rknitrrstudiovignette

Knitr: R package check error, object 'opts_chunk' not found

I am getting the following error when checking my R package

> Error: could not find function "locdata"
> Execution halted
> when running code in ‘DFSurvey.Rnw’
>   ...
> 
> > opts_chunk$set(cache = TRUE, fig.path = "DFSurveyImages/", dev = "pdf")
> 
>   When sourcing ‘DFSurvey.R’:
> Error: object 'opts_chunk' not found
> Execution halted

Yihui Xie (knitr developer) said that was because in RStudio, knitr was not set as the method for weaving .Rnw files, https://groups.google.com/forum/?fromgroups#!topic/knitr/9672CBbc8CM. I have knitr set in both the tools and build options, in the R package DESCRIPTION file I have:

VignetteBuilder: knitr
Suggests: knitr

and in the vignette I have:

%\VignetteEngine{knitr}
%\VignetteDepends{knitr,xtable,TSP}

When I use compile the pdf in RStudio or use knit("KNITR.Rnw"), it compiles correctly. When I check the package, I get the above errors for each vignette. I even put 

require(knitr)

before my opts_chunk$set statement. That did not help. I have also run the check from the command line and gotten the same error. Thank you for any help.

Knitr is a useful package. I run long simulations in vignettes, and the cache makes it possible to correct errors without running the simulations over each time. It does not have the problem of trying to find the Sweave.sty file either.

Here is my sessionInfo()

> R version 3.0.0 (2013-04-03)
> 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] tcltk     grid      stats     graphics  grDevices utils     datasets  methods  
> [9] base     
> 
> other attached packages:
>  [1] DualFrame_0.5         xtable_1.7-1          TSP_1.0-7            
>  [4] maptools_0.8-23       lattice_0.20-15       foreign_0.8-53       
>  [7] spsurvey_2.5          sp_1.0-9              stringr_0.6.2        
> [10] sqldf_0.4-6.4         RSQLite.extfuns_0.0.1 chron_2.3-43         
> [13] gsubfn_0.6-5          proto_0.3-10          RSQLite_0.11.3       
> [16] DBI_0.2-7             knitr_1.2             gpclib_1.5-5         
> 
> loaded via a namespace (and not attached):
> [1] deldir_0.0-22  digest_0.6.3   evaluate_0.4.3 formatR_0.7    MASS_7.3-26   
> [6] rgeos_0.2-17   tools_3.0.0
Solution

  • For a knitr vignette that you can compile using knit() or with the "Compile PDF" button in RStudio, but that gets an

    Error: object 'opts_chunk' not found Execution halted

    error when checking or building the package, the package check code is not recognizing that your .Rnw file should be knited and not Sweaveed. Check that you have the following:

    1. The vignettes are in the vignette directory, if you have R 3.0.0 or higher (this was the solution to this post), cran.r-project.org/doc/manuals/r-devel/R-exts.html#Non_002dSweave-vignettes

    2. Include %\VignetteEngine{knitr::knitr} in the vignette metadata, yihui.name/knitr/demo/vignette/

    3. Specify VignetteBuilder: knitr in the package DESCRIPTION file, and

    4. Add Suggests: knitr in DESCRIPTION if knitr is needed only for vignettes

    If that does not work add a require(knitr) statement before you set your global options in opts_chunk(), as Ben Bolker, Yuhui and Tyler Rinker suggested.

    If in RStudio: In BOTH the Build configuration and Tool options, set the Sweave option to knitr, www.rstudio.com/ide/docs/authoring/rnw_weave