Vignettes with plots won't built with knitr after 1.27 update: there is no package called 'magick'

[anhtr]

Hello,

Thank you for your essential package. I may have found a bug in the 1.27 release of knitr.

My package (HPAanalyze on Bioconductor) build vignette using knitr, and the Travis-CI build has been fine right up to the release of knitr 1.27 (i.e. this morning was ok, this afternoon was not.). I got the error message there is no package called 'magick'. I traced back to the line in the vignette that caused the error, and it was a function that generate plots using ggplot2 and gridExtra.

I think a change in knitr 1.27 may have caused that. The full log is as below. Please let me know what other information I should include. Thank you very much.

https://travis-ci.com/trannhatanh89/HPAanalyze/builds/144784427

Building with: R CMD build 

30.81s$ R CMD build  .

* checking for file ‘./DESCRIPTION’ ... OK

* preparing ‘HPAanalyze’:

* checking DESCRIPTION meta-information ... OK

* installing the package to build vignettes

* creating vignettes ... ERROR

--- re-building ‘a_HPAanalyze_quick_start.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 56-59 (a_HPAanalyze_quick_start.Rmd) 

Error: processing vignette 'a_HPAanalyze_quick_start.Rmd' failed with diagnostics:

there is no package called 'magick'

--- failed re-building ‘a_HPAanalyze_quick_start.Rmd’

--- re-building ‘b_HPAanalyze_indepth.Rmd’ using rmarkdown

Quitting from lines 64-65 (b_HPAanalyze_indepth.Rmd) 

Error: processing vignette 'b_HPAanalyze_indepth.Rmd' failed with diagnostics:

there is no package called 'magick'

--- failed re-building ‘b_HPAanalyze_indepth.Rmd’

--- re-building ‘c_HPAanalyze_case_query.Rmd’ using rmarkdown

Quitting from lines 54-55 (c_HPAanalyze_case_query.Rmd) 

Error: processing vignette 'c_HPAanalyze_case_query.Rmd' failed with diagnostics:

there is no package called 'magick'

--- failed re-building ‘c_HPAanalyze_case_query.Rmd’

--- re-building ‘d_HPAanalyze_case_offline_xml.Rmd’ using rmarkdown

--- finished re-building ‘d_HPAanalyze_case_offline_xml.Rmd’

--- re-building ‘e_HPAanalyze_case_json.Rmd’ using rmarkdown

--- finished re-building ‘e_HPAanalyze_case_json.Rmd’

--- re-building ‘f_HPAanalyze_case_images.Rmd’ using rmarkdown

trying URL 'https://www.proteinatlas.org/ENSG00000134057.xml'

downloaded 1.1 MB

--- finished re-building ‘f_HPAanalyze_case_images.Rmd’

--- re-building ‘z_HPAanalyze_paper_figures.Rmd’ using rmarkdown

--- finished re-building ‘z_HPAanalyze_paper_figures.Rmd’

SUMMARY: processing the following files failed:

  ‘a_HPAanalyze_quick_start.Rmd’ ‘b_HPAanalyze_indepth.Rmd’

  ‘c_HPAanalyze_case_query.Rmd’

Error: Vignette re-building failed.

Execution halted

The command "R CMD build  ." failed and exited with 1 during .

---

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[yihui]

Thanks for the report! You may add magick to Suggests in DESCRIPTION, or set knitr::opts_chunk$set(crop = NULL) in your Rmd.

This problem occurs because BiocStyle enabled plot cropping unconditionally for all its output formats:

• https://github.com/Bioconductor/BiocStyle/blob/3ffe07b03fbfdfd607c84708cfb2f410c5b435ed/R/knitr_options.R#L10
• https://github.com/Bioconductor/BiocStyle/blob/3ffe07b03fbfdfd607c84708cfb2f410c5b435ed/R/knitr_options.R#L20

That means magick needs to be declared as a Suggests dependency in packages that use BiocStyle's non-LaTeX/PDF output formats; knitr 1.27 started to use magick to crop non-PDF images, per suggestion #1785.

In rmarkdown, we only enable cropping in the pdf_document format, and we enable this feature conditionally: https://github.com/rstudio/rmarkdown/blob/3a03ed9368ee54c42eec7302fe33990b193219ef/R/output_format.R#L254 BiocStyle may need to check requireNamespace('magick', quietly = TRUE).

[anhtr]

Thank you for your answer! Setting knitr::opts_chunk$set(crop = NULL) worked perfectly for me.

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