intermediates_dir causes rename warnings

[aronatkins]

Using intermediates_dir causes rename warnings. Perhaps similar to #1190.

---
title: rename warnings
output: html_document
---

```{r echo=FALSE}
data <- c(
  red = 2,
  blue = 4,
  brown = 7,
  white = 3
)

barplot(data, col = heat.colors(length(data)), las = 2)
```

Command used to render:

rmarkdown::render(
    input = "~/Downloads/slash/index.Rmd", 
    output_dir = "~/Downloads/slash/target", 
    intermediates_dir = tempdir(), 
    envir = new.env(), 
    output_options = list(self_contained = TRUE))

Output created: index.html
Warning messages:
1: In file.rename(from, to) :
  cannot rename file '/Users/aron/Downloads/slash/target/index_files/figure-html' to '/private/var/folders/ts/s940qvdj5vj1czr9qh07fvtw0000gn/T/RtmpnYIsk2//Users/aron/Downloads/slash/target/index_files/figure-html', reason 'No such file or directory'
2: In file.rename(from, to) :
  cannot rename file '/private/var/folders/ts/s940qvdj5vj1czr9qh07fvtw0000gn/T/RtmpnYIsk2//Users/aron/Downloads/slash/target/index_files/figure-html' to '/Users/aron/Downloads/slash/target/index_files/figure-html', reason 'No such file or directory'

Removing the intermediates_dir argument eliminates the warning.

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
 [1] compiler_3.4.3  backports_1.1.1 magrittr_1.5    rprojroot_1.2   htmltools_0.3.6 tools_3.4.3    
 [7] yaml_2.1.16     Rcpp_0.12.14    stringi_1.1.6   rmarkdown_1.8.5 knitr_1.17      stringr_1.2.0  
[13] digest_0.6.12   evaluate_0.10.1

Installed rmarkdown from github; using SHA 9f45f00 to verify that this is still present in HEAD.

I then installed rmarkdown from SHA 61ec71932020b38c581bd9b9eed00b412d09a8d5; the warning does not occur.

Looks like a regression since rmarkdown-1.6.

[aronatkins]

/CC @scottmmjackson @joncfoo

[aronatkins]

This is probably duplicated by #1288. (edited to fix issue cross-reference)

[kevinushey]

This also occurs for plain old runtime: shiny documents. For example:

---
title: "Warning in file.rename(from, to)"
runtime: shiny
---

```{r}
plot(1)
```

If I try to run this document in the RStudio IDE (with Run Document) I see:

  |......................                                           |  33%
  ordinary text without R code

  |...........................................                      |  67%
label: unnamed-chunk-1


processing file: run.Rmd
  |.................................................................| 100%
  ordinary text without R code


/usr/local/bin/pandoc +RTS -K512m -RTS /private/var/folders/qt/txb728ms5012wp_4yn369wth0000gn/T/RtmpbixrWP/run.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output /private/var/folders/qt/txb728ms5012wp_4yn369wth0000gn/T/RtmpbixrWP/file535c35790a0f.html --email-obfuscation none --standalone --section-divs --template /Users/kevin/Library/R/3.5/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --id-prefix section- --variable 'theme:bootstrap' --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' 
output file: /private/var/folders/qt/txb728ms5012wp_4yn369wth0000gn/T/RtmpbixrWP/run.knit.md

Warning in file.rename(from, to) :
  cannot rename file '/private/var/folders/qt/txb728ms5012wp_4yn369wth0000gn/T/RtmpbixrWP/file535c35790a0f_files/figure-html' to '/private/var/folders/qt/txb728ms5012wp_4yn369wth0000gn/T/RtmpbixrWP//private/var/folders/qt/txb728ms5012wp_4yn369wth0000gn/T/RtmpbixrWP/file535c35790a0f_files/figure-html', reason 'No such file or directory'
Warning in file.rename(from, to) :
  cannot rename file '/private/var/folders/qt/txb728ms5012wp_4yn369wth0000gn/T/RtmpbixrWP//private/var/folders/qt/txb728ms5012wp_4yn369wth0000gn/T/RtmpbixrWP/file535c35790a0f_files/figure-html' to '/private/var/folders/qt/txb728ms5012wp_4yn369wth0000gn/T/RtmpbixrWP/file535c35790a0f_files/figure-html', reason 'No such file or directory'

Output created: /private/var/folders/qt/txb728ms5012wp_4yn369wth0000gn/T/RtmpbixrWP/file535c35790a0f.html

[yihui]

Both the original and the later shiny issues should be fixed now. Thanks for the report!

[github-actions]

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