Work around breaking change in knitr 1.39.

scripts/generate_report.R

@@ -4,7 +4,7 @@
 # Copyright © 2017, 2018 Alexander Gosdschan <[email protected]>
 # Copyright © 2017, 2018, 2019 Alexander Blume <[email protected]>
 # Copyright © 2017 Katarzyna Wreczycka <[email protected]>
-# Copyright © 2017 Ricardo Wurmus <[email protected]>
+# Copyright © 2017, 2022 Ricardo Wurmus <[email protected]>
 #
 # This file is part of the PiGx BSseq Pipeline.
 #
@@ -63,6 +63,9 @@ render2HTML <- function(reportFile,
   ## render single report
   message("rendering report from template: ", reportFile)
 
+  # knitr 1.39 changed the default behavior.
+  options(knitr.graphics.rel_path = FALSE)
+
   htmlwidgets::setWidgetIdSeed(1234)
   rmarkdown::render(
     input = reportFile,

scripts/report_functions.R

@@ -3,7 +3,7 @@
 # Copyright © 2017 Bren Osberg <[email protected]>
 # Copyright © 2017, 2018 Alexander Gosdschan <[email protected]>
 # Copyright © 2017 Katarzyna Wreczycka <[email protected]>
-# Copyright © 2017 Ricardo Wurmus <[email protected]>
+# Copyright © 2017, 2022 Ricardo Wurmus <[email protected]>
 #
 # This file is part of the PiGx BSseq Pipeline.
 #
@@ -30,7 +30,10 @@ render2HTML <- function(reportFile,
                             self.contained=TRUE,
                             logFile = NULL)
 {
-
+
+  # knitr 1.39 changed the default behavior.
+  options(knitr.graphics.rel_path = FALSE)
+
   output_format = rmarkdown::all_output_formats(reportFile, 'UTF-8')
 
   if(!dir.exists(finalReportDir)) dir.create(finalReportDir, recursive = TRUE)