do not cache chunk outputs as this triggers git lfs error

carpentries-incubator · May 23, 2024 · 6293ab0 · 6293ab0
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commit 6293ab0
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diff --git a/episodes/cell_type_annotation.Rmd b/episodes/cell_type_annotation.Rmd
@@ -23,7 +23,7 @@ editor_options:
 ## Setup
 
 ```{r chunk-opts, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE, cache = TRUE, message = FALSE, warning = FALSE)
+knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE)
 library(BiocStyle)
 ```
 

diff --git a/episodes/eda_qc.Rmd b/episodes/eda_qc.Rmd
@@ -26,7 +26,7 @@ exercises: 15 # Minutes of exercises in the lesson
 ```{r chunk-opts, include=FALSE}
 rm(list = ls())
 gc()
-knitr::opts_chunk$set(echo = TRUE, cache = TRUE, message = FALSE, warning = FALSE)
+knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE)
 library(BiocStyle)
 ```
 

diff --git a/episodes/intro-sce.Rmd b/episodes/intro-sce.Rmd
@@ -23,7 +23,7 @@ exercises: 10 # Minutes of exercises in the lesson
 ## Setup
 
 ```{r chunk-opts, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE, cache = TRUE, message = FALSE, warning = FALSE)
+knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE)
 library(BiocStyle)
 ```
 

diff --git a/episodes/large_data.Rmd b/episodes/large_data.Rmd
@@ -22,7 +22,7 @@ exercises: 2 # Minutes of exercises in the lesson
 ::::::::::::::::::::::::::::::::::::::::::::::::
 
 ```{r chunk-opts, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE, cache = TRUE, message = FALSE, warning = FALSE)
+knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE)
 library(BiocStyle)
 ```
 

diff --git a/episodes/multi-sample.Rmd b/episodes/multi-sample.Rmd
@@ -37,7 +37,7 @@ Note that this is a paired design in which for each biological replicate (pool 3
 We start by loading the data and doing a quick exploratory analysis, essentially applying the normalization and visualization techniques that we have seen in the previous lectures to all samples.
 
 ```{r chunk-opts, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE, cache = TRUE, message = FALSE, warning = FALSE)
+knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE)
 library(BiocStyle)
 ```