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

Stefan Mutter Stefan.Mutter at sahmri.com
Fri Oct 6 05:02:51 CEST 2017

?Hi Andrzej,

thanks to your help everything is working fine now.

Thanks a lot.



From: Andrzej Ole¶ <andrzej.oles at gmail.com>
Sent: Thursday, October 5, 2017 6:23 PM
To: Stefan Mutter
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Problem with html vignette in BiocStyle 2.5.39

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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