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

[Molly Elliott]

My apologies to everyone who offered assistance here. I broke my code chunks up some more, and further isolated the problem line to a different function.  

Yihui, 

Thank you for the information for running the .Rmd file within R itself, rather than RStudio. I have installed pandoc and like that I can work straight in R. 

Thierry, 

Thank you for the suggestions as well, your advice helped me to realize my mistake in posting my question. 

Jeff,

Thanks for your advice on intelligent posting! I wasn’t sure where to start, and hummed and hawed over it for a day, but better understand how the mailing list works now.

Best,
Molly 

> On Jan 12, 2015, at 8:41 AM, Yihui Xie <xie at yihui.name> wrote:
> 
> Can you try to compile your .Rmd file in the R console (instead of
> clicking the button in RStudio)?
> 
>  rmarkdown::render('your.Rmd')
> 
> If it gives the same error, please post the traceback() information. I
> just tried the following minimal example, and I was unable to
> reproduce your problem. You may also try to reinstall the package:
> BiocInstaller::biocLite('IlluminaHumanMethylation450kanno.ilmn12.hg19')
> 
> ---
> output: pdf_document
> ---
> 
> ```{r}
> library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
> data(IlluminaHumanMethylation450kanno.ilmn12.hg19)
> ```
> 
> 
> Regards,
> Yihui
> --
> Yihui Xie <xieyihui at gmail.com>
> Web: http://yihui.name
> 
> 
> On Mon, Jan 12, 2015 at 12:06 AM, 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:
>> data(IlluminaHumanMethylation450kanno.ilmn12.hg19)
>> 
>> 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!
>> 
>> Molly