[Bioc-devel] Problem with html vignette in BiocStyle 2.5.39

Stefan Mutter Stefan.Mutter at sahmri.com
Thu Oct 5 06:35:19 CEST 2017


I have a problem while generating a html vignette (html_document) with BiocStyle version 2.5.39 from the development branch. I have attached a small example markdown that replicates the problem on my machine.

I want to add an image as a figure and I would like the caption to say Figure X whereas X is the correctly numbered Figure in the document. Unfortunately, no BiocStyle figure caption is created and no number provided.

I am really grateful for your help.



Below is the output of sessioninfo:

R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

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

other attached packages:
[1] Numero_0.99.0        BiocInstaller_1.27.5

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.13        compiler_3.4.1      bitops_1.0-6
 [4] tools_3.4.1         digest_0.6.12       jsonlite_1.5
 [7] evaluate_0.10.1     memoise_1.1.0       graph_1.55.0
[10] rstudioapi_0.7      commonmark_1.4      BiocCheck_1.13.2
[13] yaml_2.1.14         curl_2.8.1          parallel_3.4.1
[16] withr_2.0.0         httr_1.3.1          stringr_1.2.0
[19] knitr_1.17          roxygen2_6.0.1      xml2_1.1.1
[22] desc_1.1.1          devtools_1.13.3     stats4_3.4.1
[25] rprojroot_1.2       getopt_1.20.0       optparse_1.4.4
[28] Biobase_2.37.2      R6_2.2.2            XML_3.98-1.9
[31] RBGL_1.53.0         rmarkdown_1.6       magrittr_1.5
[34] htmltools_0.3.6     backports_1.1.1     codetools_0.2-15
[37] biocViews_1.45.0    BiocGenerics_0.23.2 RUnit_0.4.31
[40] assertthat_0.2.0    BiocStyle_2.5.39    stringi_1.1.5
[43] RCurl_1.95-4.8      crayon_1.3.4

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