plot_crop() and the convert command from ImageMagick

[hpages]

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Hi,

We use Windows Server 2012 R2 for the Bioconductor build system to build and check Bioconductor packages. When building the vignettes, we sometimes see a warning like this one for some packages:

Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "overview_files/figure-html/unnamed-chunk-5-1.png" -trim "overview_files/figure-html/unnamed-chunk-5-1.png"' execution failed with error code 4

Tracking down this warning reveals at least 2 issues with knitr:

• The SystemRequirements field for knitr makes no mention of the dependency on ImageMagick.
• On Windows Server 2012 R2 (and maybe on other Windows flavors), if ImageMagick is not installed Sys.which("convert") returns:

   > Sys.which("convert")
                               convert
  "C:\\Windows\\SYSTEM32\\convert.exe"
  

  This convert.exe command is a Microsoft utility for converting a file-system from FAT to NTFS (see https://docs.microsoft.com/en-us/windows-server/administration/windows-commands/convert). Unfortunately this is what knitr::plot_crop() picks up which is why we get the above warnings.

Since knitr already suggests CRAN package magick (since knitr 1.22), I wonder if there is any reason to not use this in plot_crop() instead of a system call to the convert command from ImageMagick. That way knitr would no longer depend on ImageMagick and the risk to pick up the wrong convert command would be eliminated, making knitr::plot_crop() more robust and platform independent.

Thanks,
H.

> xfun::session_info('knitr')
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2012 R2 x64 (build 9600)

Locale:
  LC_COLLATE=English_United States.1252
  LC_CTYPE=English_United States.1252
  LC_MONETARY=English_United States.1252
  LC_NUMERIC=C
  LC_TIME=English_United States.1252

Package version:
  evaluate_0.14   glue_1.3.1      graphics_3.6.1  grDevices_3.6.1
  highr_0.8       knitr_1.26      magrittr_1.5    markdown_1.1
  methods_3.6.1   mime_0.7        stats_3.6.1     stringi_1.4.3
  stringr_1.4.0   tools_3.6.1     utils_3.6.1     xfun_0.11
  yaml_2.2.0

[yihui]

Thanks for the report! The plot_crop() function existed long before the magick package. That's why it didn't use magick. Now it definitely should. I'll make the change.

[github-actions]

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