Closed nr0cinu closed 8 years ago
Sorry but I did not get it. What exactly was not working?
Hi,
so:
this seems to happen if the files are named identical but in different folders. I observed this by using the RStudio Knit button as well as calling rmarkdown::render.
See demo below.
I hope that makes it clear.
Thanks again! Bela
Demo:
$ ls -l *
folder1:
total 4
-rw-r--r-- 1 bela bela 709 Apr 1 06:58 file.Rmd
folder2:
total 0
lrwxrwxrwx 1 bela bela 19 Apr 1 07:00 file.Rmd -> ../folder1/file.Rmd
$ R --slave -e "rmarkdown::render('folder1/file.Rmd')"
processing file: file.Rmd
|............. | 20%
ordinary text without R code
|.......................... | 40%
label: unnamed-chunk-1
|....................................... | 60%
ordinary text without R code
|.................................................... | 80%
label: unnamed-chunk-2 (with options)
List of 1
$ echo: logi FALSE
|.................................................................| 100%
ordinary text without R code
output file: file.knit.md
/usr/bin/pandoc file.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output file.html --smart --email-obfuscation none --self-contained --standalone --section-divs --template /home/bela/.R/x86_64-pc-linux-gnu-library/3.1/rmarkdown/rmd/h/default.html --variable 'theme:bootstrap' --include-in-header /tmp/RtmpUOzCtz/rmarkdown-str7793c45f4e2.html --mathjax --variable 'mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --no-highlight --variable highlightjs=/home/bela/.R/x86_64-pc-linux-gnu-library/3.1/rmarkdown/rmd/h/highlight
Output created: file.html
$ ls -l *
folder1:
total 664
-rw-r--r-- 1 bela bela 675296 Apr 1 07:01 file.html
-rw-r--r-- 1 bela bela 709 Apr 1 06:58 file.Rmd
folder2:
total 0
lrwxrwxrwx 1 bela bela 19 Apr 1 07:00 file.Rmd -> ../folder1/file.Rmd
$ rm folder1/file.html
removed ‘folder1/file.html’
$ R --slave -e "rmarkdown::render('folder2/file.Rmd')"
processing file: file.Rmd
|............. | 20%
ordinary text without R code
|.......................... | 40%
label: unnamed-chunk-1
|....................................... | 60%
ordinary text without R code
|.................................................... | 80%
label: unnamed-chunk-2 (with options)
List of 1
$ echo: logi FALSE
|.................................................................| 100%
ordinary text without R code
output file: file.knit.md
/usr/bin/pandoc file.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output file.html --smart --email-obfuscation none --self-contained --standalone --section-divs --template /home/bela/.R/x86_64-pc-linux-gnu-library/3.1/rmarkdown/rmd/h/default.html --variable 'theme:bootstrap' --include-in-header /tmp/RtmpaA98jT/rmarkdown-str79060dfba77.html --mathjax --variable 'mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --no-highlight --variable highlightjs=/home/bela/.R/x86_64-pc-linux-gnu-library/3.1/rmarkdown/rmd/h/highlight
Output created: file.html
$ ls -l *
folder1:
total 664
-rw-r--r-- 1 bela bela 675296 Apr 1 07:01 file.html
-rw-r--r-- 1 bela bela 709 Apr 1 06:58 file.Rmd
folder2:
total 0
lrwxrwxrwx 1 bela bela 19 Apr 1 07:00 file.Rmd -> ../folder1/file.Rmd
I can reproduce it, but it appears to be an rmarkdown issue instead of knitr. knitr::knit()
works fine. I guess rmarkdown::render()
used normalizePath()
somewhere and the symlink will be resolved.
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Hi!
Not sure if this is a knitr issue, so I hope that fits here.
Let’s say I have a Rmd file in one directory, and then a symlink to that file in a subdirectory:
If I then proceed to knit
a_dir/test.Rmd
the working directory is the base directory. If I just copy the Rmd file to the subdirectory the working directory is the subdirectory.It also works with hardlinks, but I would really prefer to use symlinks.
Thanks! Bela