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