Cannot use include_graphics to insert png in Rmarkdown (error: file is not in PNG format)

Question

This error is very strange. When I knitr the doc, I got the following error:

Quitting from lines 42-43 (sigminer-doc.Rmd) 
Error in png::readPNG(path, native = TRUE, info = TRUE) : 
  file is not in PNG format

However, I can read the png by png::readPNG and it also works when I run the chunk in RStudio.

Use the knitr button in RStudio for index.Rmd cannot work.

I also reinstall the png, knitr package, the idea cannot work.

UPDATE:

I tried to debug the working directory and add the following code to the header.

knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
knitr::knit_hooks$set(debug = function(before, options, envir) {
  if (!before) {
    envir = as.list(envir)
    message("Objects: ", paste(names(envir), collapse = " "))
    for (i in names(envir)) {
      if (!startsWith(i, ".")) {
        message(
          i, " = ", envir[[i]]
        )
      }
    }
  }
})

The working directory is as expected.

Objects: workdir root.dir
workdir = /Users/wsx/Documents/GitHub/sigminer-doc
root.dir = /Users/wsx/Documents/GitHub/sigminer-doc
  |.....                                                                                                                                 |   4%
  ordinary text without R code

  |......                                                                                                                                |   5%
label: unnamed-chunk-3 (with options) 
List of 2
 $ echo   : logi FALSE
 $ fig.cap: chr "The illustration of SBS signature, fig source: https://www.nature.com/articles/nrg3729"

Quitting from lines 64-65 (sigminer-doc.Rmd) 
Error in png::readPNG(path, native = TRUE, info = TRUE) : 
  file is not in PNG format

The knitr also did not stop in code chunk

stopifnot(file.exists("fig/sbs_signature_overview_nat_review.png"))

I found that this issue comes from the figures.

> png::readPNG("fig/sbs_signature_overview.png")
 [ reached getOption("max.print") -- omitted 3 matrix slice(s) ]
Warning message:
In png::readPNG("fig/sbs_signature_overview.png") :
  libpng warning: iCCP: known incorrect sRGB profile
> png::readPNG("fig/sbs_signature_overview_nat_review.png")
Error in png::readPNG("fig/sbs_signature_overview_nat_review.png") : 
  file is not in PNG format

However, I can correctly knit this document before...

My session:

> devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.0 (2020-04-24)
 os       macOS High Sierra 10.13.6   
 system   x86_64, darwin17.0          
 ui       RStudio                     
 language (EN)                        
 collate  zh_CN.UTF-8                 
 ctype    zh_CN.UTF-8                 
 tz       Asia/Shanghai               
 date     2020-05-11                  

