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 -------------- next part -------------- A non-text attachment was scrubbed... Name: split.png Type: image/png Size: 151381 bytes Desc: split.png URL: <https://stat.ethz.ch/pipermail/bioc-devel/attachments/20171005/4070bf3c/attachment.png>
[Bioc-devel] Problem with html vignette in BiocStyle 2.5.39
3 messages · Stefan Mutter, 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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?Hi Andrzej, thanks to your help everything is working fine now. Thanks a lot. Cheers, Stefan
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
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.
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<mailto: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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