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Question: Error in Knit R Markdown document (could not find function "Biocexptpkg")
0
gravatar for Jon Bråte
13 months ago by
Jon Bråte130
Norway
Jon Bråte130 wrote:

Hi,

I am trying to Knit my Rmarkdown file in R Studio, but get this message:

Quitting from lines 12-55 (MBV-INFX410-transcriptomics.Rmd)
Error in eval(expr, envir, enclos) :
  could not find function "Biocexptpkg"
Calls: <Anonymous> ... in_dir -> inline_exec -> withVisible -> eval -> eval
Execution halted

Line 12 only contains this ## Experimental

Thanks, Jon

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

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     

loaded via a namespace (and not attached):
 [1] magrittr_1.5    htmltools_0.3.5 tools_3.3.1     yaml_2.1.13     Rcpp_0.12.7     stringi_1.1.2   rmarkdown_1.0   knitr_1.14     
 [9] stringr_1.1.0   digest_0.6.10   evaluate_0.10 

 

ADD COMMENTlink modified 13 months ago • written 13 months ago by Jon Bråte130
2
gravatar for James W. MacDonald
13 months ago by
United States
James W. MacDonald45k wrote:

You need to load the BiocStyle package if you want to call functions from that package, which includes using that set of styles for your rmarkdown file.

ADD COMMENTlink written 13 months ago by James W. MacDonald45k
1
gravatar for Steve Lianoglou
13 months ago by
Genentech
Steve Lianoglou12k wrote:

Hard to tell what's going on, not enough info here, but:

I'm pretty sure that Rmd errors usually give the range of the chunk that threw the error, so the code is in lines 12-55 (not just line 12)

Run the chunks of your Rmd file one by one until you get to the code block that is giving the error. Step through that line by line and debug from there.

If you are in RStudio, this process is made easy with its "run all chunks above" and other run functions available from the toolbar in the editor.

ADD COMMENTlink written 13 months ago by Steve Lianoglou12k
0
gravatar for Jon Bråte
13 months ago by
Jon Bråte130
Norway
Jon Bråte130 wrote:

Thanks a lot! Problem solved! :)

ADD COMMENTlink written 13 months ago by Jon Bråte130
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