knitr markdown removes image file from project folder - r

Question

I have this basic R markdown file:
---
title: 'test'
output:
html_document
---
![myimage](test.png)
The file test.png can be found in the project folder. If I compile the document the first time all is good:
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ordinary text without R code
/Applications/RStudio.app/Contents/MacOS/pandoc/pandoc +RTS -K512m -RTS /Users/nf/test/test_file.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output test_file.html --smart --email-obfuscation none --self-contained --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rmarkdown/rmd/h/default.html --variable 'theme:bootstrap' --include-in-header /var/folders/x0/87l48swx73lg569_81cctqt00000gp/T//RtmpYYJgwp/rmarkdown-stree426f43954e.html --mathjax --variable 'mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --no-highlight --variable highlightjs=/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rmarkdown/rmd/h/highlight
processing file: test_file.Rmd
output file: /Users/nf/test/test_file.knit.md
Output created: test_file.html
But if I compile it the second time (without changing anything) I get this error:
|.................................................................| 100%
ordinary text without R code
processing file: test_file.Rmd
output file: /Users/nf/test/test_file.knit.md
/Applications/RStudio.app/Contents/MacOS/pandoc/pandoc +RTS -K512m -RTS /Users/nf/test/test_file.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output test_file.html --smart --email-obfuscation none --self-contained --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rmarkdown/rmd/h/default.html --variable 'theme:bootstrap' --include-in-header /var/folders/x0/87l48swx73lg569_81cctqt00000gp/T//RtmprFBDzb/rmarkdown-streef56b8e7e99.html --mathjax --variable 'mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --no-highlight --variable highlightjs=/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rmarkdown/rmd/h/highlight
pandoc: Could not fetch test.png
test.png: openBinaryFile: does not exist (No such file or directory)
Error: pandoc document conversion failed with error 67
Execution halted
If I look into my project folder the image test.png is gone. In the process of the first compilation of the document the image get's deleted. I can reproduce it every time. And then of course it is missing for the second compilation. This also happens with .RData files I load inside R chunks. I even tried to keep the files in a separate folder and copy them every time inside my project folder I compile my document (with the command file.copy()). But then the files in the outside folder disappear as well. It seems that every file mentioned in the markdown document gets deleted or moved somewhere else.
What I found out is that this happens only if the name of the markdown file contains spaces like test file.Rmd. Html pages produced from this file are formated test_file.html so I guess some transformation to a filename without spaces takes place.
I think this is a bug I should report on some bug tracker, but since I don't know whether this is about rmarkdown, knitr, pandoc, RStudio or something else I post it here.
My session info:
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.2 (El Capitan)
locale:
[1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] knitr_1.11
loaded via a namespace (and not attached):
[1] tools_3.2.2

Answer 1

Updating to rmarkdown_0.9.2 fixed the problem according to this issue: https://github.com/rstudio/rmarkdown/issues/580