WHY THIS LAB
Setup is part of the research workflow.
A path error, missing package, or closed project can make correct code fail. This installation clinic is our first reproducibility exercise.
Work on your own laptop and keep the complete error text visible. Classmates and instructors may help diagnose. Every student runs the final check personally. Students who finish early help someone else gather evidence.
The checker prints RESULT: GREEN, RStudio shows the
course project, and Codex can read START-HERE.md in
that same folder.
00–05 MINUTES
Show your status before repairing anything.
-
01Open
math-camp-2026.Rprojin RStudio. - 02Open the Terminal tab.
-
03Run
Rscript code/check_setup.R. - 04Display green, yellow, or red.
Keep the exact error, command, complete output, operating system, and project path visible so the room can route you to the right help lane.
05–50 MINUTES
Repair one layer at a time.
Extract the ZIP, open the .Rproj, and confirm R
4.2 or newer.
Install only the packages named by the checker, then rerun it.
Install Quarto, restart RStudio, and confirm it is on
PATH.
Confirm the complete repository contains the frozen CSV.
Sign in with the Harvard-supported account and open the course project.
| Lane | Common symptom | First repair |
|---|---|---|
| Windows | Project or data not found. | Extract the ZIP fully; do not work inside the compressed folder. |
| macOS | Installer blocked or Quarto missing. | Use the official installer, reopen through System Settings if prompted, then restart RStudio. |
| Packages | The checker names missing libraries. |
Copy the reported install.packages() command
into the R console.
|
| Account | Codex cannot open or cannot see the project. |
Confirm the Harvard-supported sign-in, then open the
folder containing START-HERE.md.
|
50–57 MINUTES
Run the complete readiness gate.
Rscript code/check_setup.R --codex-confirmedThe gate checks the project root, R version, required packages, Quarto, the frozen data file, and your confirmation that Codex opens with the project.
-
□The final line says
RESULT: GREEN. -
□RStudio shows
math-camp-2026as the open project. -
□Codex can read
START-HERE.md. - □You know whether your earlier failure came from the project, R, packages, Quarto, data, or account layer.
OPTIONAL · 8–10 MINUTES · AFTER YOUR GATE IS GREEN
Prove that the agent and the student see the same project.
This optional 8–10 minute extension runs while setup repairs continue. Open the course project in Codex and give it a read-only request:
Read this project without changing files or running commands. Locate (1) the course start instructions, (2) the frozen WDI data, and (3) the indicator dictionary. Return each exact file path and one sentence about what the file contains. Separate statements you read from the files from inferences you made.
- 01Check each path manually. Use RStudio’s Files pane rather than accepting the answer from memory.
- 02Open one named file. Confirm that the description matches what the file actually contains.
- 03Name the boundary. Write one sentence distinguishing what the agent learned from files from what it inferred.
This is a first supervised agent exercise, not a race and not a graded artifact. If your machine is not green, continue repairing setup instead.
57–60 MINUTES
Every red result leaves with an owned repair.
If the result is red, save a four-part repair record:
- 01Machine. Operating system and version.
- 02Evidence. Exact command and complete output.
- 03Next step. One concrete repair to try.
- 04Owner. The instructor or ICA who will follow up.
There is no submission and no grade. The operational rule is simple: leave green, or leave with an owned repair plan that gets you to green before Lesson 2.