try highr package instead of highlight package

gagneurlab · Jul 22, 2024 · f0fd1c0 · f0fd1c0
1 parent bf875f7
commit f0fd1c0
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -148,6 +148,7 @@ jobs:
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
         run: |
+          install.packages("highr")
           ## Edit below if you have any Windows system dependencies
         shell: Rscript {0}
 
@@ -159,7 +160,7 @@ jobs:
           system("tlmgr --version")
           install.packages("tinytex")
           tinytex::tlmgr_install(pkgs = c("bera", "caption", "changepage", "enumitem", "everysel", "fancyhdr", "footmisc", "grfext", "index", "marginfix", "mathtools", 
-                                 "ms", "nowidow", "parnotes", "parskip", "placeins", "preprint", "ragged2e", "side", "soul", "titlesec", "tocbibind", "xstring", "highlight"))
+                                 "ms", "nowidow", "parnotes", "parskip", "placeins", "preprint", "ragged2e", "side", "soul", "titlesec", "tocbibind", "xstring"))
         shell: Rscript {0}
 
       - name: Install BiocManager

diff --git a/vignettes/OUTRIDER.Rnw b/vignettes/OUTRIDER.Rnw
@@ -6,14 +6,14 @@
 \documentclass[11pt]{article}
 \usepackage{xcolor}
 \definecolor{fgcolor}{rgb}{0,0,0}
-\usepackage{highlight}
 
 <<style-knitr, eval=TRUE, echo=FALSE, cache=FALSE, results="asis">>=
 BiocStyle::latex()
 @
 
 <<knitr, echo=FALSE, cache=FALSE, results="hide">>=
 library(knitr)
+library(highr)
 opts_chunk$set(
     tidy=FALSE,
     dev="png",