From f5afe3a8a0ab44dd06812a16c3a80a9b627da6dc Mon Sep 17 00:00:00 2001
From: hosseinvk <h.valipour.k@gmail.com>
Date: Mon, 10 Aug 2026 22:36:43 +1000
Subject: [PATCH] Disable multienrichjam install code, exclude it from
 workshop.R

Comments out the install.packages/remotes/library/help lines in the
optional multienrichjam install chunk so they can't be accidentally
run, and wraps the whole chunk in <!--omit-begin/end--> so it's
excluded from the generated workshop.R entirely while remaining
visible in the rendered book chapter.
---
 10-clusterprofiler.Rmd | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/10-clusterprofiler.Rmd b/10-clusterprofiler.Rmd
index 1c0fa3f..d3fe315 100644
--- a/10-clusterprofiler.Rmd
+++ b/10-clusterprofiler.Rmd
@@ -327,18 +327,20 @@ Unfortunately, `enrichplot` is only compatible with the enrichment results from
 `multienrichjam` has a lot of dependencies and has not been installed on these VMs so we will not be performing this today. However, this functionality and flexibility is pretty cool, so if you wanted to install this on your own computer outside the workshop, below is the code for installing :-)
 
 
+<!--omit-begin-->
 ```{r install multienrichjam, eval = FALSE}
 # github remotes package required:
-install.packages("remotes")
-library(remotes)
+# install.packages("remotes")
+# library(remotes)
 
 # install multienrichjam:
-remotes::install_github("jmw86069/multienrichjam", dependencies = TRUE)
-library(multienrichjam)
+# remotes::install_github("jmw86069/multienrichjam", dependencies = TRUE)
+# library(multienrichjam)
 
 # check function help:
-?enrichDF2enrichResult
+# ?enrichDF2enrichResult
 ```
+<!--omit-end-->
 
 
 #### dotplot