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

5 messages · ONKELINX, Thierry, Jeff Newmiller, Yihui Xie +1 more

Original
Molly Elliott
# 
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
ONKELINX, Thierry
# 
Dear Molly,

Is the package in which the data is stored loaded in the Rmd? If not try

library(yourPackage)
data(yourData)

or

data(yourData, package = "yourPackage")

If this doesn't solve your problem, please provide a minimal reproducible example of the problem.

Best regards,

Thierry

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
Thierry.Onkelinx at inbo.be
www.inbo.be

To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

-----Oorspronkelijk bericht-----
Van: R-help [mailto:r-help-bounces at r-project.org] Namens Molly Elliott
Verzonden: maandag 12 januari 2015 7:06
Aan: r-help at r-project.org
Onderwerp: [R] Suggestions for workaround for R Markdown problem with data() ?

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
Jeff Newmiller
# 
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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On January 11, 2015 10:06:21 PM PST, Molly Elliott <elliotmo at onid.oregonstate.edu> wrote:
Yihui Xie
# 
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:
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