Add crop = NULL to all template Rmarkdown files. Drop magick as adepencency since cropping is not used on the reports (as done throughBiocStyle by default). This is again related to responding to -devel/2020-April/016645.html.
These flags are redundant in versions 0.9.5 and above. They provided some coarse control over the behaviour of the sorting algorithm in earlier versions, which was sometimes useful. 0.9.5 and above have an improved algorithm which renders these flags irrelevant. 2b1af7f3a8