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

Jeff Newmiller jdnewmil at dcn.davis.CA.us
Mon Jan 12 09:41:43 CET 2015

When you start off by saying it works fine in the console, it starts sounding like not a question that belongs here. It actually is possible to run knitr/rmarkdown in the console without RStudio, so you could try that but to me it sounds suspiciously like a bug in RStudio. Ask on their support forums with a reproducible example. If it turns out to be a bug in the package, keep in mind that that is a Bioconductor package and they, too, have their own support forum.
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Sent from my phone. Please excuse my brevity.

On January 11, 2015 10:06:21 PM PST, Molly Elliott <elliotmo at onid.oregonstate.edu> wrote:
>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!
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>PLEASE do read the posting guide
>and provide commented, minimal, self-contained, reproducible code.

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