I recently upgraded to pandoc 3 and now BiocStyle looks terrible. Notice the lack of background for the output chunks, as well as the loss of vertical padding around the code chunks.
Compare this to the vignette built with the BBS, presumably on an earlier pandoc. The top/bottom padding around the blocks is present and the output chunks are well-distinguished from the text with its own background. (Would be even nicer if the text or background color for output chunks was subtly different, so as to better distinguish from code chunks.)
I suspect that the problem occurs at pandoc < 3, actually. I previously had 2.17 but I was seeing this show up in systems with 2.19.
Session information
> sessionInfo()
R Under development (unstable) (2022-11-08 r83316)
Platform: x86_64-apple-darwin19.6.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /Users/luna/Software/R/trunk/lib/libRblas.dylib
LAPACK: /Users/luna/Software/R/trunk/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ResidualMatrix_1.9.0 Matrix_1.5-3 BiocStyle_2.27.1
loaded via a namespace (and not attached):
[1] cli_3.6.0 knitr_1.42 rsvd_1.0.5
[4] magick_2.7.3 rlang_1.0.6 xfun_0.36
[7] highr_0.10 jsonlite_1.8.4 DelayedArray_0.25.0
[10] BiocSingular_1.15.0 S4Vectors_0.37.3 htmltools_0.5.4
[13] sass_0.4.4 stats4_4.3.0 MatrixGenerics_1.11.0
[16] rmarkdown_2.20 grid_4.3.0 evaluate_0.20
[19] jquerylib_0.1.4 fastmap_1.1.0 IRanges_2.33.0
[22] yaml_2.3.7 bookdown_0.32 BiocManager_1.30.19
[25] compiler_4.3.0 codetools_0.2-18 irlba_2.3.5.1
[28] Rcpp_1.0.10 BiocParallel_1.33.9 lattice_0.20-45
[31] digest_0.6.31 R6_2.5.1 parallel_4.3.0
[34] magrittr_2.0.3 bslib_0.4.2 tools_4.3.0
[37] beachmat_2.15.0 ScaledMatrix_1.7.0 matrixStats_0.63.0
[40] BiocGenerics_0.45.0 cachem_1.0.6
I recently upgraded to pandoc 3 and now BiocStyle looks terrible. Notice the lack of background for the output chunks, as well as the loss of vertical padding around the code chunks.
Compare this to the vignette built with the BBS, presumably on an earlier pandoc. The top/bottom padding around the blocks is present and the output chunks are well-distinguished from the text with its own background. (Would be even nicer if the text or background color for output chunks was subtly different, so as to better distinguish from code chunks.)
I suspect that the problem occurs at pandoc < 3, actually. I previously had 2.17 but I was seeing this show up in systems with 2.19.
Session information