From 44f1cf4e95ae1a3bb98bc5c9442d8aba1d399a6b Mon Sep 17 00:00:00 2001
From: AtaJadidAhari <atajadidahari@gmail.com>
Date: Tue, 30 Jul 2024 11:13:35 +0200
Subject: [PATCH] fall back to knitr instead of rmarkdown, echo pandoc version

---
 .github/workflows/check-bioc.yml | 3 +--
 vignettes/OUTRIDER.Rnw           | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
index bdf38cc..038373d 100644
--- a/.github/workflows/check-bioc.yml
+++ b/.github/workflows/check-bioc.yml
@@ -131,7 +131,7 @@ jobs:
           ## Enable installing XML from source if needed
           brew install libxml2
           echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
-
+          message(pandoc --version)
           ## Required to install magick as noted at
           ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
           brew install imagemagick@6
@@ -144,7 +144,6 @@ jobs:
 
           ## Required for tcltk
           brew install xquartz --cask
-          brew install Caskroom/cask/mactex
 
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
diff --git a/vignettes/OUTRIDER.Rnw b/vignettes/OUTRIDER.Rnw
index 2bd25d9..b1367d9 100644
--- a/vignettes/OUTRIDER.Rnw
+++ b/vignettes/OUTRIDER.Rnw
@@ -1,6 +1,6 @@
 %\VignetteIndexEntry{OUTRIDER: OUTlier in RNA-seq fInDER}
 %\VignettePackage{OUTRIDER}
-%\VignetteEngine{knitr::rmarkdown}
+%\VignetteEngine{knitr::knitr}
 %\VignetteEncoding{UTF-8}
 
 \documentclass[11pt]{article}