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package      * version date       lib source        
 assertthat     0.2.1   2019-03-21 [1] CRAN (R 4.0.0)
 backports      1.1.6   2020-04-05 [1] CRAN (R 4.0.0)
 bibtex         0.4.2.2 2020-01-02 [1] CRAN (R 4.0.0)
 Biobase      * 2.48.0  2020-04-27 [1] Bioconductor  
 BiocGenerics * 0.34.0  2020-04-27 [1] Bioconductor  
 bookdown       0.18    2020-03-05 [1] CRAN (R 4.0.0)
 callr          3.4.3   2020-03-28 [1] CRAN (R 4.0.0)
 cli            2.0.2   2020-02-28 [1] CRAN (R 4.0.0)
 cluster      * 2.1.0   2019-06-19 [2] CRAN (R 4.0.0)
 codetools      0.2-16  2018-12-24 [2] CRAN (R 4.0.0)
 colorspace     1.4-1   2019-03-18 [1] CRAN (R 4.0.0)
 crayon         1.3.4   2017-09-16 [1] CRAN (R 4.0.0)
 data.table     1.12.8  2019-12-09 [1] CRAN (R 4.0.0)
 desc           1.2.0   2018-05-01 [1] CRAN (R 4.0.0)
 devtools       2.3.0   2020-04-10 [1] CRAN (R 4.0.0)
 digest         0.6.25  2020-02-23 [1] CRAN (R 4.0.0)
 doParallel     1.0.15  2019-08-02 [1] CRAN (R 4.0.0)
 dplyr          0.8.5   2020-03-07 [1] CRAN (R 4.0.0)
 ellipsis       0.3.0   2019-09-20 [1] CRAN (R 4.0.0)
 evaluate       0.14    2019-05-28 [1] CRAN (R 4.0.0)
 fansi          0.4.1   2020-01-08 [1] CRAN (R 4.0.0)
 foreach        1.5.0   2020-03-30 [1] CRAN (R 4.0.0)
 fs             1.4.1   2020-04-04 [1] CRAN (R 4.0.0)
 furrr          0.1.0   2018-05-16 [1] CRAN (R 4.0.0)
 future         1.17.0  2020-04-18 [1] CRAN (R 4.0.0)
 ggplot2        3.3.0   2020-03-05 [1] CRAN (R 4.0.0)
 globals        0.12.5  2019-12-07 [1] CRAN (R 4.0.0)
 glue           1.4.0   2020-04-03 [1] CRAN (R 4.0.0)
 gridBase       0.4-7   2014-02-24 [1] CRAN (R 4.0.0)
 gtable         0.3.0   2019-03-25 [1] CRAN (R 4.0.0)
 htmltools      0.4.0   2019-10-04 [1] CRAN (R 4.0.0)
 iterators      1.0.12  2019-07-26 [1] CRAN (R 4.0.0)
 knitr          1.28    2020-02-06 [1] CRAN (R 4.0.0)
 lifecycle      0.2.0   2020-03-06 [1] CRAN (R 4.0.0)
 listenv        0.8.0   2019-12-05 [1] CRAN (R 4.0.0)
 magrittr       1.5     2014-11-22 [1] CRAN (R 4.0.0)
 memoise        1.1.0   2017-04-21 [1] CRAN (R 4.0.0)
 munsell        0.5.0   2018-06-12 [1] CRAN (R 4.0.0)
 NMF          * 0.22.0  2020-02-12 [1] CRAN (R 4.0.0)
 pacman       * 0.5.1   2019-03-11 [1] CRAN (R 4.0.0)
 pheatmap       1.0.12  2019-01-04 [1] CRAN (R 4.0.0)
 pillar         1.4.4   2020-05-05 [1] CRAN (R 4.0.0)
 pkgbuild       1.0.8   2020-05-07 [1] CRAN (R 4.0.0)
 pkgconfig      2.0.3   2019-09-22 [1] CRAN (R 4.0.0)
 pkgload        1.0.2   2018-10-29 [1] CRAN (R 4.0.0)
 pkgmaker     * 0.31.1  2020-03-19 [1] CRAN (R 4.0.0)
 plyr           1.8.6   2020-03-03 [1] CRAN (R 4.0.0)
 png            0.1-7   2013-12-03 [1] CRAN (R 4.0.0)
 prettyunits    1.1.1   2020-01-24 [1] CRAN (R 4.0.0)
 processx       3.4.2   2020-02-09 [1] CRAN (R 4.0.0)
 ps             1.3.2   2020-02-13 [1] CRAN (R 4.0.0)
 purrr          0.3.4   2020-04-17 [1] CRAN (R 4.0.0)
 R.cache        0.14.0  2019-12-06 [1] CRAN (R 4.0.0)
 R.methodsS3    1.8.0   2020-02-14 [1] CRAN (R 4.0.0)
 R.oo           1.23.0  2019-11-03 [1] CRAN (R 4.0.0)
 R.utils        2.9.2   2019-12-08 [1] CRAN (R 4.0.0)
 R6             2.4.1   2019-11-12 [1] CRAN (R 4.0.0)
 RColorBrewer   1.1-2   2014-12-07 [1] CRAN (R 4.0.0)
 Rcpp           1.0.4.6 2020-04-09 [1] CRAN (R 4.0.0)
 registry     * 0.5-1   2019-03-05 [1] CRAN (R 4.0.0)
 remotes        2.1.1   2020-02-15 [1] CRAN (R 4.0.0)
 reshape2       1.4.4   2020-04-09 [1] CRAN (R 4.0.0)
 rlang          0.4.6   2020-05-02 [1] CRAN (R 4.0.0)
 rmarkdown      2.1     2020-01-20 [1] CRAN (R 4.0.0)
 rngtools     * 1.5     2020-01-23 [1] CRAN (R 4.0.0)
 rprojroot      1.3-2   2018-01-03 [1] CRAN (R 4.0.0)
 rstudioapi     0.11    2020-02-07 [1] CRAN (R 4.0.0)
 scales         1.1.0   2019-11-18 [1] CRAN (R 4.0.0)
 sessioninfo    1.1.1   2018-11-05 [1] CRAN (R 4.0.0)
 sigminer     * 1.0.5   2020-05-09 [1] local         
 stringi        1.4.6   2020-02-17 [1] CRAN (R 4.0.0)
 stringr        1.4.0   2019-02-10 [1] CRAN (R 4.0.0)
 styler         1.3.2   2020-02-23 [1] CRAN (R 4.0.0)
 testthat       2.3.2   2020-03-02 [1] CRAN (R 4.0.0)
 tibble         3.0.1   2020-04-20 [1] CRAN (R 4.0.0)
 tidyselect     1.0.0   2020-01-27 [1] CRAN (R 4.0.0)
 usethis        1.6.1   2020-04-29 [1] CRAN (R 4.0.0)
 vctrs          0.2.4   2020-03-10 [1] CRAN (R 4.0.0)
 withr          2.2.0   2020-04-20 [1] CRAN (R 4.0.0)
 xfun           0.13    2020-04-13 [1] CRAN (R 4.0.0)
 xtable         1.8-4   2019-04-21 [1] CRAN (R 4.0.0)
 yaml           2.2.1   2020-02-01 [1] CRAN (R 4.0.0)

[1] /Users/wsx/R_library
[2] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

score 2 · Accepted Answer · answered May 11 '20 at 07:01

The problem is caused by the wrong file format. Although I save the error file with '.png' file extension before, it is not in png format. I still don't know why this file can be read by png package sometimes.

I correct the format and the issue is gone.

> error_file = magick::image_read("fig/sbs_signature_overview_nat_review.png")
> print(error_file)
  format width height colorspace matte filesize density
1   WEBP   685    521       sRGB FALSE    18390   72x72
> right_png <- magick::image_convert(error_file, "png")
> right_png
  format width height colorspace matte filesize density
1    PNG   685    521       sRGB FALSE        0   72x72
> magick::image_write(right_png, path = "fig/sbs_signature_overview_nat_review2.png", format = "png")

I learn a little magick and debugging knitr here. Thanks for the authors.

score 1 · Answer 2 · answered May 11 '20 at 04:17

1

I think that the issue might be where your Rmd is located. The working directory automatically gets changed to that location when knitting. You could either change the root directory (Setting work directory in knitr using opts_chunk$set(root.dir = ...) doesn't work), or simply use paths that first go "up" to the main directory of your R project ("../figure.png").

answered May 11 '20 at 04:17

Marc in the box

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It cannot work. As yihui written in https://yihui.org/knitr/options/, the default root dir is the directory of the input document. It is right. And I also tried `knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())`. Is there debug method to print the info in the chunk? So I can confirm if the root directory is right. – Shixiang Wang May 11 '20 at 06:00

Cannot use include_graphics to insert png in Rmarkdown (error: file is not in PNG format)

2 Answers2

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