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Disable learnr exercise checker in R Markdown templates #187

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Disable learnr exercise checker in R Markdown templates #187

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564186e
Initial plan
Copilot Jan 15, 2026
37597c5
Disable tutorial exercise checker in R Markdown templates
Copilot Jan 15, 2026
d44c88a
Add exercise checker disable to all vignettes
Copilot Jan 15, 2026
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5 changes: 5 additions & 0 deletions inst/rmarkdown/index.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,11 @@ params:
library(knitr)
options(width=400)
scigenex::set_verbosity(0)

# Disable tutorial exercise checking to prevent chunks ending in
# '-check' from being interpreted as learnr exercise check chunks
options(tutorial.exercise.checker = NULL)

knitr::opts_chunk$set(
fig.path="all_",
fig.align = "center",
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4 changes: 4 additions & 0 deletions inst/rmarkdown/module.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,10 @@ scigenex::set_verbosity(0)
library(knitr)
options(width=400)

# Disable tutorial exercise checking to prevent chunks ending in
# '-check' from being interpreted as learnr exercise check chunks
options(tutorial.exercise.checker = NULL)

knitr::opts_chunk$set(
fig.path="FIG_PATH",
fig.align = "center",
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6 changes: 6 additions & 0 deletions vignettes/report.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,12 @@ vignette: >
%\usepackage[UTF-8]{inputenc}
---

```{r setup, include=FALSE}
# Disable tutorial exercise checking to prevent any chunks ending in
# '-check' from being interpreted as learnr exercise check chunks
options(tutorial.exercise.checker = NULL)
knitr::opts_chunk$set(echo = TRUE)
```

## Introduction

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7 changes: 7 additions & 0 deletions vignettes/spatial.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,13 @@ vignette: >
%\usepackage[UTF-8]{inputenc}
---

```{r setup, include=FALSE}
# Disable tutorial exercise checking to prevent any chunks ending in
# '-check' from being interpreted as learnr exercise check chunks
options(tutorial.exercise.checker = NULL)
knitr::opts_chunk$set(echo = TRUE)
```

## Working with spatial transcriptomics datasets

The scigenex package offers a certain number of functions dedicated to spatial transcriptomic data analysis. At the moment these functions have been mainly developed to analyse VISIUM technology (10X Genomics).
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7 changes: 7 additions & 0 deletions vignettes/usage.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,13 @@ vignette: >
%\usepackage[UTF-8]{inputenc}
---

```{r setup, include=FALSE}
# Disable tutorial exercise checking to prevent any chunks ending in
# '-check' from being interpreted as learnr exercise check chunks
options(tutorial.exercise.checker = NULL)
knitr::opts_chunk$set(echo = TRUE)
```

# Guided tutorial

The easiest way to use scigenex is to perform the following steps using the Seurat R package:
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