error when uploading to bookdown.org

I tried to upload my book to bookdown.org. After half an hour (I am wondering why there are so many files uploaded to RStudio Connect) I got an error

2017/10/09 18:46:51.957709974 Quitting from lines 28-38 (wiss-arbeiten.Rmd) 2017/10/09 18:46:51.957825693 Error in loadNamespace(name) : there is no package called 'BiocInstaller' 2017/10/09 18:46:51.957885047 Calls: local ... try_bioc -> suppressMessages -> withCallingHandlers 2017/10/09 18:46:51.958782481 2017/10/09 18:46:51.960108826 Execution halted

I installed BiocInstaller and tried it several times again with the same error message.

To provide a reprex I installed bookdown from scratch and tried to upload it. I didn't succeed but this time with another error message:

    2017/10/09 21:52:18.435444168 output file: test-bookdown.knit.md
2017/10/09 21:52:18.435449884
2017/10/09 21:52:19.249176890 Latexmk: -latexoption=-halt-on-error bad option
2017/10/09 21:52:19.249238308 Latexmk: -interaction=batchmode bad option
2017/10/09 21:52:19.249408997
2017/10/09 21:52:19.249413953 Latexmk: Bad options specified
2017/10/09 21:52:19.249436980 Use
2017/10/09 21:52:19.249439476    latexmk -help
2017/10/09 21:52:19.249455810 to get usage information
GET /__api__/tasks/eHORYjLKgZlV4pom?first_status=137 524ms
2017/10/09 21:52:19.644109397
2017/10/09 21:52:19.644123280 Latexmk, John Collins, 7 May 2011. Version 4.24
2017/10/09 21:52:19.647906139 Error: Failed to compile test-bookdown.tex.
2017/10/09 21:52:19.647978929 In addition: Warning message:
2017/10/09 21:52:19.648059206 Your latexmk version seems to be too low. You may need to update the latexmk package or your LaTeX distribution.
2017/10/09 21:52:19.658900711 Please delete test-bookdown.Rmd after you finish debugging the error.
2017/10/09 21:52:19.658977638 Execution halted

but it seems to me that my latex-versions are ok: pdfTeX 3.14159265-2.6-1.40.18 (TeX Live 2017) and Latexmk, John Collins, 19 Jan. 2017. Version 4.52c

I am using RStudio Version 1.1.383 and R version 3.4.2 (2017-09-28) -- "Short Summer", Platform: x86_64-apple-darwin15.6.0 (64-bit) and bookdown 0.5.4

Any idea what could be wrong?

Solution

This question was cross-posted at https://github.com/rstudio/bookdown/issues/474 and solved there. In short, you used bookdown::publish_book(render = "server"), which is not well supported at the moment on bookdown.org. You should render the book locally and use the default bookdown::publish_book(render = "none") instead.