knitr compile problems with RStudio (windows)

Question

i have a knitr based Rnw file that is compiling to pdf perfectly fine in RStudio on mac (v0.97.316) and knitr (v1.1) but in a windows enviornment (same versions) i get a compilation error. I've checked the options in RStudio in both environments and they are consistent.

It appears that the windows setup is always injecting: "\SweaveOpts{concordance=TRUE}" into the ".tex" file even though i have no such flag in the Rnw file, and/or if i toggle the settings in the preferences, and/or if i add the "opts_knit$set(concordance=FALSE)" options to a knitr settings chunk. If i drop the line from the ".tex" file and compile it manually at the cmd prompt the output is generated as expected.

I'm not sure if this is an RStudio or knitr problem, but any pointers would be appreciated.

Note, i've also posted this question on the RStudio support board (http://support.rstudio.org/help/discussions/problems/5039-knitr-compile-problems-with-rstudio-windows?unresolve=true).

Answer 1

The reason that it was injecting \SweaveOpts{concordance=TRUE} is likely to be your weaver was Sweave instead of knitr, and you also enabled Rnw concordance: http://www.rstudio.com/ide/docs/authoring/rnw_weave But I cannot say for sure it is not a bug for the Windows version of RStudio. Anyway, it is easy to verify if it is an RStudio problem -- open the Compile PDF panel and you should see the log like this:

If your weaver was Sweave, you will see something like this instead:

This is my configuration (I'm under Ubuntu):

If you are using knitr indeed, and RStudio still inserts \SweaveOpts{concordance=TRUE}, I guess it must be a bug of RStudio.

Answer 2

I encountered this problem with "R CMD build KFAS-master" downloaded 2016-04-24 as "KFAS-master.zip" clicking "Download ZIP" from KFAS on GitHub (https://github.com/helske/KFAS). I'm unable to replicate the problem, but the work around I used was to find the line mentioned in the pop-up (copied below), and comment it out by preceding it with "%%".

After downloading it, I unzipped it and changed the name of the folder to "KFAS". Then I got a command prompt and navigated to the directory containing the KFAS-master folder renamed as KFAS. This time "R CMD build KFAS" worked as expected. Then I opened ~KFAS/vignettes/KFAS.Rmw in RStudio 0.99.893, the current version as of 2016-04-26. I changed something and saved the result. When I repeated "R CMD build KFAS", I got the problem portrayed in the image below.

Jouni Helske directed me to this post. I commented out line 69 mentioned in the screen shot below by prepending "%%" to "\SweaveOpts{concordance=TRUE}". I saved the result, and "R CMD build KFAS" worked.

Something seems to occasionally insert a line like "\SweaveOpts{concordance=TRUE}" into a *.Rnw file, but I don't know what it is. I'm running R 3.2.4 on a MacBook Pro with OS X 10.11.2.

Thanks to Yihui and others for earlier posts in this thread.

screen shot showing pop-up complaining, "It seems you are using the Sweave-specific syntax in line(s) 69... ."

Answer 3

I had the same problem even when knitr was set for "Weave Rnw files using" by default.

I solved it by going to Tools/Global Options/Sweave and setting "Weave Rnw files using" to Sweave and pressing Ok. Then, I went back and set it back to knitr, and everything works fine now.

I guess it was indeed Rstudio bug