BiocStyle not working
1
Entering edit mode
29 days ago

I used BiocStyle for a couple of days and it worked perfectly. Suddenly it stop working without any change in my script. I receive the following error:

Quitting from lines 43-44 (Untitled.Rmd) Error in if is.na(options$out.width.px)) options$out.width.px = options$fig.width * : the argument has length zero Calls: <anonymous> ... processgroup.block -> callblock -> as.strict_list -> hook Execution interrupted

Any reason why? Thanks!

sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale: [1] itIT.UTF-8/itIT.UTF-8/itIT.UTF-8/C/itIT.UTF-8/it_IT.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] Rcpp1.0.5 locfit1.5-9.4
[3] lattice0.20-41 assertthat0.2.1
[5] digest0.6.25 R62.4.1
[7] GenomeInfoDb1.25.11 stats44.0.2
[9] RSQLite2.2.0 evaluate0.14
[11] ggplot23.3.2 pillar1.4.6
[13] zlibbioc1.35.0 rlang0.4.7
[15] rstudioapi0.11 annotate1.67.1
[17] blob1.2.1 S4Vectors0.27.13
[19] Matrix1.2-18 rmarkdown2.3
[21] splines4.0.2 BiocParallel1.23.2
[23] geneplotter1.67.0 RCurl1.98-1.2
[25] bit4.0.4 munsell0.5.0
[27] DelayedArray0.15.8 compiler4.0.2
[29] xfun0.17 pkgconfig2.0.3
[31] BiocGenerics0.35.4 htmltools0.5.0
[33] tidyselect1.1.0 SummarizedExperiment1.19.6 [35] tibble3.0.3 GenomeInfoDbData1.2.3
[37] IRanges2.23.10 matrixStats0.56.0
[39] XML3.99-0.5 fansi0.4.1
[41] crayon1.3.4 dplyr1.0.2
[43] dbplyr1.4.4 bitops1.0-6
[45] grid4.0.2 xtable1.8-4
[47] gtable0.3.0 lifecycle0.2.0
[49] DBI1.1.0 magrittr1.5
[51] scales1.1.1 cli2.0.2
[53] XVector0.29.3 genefilter1.71.0
[55] ellipsis0.3.1 generics0.0.2
[57] vctrs0.3.4 cowplot1.1.0
[59] BiocStyle2.17.0 RColorBrewer1.1-2
[61] tools4.0.2 bit644.0.5
[63] Biobase2.49.1 glue1.4.2
[65] DESeq21.29.13 purrr0.3.4
[67] parallel4.0.2 survival3.2-3
[69] yaml2.2.1 AnnotationDbi1.51.3
[71] colorspace1.4-1 BiocManager1.30.10
[73] GenomicRanges1.41.6 memoise1.1.0
[75] knitr_1.30

BiocStyle • 98 views
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Entering edit mode
15 minutes ago
Mike Smith ♦ 4.7k
EMBL Heidelberg / de.NBI

This is caused by an update to knitr, which in turn broke BiocStyle. If you update your BiocStyle to version 2.17.1 the error should be fixed.

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