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

[Andrzej Oleś]

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.

Best,
Andrzej


---
output: BiocStyle::html_document
---

```{r, echo=FALSE, fig.cap="Figure title. Detailed description"}
knitr::include_graphics("split.png")
```



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

> Hi,
>
>
> 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.
>
>
> Regards,
>
> Stefan
>
>
> 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
>
> locale:
> [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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>

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