Can't knit from Bioconductor HTML template

[EricMarcon]

Hello,

I'm trying to use the Bioconductor vignette template.
When knitting, I get

ParamŠtre non valide - /figure-html

in the R Markdown window of RStudio each time a chunk produces a plot.
Finally, warnings claim that convert failed : (...) execution failed with error code 4

The HTML is produced and seems correct so this would not be a serious issue but the checking procedure of the package fails for that reason.

In details:

• I use Windows 10, up-to-date
• R Studio 1.1.383 ; R 3.4-2
• I installed the package BiocStyle from Bioconductor:

source("https://bioconductor.org/biocLite.R")
biocLite("BiocStyle")

Then I created a new R Markdown, from Template : 'Bioconductor HTML Vignette' and I knitted it. I saved it as a.Rmd. The vignette is produced. This is the R Markown Window:

processing file: a.Rmd
  |........                                                           |  12%
   inline R code fragments

  |.................                                                  |  25%
label: plot (with options) 
List of 2
 $ fig.cap: chr "Regular figure. The first sentence of the figure caption is automatically emphasized to serve as figure title."
 $ echo   : logi FALSE

ParamŠtre non valide - /figure-html
  |.........................                                          |  38%
  ordinary text without R code

  |..................................                                 |  50%
label: small (with options) 
List of 3
 $ fig.cap  : chr "Small figure. A plot produced by a code chunk with option `fig.small = TRUE`."
 $ fig.small: logi TRUE
 $ echo     : logi FALSE

  |..........................................                         |  62%
  ordinary text without R code

  |..................................................                 |  75%
label: wide (with options) 
List of 3
 $ fig.cap : chr "Wide figure. A plot produced by a code chunk with option `fig.wide = TRUE`."
 $ fig.wide: logi TRUE
 $ echo    : logi FALSE

ParamŠtre non valide - /figure-html
ParamŠtre non valide - /figure-html
  |...........................................................        |  88%
  ordinary text without R code

  |...................................................................| 100%
label: sessionInfo (with options) 
List of 1
 $ echo: logi FALSE


output file: a.knit.md

"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS a.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output pandocf842c01931.html --smart --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 3 --template "C:\Users\ERIC~1.MAR\AppData\Local\Temp\RtmpSmnSpT/BiocStyle/template.html" --no-highlight --variable highlightjs=1 --number-sections --css "C:\PROGRA~1\R\R-34~1.2\library\BIOCST~1\RESOUR~1\html\BIOCON~2.CSS" --variable "theme:bootstrap" --include-in-header "C:\Users\ERIC~1.MAR\AppData\Local\Temp\RtmpSmnSpT\rmarkdown-strf84dcd349a.html" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" 

Output created: C:/Users/Eric.Marcon/AppData/Local/Temp/RtmpO0xNH3/preview-1e5476bf4d85.dir/a.html
Warning messages:
1: l'exécution de la commande 'C:\WINDOWS\system32\cmd.exe /c convert "C:\Users\Eric.Marcon\AppData\Local\Temp\RtmpO0xNH3\preview-1e5476bf4d85.dir\a_files/figure-html/plot-1.png" -trim "C:\Users\Eric.Marcon\AppData\Local\Temp\RtmpO0xNH3\preview-1e5476bf4d85.dir\a_files/figure-html/plot-1.png"' renvoie un statut 4 
2: In shell(paste(c(cmd, args), collapse = " ")) :
  'convert "C:\Users\Eric.Marcon\AppData\Local\Temp\RtmpO0xNH3\preview-1e5476bf4d85.dir\a_files/figure-html/plot-1.png" -trim "C:\Users\Eric.Marcon\AppData\Local\Temp\RtmpO0xNH3\preview-1e5476bf4d85.dir\a_files/figure-html/plot-1.png"' execution failed with error code 4
3: l'exécution de la commande 'C:\WINDOWS\system32\cmd.exe /c convert "C:\Users\Eric.Marcon\AppData\Local\Temp\RtmpO0xNH3\preview-1e5476bf4d85.dir\a_files/figure-html/small-1.png" -trim "C:\Users\Eric.Marcon\AppData\Local\Temp\RtmpO0xNH3\preview-1e5476bf4d85.dir\a_files/figure-html/small-1.png"' renvoie un statut 4 
4: In shell(paste(c(cmd, args), collapse = " ")) :
  'convert "C:\Users\Eric.Marcon\AppData\Local\Temp\RtmpO0xNH3\preview-1e5476bf4d85.dir\a_files/figure-html/small-1.png" -trim "C:\Users\Eric.Marcon\AppData\Local\Temp\RtmpO0xNH3\preview-1e5476bf4d85.dir\a_files/figure-html/small-1.png"' execution failed with error code 4
5: l'exécution de la commande 'C:\WINDOWS\system32\cmd.exe /c convert "C:\Users\Eric.Marcon\AppData\Local\Temp\RtmpO0xNH3\preview-1e5476bf4d85.dir\a_files/figure-html/wide-1.png" -trim "C:\Users\Eric.Marcon\AppData\Local\Temp\RtmpO0xNH3\preview-1e5476bf4d85.dir\a_files/figure-html/wide-1.png"' renvoie un statut 4 
6: In shell(paste(c(cmd, args), collapse = " ")) :
  'convert "C:\Users\Eric.Marcon\AppData\Local\Temp\RtmpO0xNH3\preview-1e5476bf4d85.dir\a_files/figure-html/wide-1.png" -trim "C:\Users\Eric.Marcon\AppData\Local\Temp\RtmpO0xNH3\preview-1e5476bf4d85.dir\a_files/figure-html/wide-1.png"' execution failed with error code 4

Thanks for your efforts.

[yihui]

Have you reported to the authors of BiocStyle? It seems they enabled the knitr hook knitr::hook_pdfcrop unconditionally (i.e. without checking if ImageMagick has been installed).

Anyway, this is the repo of the rmarkdown package. If you run into problems by using output formats from other packages, please contact maintainers of those packages first. We cannot maintain their packages.

[github-actions]

This old thread has been automatically locked. If you think you have found something related to this, please open a new issue by following the issue guide (https://yihui.org/issue/), and link to this old issue if necessary.