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

Stefan Mutter Stefan.Mutter at sahmri.com
Thu Oct 5 12:42:28 CEST 2017

Hi Andrzej,

Thanks for your quick reply. It's very well possible I forgot to attach the file. Sorry for that. I will double check but I also realised that I have included the figure into markdown with a different and most likely incorrect syntax. I will try your way and if the problem persists, I will get back to you with everything attached.

Thank you very much for taking the time to reply. I really appreciate it.


On 5 Oct 2017 18:23, Andrzej Oleś <andrzej.oles at gmail.com> wrote:
Dear Stefan,

Thanks for your feedback. I didn't find the R Markdown sample document you mentioned, maybe you forgot to attach it.

The following minimal example illustrates how to include figures from external files such that they are numbered and contain captions.


output: BiocStyle::html_document

```{r, echo=FALSE, fig.cap="Figure title. Detailed description"}

On Thu, Oct 5, 2017 at 6:35 AM, Stefan Mutter <Stefan.Mutter at sahmri.com<mailto:Stefan.Mutter at sahmri.com>> wrote:

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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