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 <xieyi...@gmail.com>
Web: http://yihui.name
On Mon, Jan 12, 2015 at 12:06 AM, Molly Elliott
<ellio...@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
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