Currently broken, most likely due to changes in `rmarkdown` 0.1.73

Question

Currently broken, most likely due to changes in `rmarkdown` 0.1.73

lcolladotor opened this issue 10 years ago · comments

Leonardo Collado-Torres commented 10 years ago

Hello,

With the newest version of rmarkdown (0.1.73), knitrBootstrap is broken as shown below.

Using a very simple test.Rmd file (see https://gist.github.com/10429813) produces the following error

> library(knitrBootstrap)
> library(rmarkdown)
> render("test.Rmd", bootstrap_document())


processing file: test.Rmd
  |......................                                           |  33%
  ordinary text without R code

  |...........................................                      |  67%
label: unnamed-chunk-1
  |.................................................................| 100%
  ordinary text without R code


output file: test.knit.md

Error in knitr::knit_meta(class = "rmd_warning", clean = TRUE) :
  unused argument (class = "rmd_warning")
> sessionInfo()
R version 3.1.0 beta (2014-03-26 r65301)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

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

other attached packages:
[1] rmarkdown_0.1.73     knitrBootstrap_1.0.0 colorout_1.0-2

loaded via a namespace (and not attached):
[1] evaluate_0.5.3 formatR_0.10   knitr_1.5.25   markdown_0.6.5 stringr_0.6.2
[6] tools_3.1.0

This is most likely due to the recent changes in the rmarkdown package, which I can see is under heavy development. It might be best to double check with the authors (@jjallaire) so hopefully new changes in rmarkdown won't break knitrBootstrap.

Leonardo Collado-Torres · Answer 1 · Fri Apr 11 2014 07:10:56 GMT+0800 (China Standard Time)

This has to be a very recent change because using the rmarkdown version when they bumped from 0.1.72 to 0.1.73 (see commit rstudio/rmarkdown@73ddc8d) does work

library(devtools)
install_github('rstudio/rmarkdown', ref="73ddc8d4465ea212defb3389ae8203a0b9dcf9af")

Leonardo Collado-Torres · Answer 2 · Fri Apr 11 2014 07:14:09 GMT+0800 (China Standard Time)

Maybe it's due to

rstudio/rmarkdown@2cd5d87
or
rstudio/rmarkdown@1754ef8

J.J. Allaire · Answer 3 · Fri Apr 11 2014 07:17:59 GMT+0800 (China Standard Time)

We know what the issue is, should have a fix in shortly

On Apr 10, 2014, at 7:14 PM, Leonardo Collado-Torres <
notifications@github.com> wrote:

Maybe it's due to

rstudio/rmarkdown@2cd5d87rstudio/rmarkdown@2cd5d87
or
rstudio/rmarkdown@1754ef8rstudio/rmarkdown@1754ef8

Reply to this email directly or view it on
GitHubhttps://github.com//issues/43#issuecomment-40153915
.

Leonardo Collado-Torres · Answer 4 · Fri Apr 11 2014 07:21:37 GMT+0800 (China Standard Time)

Excellent! Thank you for the fast reply!

Jonathan · Answer 5 · Fri Apr 11 2014 07:27:55 GMT+0800 (China Standard Time)

Fix is in, let us know if this doesn't resolve the problem for you!

rstudio/rmarkdown@a4ffc9c

Leonardo Collado-Torres · Answer 6 · Fri Apr 11 2014 07:40:31 GMT+0800 (China Standard Time)

Hm... it's not working for me yet. Is the knit_meta(class) feature something that is from knitr 1.5.25 or 1.5.26 (not yet on R-forge)?

## Making sure I have the latest knitr and rmarkdown
> update.packages(ask = FALSE, repos = 'http://cran.rstudio.org')
> install.packages('knitr', repos = c('http://rforge.net', 'http://cran.rstudio.org'),
> library(devtools)
> install_github("rstudio/rmarkdown")

## Error
> library(rmarkdown)
> library(knitrBootstrap)
> render("test.Rmd", bootstrap_document())
Error in knitr::knit_meta(class, clean = TRUE) : unused argument (class)
> sessionInfo()
R version 3.1.0 beta (2014-03-26 r65301)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

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

other attached packages:
[1] knitrBootstrap_1.0.0 rmarkdown_0.1.73     devtools_1.5
[4] colorout_1.0-2

loaded via a namespace (and not attached):
 [1] digest_0.6.4   evaluate_0.5.3 formatR_0.10   httr_0.3       knitr_1.5.25
 [6] markdown_0.6.5 memoise_0.1    parallel_3.1.0 RCurl_1.95-4.1 stringr_0.6.2
[11] tools_3.1.0    whisker_0.3-2
>

J.J. Allaire · Answer 7 · Fri Apr 11 2014 08:10:12 GMT+0800 (China Standard Time)

Try again (just made another change).

On Thu, Apr 10, 2014 at 7:40 PM, Leonardo Collado-Torres <
notifications@github.com> wrote:

Hm... it's not working for me yet. Is the knit_meta(class) feature
something that is from knitr 1.5.25 or 1.5.26 (not yet on R-forge)?

Making sure I have the latest knitr and rmarkdown> update.packages(ask = FALSE, repos = 'http://cran.rstudio.org')> install.packages('knitr', repos = c('http://rforge.net', 'http://cran.rstudio.org'),> library(devtools)> install_github("rstudio/rmarkdown")

Error> library(rmarkdown)> library(knitrBootstrap)> render("test.Rmd", bootstrap_document())

Error in knitr::knit_meta(class, clean = TRUE) : unused argument (class)

sessionInfo()
R version 3.1.0 beta (2014-03-26 r65301)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

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

other attached packages:
[1] knitrBootstrap_1.0.0 rmarkdown_0.1.73 devtools_1.5[4] colorout_1.0-2

loaded via a namespace (and not attached):

[1] digest_0.6.4 evaluate_0.5.3 formatR_0.10 httr_0.3 knitr_1.5.25
[6] markdown_0.6.5 memoise_0.1 parallel_3.1.0 RCurl_1.95-4.1 stringr_0.6.2[11] tools_3.1.0 whisker_0.3-2>

Reply to this email directly or view it on GitHubhttps://github.com//issues/43#issuecomment-40155568
.

Leonardo Collado-Torres · Answer 8 · Fri Apr 11 2014 22:51:52 GMT+0800 (China Standard Time)

Works now =)

Just for the record in this thread, the working version is rmarkdown 0.1.74. This was the actual fix rstudio/rmarkdown@0df1fcf

Jim Hester · Answer 9 · Fri Apr 11 2014 23:44:59 GMT+0800 (China Standard Time)

Thanks to everyone for diagnosing and fixing this so fast!