From 965d1e99aba41be8526d79ffc732dfcb66860e01 Mon Sep 17 00:00:00 2001
From: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: Thu, 15 Jan 2026 13:40:51 +0200
Subject: [PATCH 1/2] Revert "Disable chunks (#831)"

This reverts commit 7efff771bcd600f5877e51723e706378281c1da6.
---
 DESCRIPTION                           |  3 ++-
 inst/pages/differential_abundance.qmd | 10 ----------
 inst/pages/integrated_learner.qmd     |  5 -----
 inst/pages/mmuphin_meta_analysis.qmd  |  5 -----
 inst/pages/msea.qmd                   |  5 -----
 5 files changed, 2 insertions(+), 26 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0a44525a..b8fa7d10 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -114,7 +114,8 @@ Remotes:
     github::stefpeschel/NetCoMi,
     github::zdk123/SpiecEasi,
     github::GraceYoon/SPRING,
-    github::himelmallick/IntegratedLearner
+    github::himelmallick/IntegratedLearner,
+    github::biobakery/Maaslin2
 VignetteBuilder: knitr
 RoxygenNote: 7.3.2
 BiocType: Book
diff --git a/inst/pages/differential_abundance.qmd b/inst/pages/differential_abundance.qmd
index ce29e849..45083c2b 100644
--- a/inst/pages/differential_abundance.qmd
+++ b/inst/pages/differential_abundance.qmd
@@ -199,11 +199,6 @@ folder for some output files. Lastly, we prevent `Maaslin2()` to create certain
 plots. (Note that `Maaslin2()` prints a lot of some output
 which is suppressed here for convenience.)
 
-```{r}
-#| label: disable_chunks
-knitr::opts_chunk$set(eval = FALSE)
-```
-
 ```{r}
 #| label: run_daa_basic
 #| results: hide
@@ -558,11 +553,6 @@ cohort).
 Note that a similar plot could also be used to illustrate a possible confounding
 effect.
 
-```{r}
-#| label: enable_chunks
-knitr::opts_chunk$set(eval = TRUE)
-```
-
 ### Differential prevalence analysis (DPA) {#sec-DPA}
 
 We show here how to perform DPA with logistic regression. We show the case
diff --git a/inst/pages/integrated_learner.qmd b/inst/pages/integrated_learner.qmd
index 6031ebc5..286f30e8 100644
--- a/inst/pages/integrated_learner.qmd
+++ b/inst/pages/integrated_learner.qmd
@@ -146,11 +146,6 @@ integrates the outputs from these individual models to make the final
 predictions. For "base learners" and "meta learner", we use _random forest_
 and _rank loss minimization_ models, respectively.
 
-```{r}
-#| label: disable_chunks
-knitr::opts_chunk$set(eval = FALSE)
-```
-
 ```{r}
 #| label: fit_model
 
diff --git a/inst/pages/mmuphin_meta_analysis.qmd b/inst/pages/mmuphin_meta_analysis.qmd
index 900e66f2..dfd9466a 100644
--- a/inst/pages/mmuphin_meta_analysis.qmd
+++ b/inst/pages/mmuphin_meta_analysis.qmd
@@ -130,11 +130,6 @@ abundance file, which includes the study names and overall response rate
 (ORR) the response variable along with other metadata. By the end of
 this step, we obtain a batch-adjusted relative abundance matrix.
 
-```{r}
-#| label: disable_chunks
-knitr::opts_chunk$set(eval = FALSE)
-```
-
 ```{r}
 #| label: prepare_input_data
 
diff --git a/inst/pages/msea.qmd b/inst/pages/msea.qmd
index d42b72f6..2fdd35d8 100644
--- a/inst/pages/msea.qmd
+++ b/inst/pages/msea.qmd
@@ -98,11 +98,6 @@ microbial species abundance versus IBD diagnosis. The analysis method we use
 here is "LM", which is the default setting. We also adjust for age and
 antibiotic usage, following the original study.
 
-```{r}
-#| label: disable_chunks
-knitr::opts_chunk$set(eval = FALSE)
-```
-
 ```{r}
 #| label: fit_model_Maaslin2
 

From c7fd9bdfa73d2e1bb9d4613431d34a294fdb71e6 Mon Sep 17 00:00:00 2001
From: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: Thu, 15 Jan 2026 13:41:23 +0200
Subject: [PATCH 2/2] Update DESCRIPTION

---
 DESCRIPTION | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b8fa7d10..0a44525a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -114,8 +114,7 @@ Remotes:
     github::stefpeschel/NetCoMi,
     github::zdk123/SpiecEasi,
     github::GraceYoon/SPRING,
-    github::himelmallick/IntegratedLearner,
-    github::biobakery/Maaslin2
+    github::himelmallick/IntegratedLearner
 VignetteBuilder: knitr
 RoxygenNote: 7.3.2
 BiocType: Book