[R] Suggestions for workaround for R Markdown problem with data() ?

Molly Elliott elliotmo at onid.oregonstate.edu
Mon Jan 12 07:06:21 CET 2015

R version: 3.1.2 (2014-10-31)
RStudio version: 0.98.1091
MacOS X Yosemite v. 10.10.1

When I run the following in the console, all is well:

Yet, when I compile in my .Rmd file, in RStudio (knit to PDF), I get the following error:
Error in file(file, "rt") : cannot open the connection
Calls: <Anonymous> ... withVisible -> eval -> eval -> read.delim -> read.table -> file
Execution halted

From what I have read, this could be alleviated by pointing the the source file for data(IlluminaHumanMethylation450kanno.ilmn12.hg19) as opposed to LazyLoading with the data() function.  Yet, I’m not sure how to work around this. (This is my first R project ever) The data(IlluminaHumanMethylation450kanno.ilmn12.hg19) is just loading an annotation file from library(IlluminaHumanMethylation450kanno.ilmn12.hg19), and I’m not sure of the file type the data are stored under (.txt, .csv, etc). 

Thanks in advance!


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