GitLab

I noticed that when creating reports the resulting html would sometimes contain an extra header (see images in Reprex). This behaviour depended on the environment in which rend.R was called (conda env dge_BioC3.8 vs vanilla bash in falcon vs local bash), but not on the package versions of rmarkdown or knitr.

Ultimately I traced this behaviour to the pandoc version in use. This is a bug created in pandoc v2.9 and as long as we use v2.5 the reports are generated as expected. This might need to be investagated further if we we ever need to upgrade pandoc, but not critical for the time being.

Reprex

pandoc 2.5

conda create -n pandoc_2.5 --yes -c conda-forge pandoc=2.5
conda activate pandoc_2.5
# conda install

rend.R -e test_header.R

Output file has the expected header:

pandoc 2.9

conda create -n pandoc_2.9.2 --yes -c conda-forge pandoc=2.9.2
conda activate pandoc_2.9.2
# conda install

rend.R -e test_header.R

Output report has two separated headers:

---

test_header.R:

#!/usr/bin/env Rscript

#' # Differential Expression Analysis
#'
#' Contents
#'
#' - [Data Preparation](#data-preparation)
#' - [Quality Control](#quality-control)
#'     - [Size Factors](#size-factors)
#'     - [Global Dispersion Model](#global-dispersion-model)
#' - [PCA and Clustering](#pca-and-clustering)
#' - [Differential Expression Test](#differential-expression-test)
#'     - [MA and Volcano plots](#ma-and-volcano-plots)
#'     - [Count Outlier Analysis](#count-outlier-analysis)
#' - [Hits Summary](#hits-summary)
#' - [Exported Data](#exported-data)
#'

# to rebuild toc do knitr::spin("featcounts_deseq_mf.R", FALSE)

#' Created by: `r system("whoami", intern=T)`
#'
#' Created at: `r format(Sys.Date(), format="%B %d %Y")`

plot(1:10)