Rendering error for Rmd vignettes using knitr::include_graphics

[hpages]

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---

Hi,

Starting with knitr 1.27 we started to see new vignette errors in several Bioconductor packages in release (BioC 3.10, based on R 3.6) and devel (BioC 3.11, based on R 4.0).

Here is how to reproduce:

1. Create a minimalist Rmd vignette that uses knitr::include_graphics:

   jpeg(file="myplot.jpeg")
   plot(1:10)
   rect(1, 5, 3, 7, col = "white")
   dev.off()
   
   Test_vignette.Rmd <- c(
       "---",
       "title: \"Test vignette\"",
       "---",
       "```{r chunk1}",
       "knitr::include_graphics(\"myplot.jpeg\")",
       "```")
   cat(Test_vignette.Rmd, sep="\n", file="Test_vignette.Rmd")
   

2. Rendering the vignette with rmarkdown::html_document works fine:

   library(rmarkdown)
   rmarkdown::render("Test_vignette.Rmd", rmarkdown::html_document())
   

3. Rendering the vignette with rmarkdown::pdf_document triggers a non-fatal error:

   rmarkdown::render("Test_vignette.Rmd", rmarkdown::pdf_document())
   

   Output:

   processing file: Test_vignette.Rmd
     |...................................                                   |  50%
     ordinary text without R code
   
     |......................................................................| 100%
   label: chunk1
   !!! Error: Input file `Test_vignette_files/figure-latex/chunk1-1.pdf' not found!
   
   output file: Test_vignette.knit.md
   
   /usr/bin/pandoc +RTS -K512m -RTS Test_vignette.utf8.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output Test_vignette.tex --self-contained --highlight-style tango --pdf-engine pdflatex --variable graphics --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.10-bioc/R/library/rmarkdown/rmd/lua/latex-div.lua --variable 'geometry:margin=1in' 
   
   Output created: Test_vignette.pdf
   

4. Trying to render the vignette again with rmarkdown::html_document after enabling cropping now produces a fatal error:

   html_document_crop <- rmarkdown::html_document()
   html_document_crop$knitr$knit_hooks <- list(crop=knitr::hook_pdfcrop)
   html_document_crop$knitr$opts_chunk$crop <- TRUE
   rmarkdown::render("Test_vignette.Rmd", html_document_crop)
   

   Output:

   processing file: Test_vignette.Rmd
     |...................................                                   |  50%
     ordinary text without R code
   
     |......................................................................| 100%
   label: chunk1
   Quitting from lines 5-6 (Test_vignette.Rmd) 
   Error in magick_image_readpath(enc2native(path), density, depth, strip) : 
     Magick: unable to open image `Test_vignette_files/figure-html/chunk1-1.png': No such file or directory @ error/blob.c/OpenBlob/2701
   

magick is installed (see sessionInfo() below) so this is not the same as issue #1796

Note that the issue was originally reported as a BiocStyle issue but the self-contained example above seems to exonerate BiocStyle.

Thanks,
H.

sessionInfo:

R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /home/biocbuild/bbs-3.10-bioc/R/lib/libRblas.so
LAPACK: /home/biocbuild/bbs-3.10-bioc/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rmarkdown_2.0

loaded via a namespace (and not attached):
 [1] compiler_3.6.2  magrittr_1.5    magick_2.2      tools_3.6.2    
 [5] htmltools_0.4.0 yaml_2.2.0      Rcpp_1.0.3      stringi_1.4.5  
 [9] jpeg_0.1-8.1    knitr_1.27      stringr_1.4.0   xfun_0.12      
[13] digest_0.6.23   rlang_0.4.2     evaluate_0.14  

[yihui]

Should be fixed now. Thanks for the report! You may try the dev version for now:

remotes::install_github('yihui/knitr')

[salim-b]

@yihui I also ran into this bug after updating to knitr 1.27. Then I updated to the dev version (1.27.2) and stumpled upon another issue I'd call a bug, too:

It seems that knitr is always overwriting the file included through knitr::include_graphics(). I don't know if this was already the case before knitr 1.27. I noticed it because I tried to build an MVE for the original bug using knitr's reference card PDF vignette as follows:

knitr::include_graphics(paste0(find.package(package = "knitr"), "/doc/knitr-refcard.pdf"))

Since I've installed knitr through Michael Rutter's PPA (Ubuntu Linux), on my system the above is equivalent to:

knitr::include_graphics("/usr/lib/R/site-library/knitr/doc/knitr-refcard.pdf")

When I try to build this, the following error is thrown:

!!! Error: Cannot move `tmp-pdfcrop-6024.pdf' to `/usr/lib/R/site-library/knitr/doc/knitr-refcard.pdf'!

This is of course because knitr isn't run as root, but the file is owned by root and knitr doesn't have write permission:

$ ls -1l /usr/lib/R/site-library/knitr/doc/knitr-refcard.pdf
-rw-r--r-- 1 root root 79531 Jan 19 04:04 /usr/lib/R/site-library/knitr/doc/knitr-refcard.pdf

I verified this with a file knitr actually has write permission to – it gets overwritten when included through knitr::include_graphics()! The documentation of knitr::include_graphics() doesn't say anything about possible file modifications of param path and I believe it was never really intended to overwrite path, right?

---

Addendum: I've just read about the crop option in #1796 and setting knitr::opts_chunk$set(crop = NULL) avoids knitr's attempt to overwrite the included PDF.

I think it's fine that knitr automatically crops whitespace around the files specified in knitr::include_graphics() but it should still never overwrite the original files!

And is there a specific reason why crop isn't a "proper" chunk options like e.g. fig.path?

[hpages]

and stumpled upon another issue

Have you considered opening a new issue for that?

[salim-b]

Have you considered opening a new issue for that?

I thought it might make sense to report it here since it seems closely related to the original issue you reported. But of course I can open a new issue if that's preferred...

[hpages]

I think it's preferred, especially since the specific issue I reported here has been fixed and closed. Thanks!

[salim-b]

I think it's preferred, especially since the specific issue I reported here has been fixed and closed. Thanks!

Ok then: #1800

[yihui]

@salim-b Your issue is slightly related to @hpages's issue. If you are unsure, it is always a good idea to file a new issue (so the original poster won't receive unnecessary notifications), and as a hint to the developers, you could mention that the new issue might be related to this issue. Thanks!

And is there a specific reason why crop isn't a "proper" chunk options like e.g. fig.path?

Because cropping images require additional software packages, and I tend to let users opt-in after they know how to install these packages, instead of "officially" supporting this feature.

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