:
    documentclass: article
    papersize: letterpaper
    fontsize: 12pt
    indent: true
    number-sections: false
    margin-top: 1in
    margin-left: 1in
    margin-right: 1in
    margin-bottom: 1in
    toc: true
editor: visual
header-includes:
  - usepackage{pdfpages}
  - usepackage{hyperref}
  - hypersetup{colorlinks=true, linkcolor=blue, filecolor=magenta, urlcolor=cyan,}
  - urlstyle{same}
  - usepackage{amsmath}
  - usepackage{amsfonts}
  - usepackage{amssymb}
  - usepackage[version=4]{mhchem}
  - usepackage{stmaryrd}
  - usepackage{indentfirst}
  - usepackage{setspace}
  - usepackage{float}
  - doublespace
---

*Side note: this version produces the error but originally pdfpages was called just before double space command and I also had - usepackage[utf8]{inputenc} as the first package.

and here is the YAML that worked

---
title: "Teaching Portfolio"
author: "me"
format: 
  pdf:
    documentclass: article
    papersize: letterpaper
    fontsize: 12pt
    indent: true
    number-sections: false
    margin-top: 1in
    margin-left: 1in
    margin-right: 1in
    margin-bottom: 1in
    toc: true
editor: visual
header-includes:
  - usepackage[utf8]{inputenc}
  - usepackage{indentfirst}
  - usepackage{hyperref}
  - hypersetup{colorlinks=true, linkcolor=blue, filecolor=magenta, urlcolor=cyan,}
  - urlstyle{same}
  - usepackage{amsmath}
  - usepackage{amsfonts}
  - usepackage{amssymb}
  - usepackage[version=4]{mhchem}
  - usepackage{stmaryrd}
  - usepackage{setspace}
  - usepackage{float}
  - usepackage{pdfpages}
---

What gives? And how can I avoid this issue in the future? Thanks for your consideration!

I tried shuffling the order of the packages, removing some extraneous ones, I even commented out my figure caption, I also tried explicitly loading the “caption” package but then a new error that was basically the same but now with “subcaption” package. Also each time I change the number of packages the error remains but the number before “…ageloaded{caption}{}{usepackage{caption}}” changes e.g. l.91 then l.90 then l.89 etc