R help - Jan 2015 - 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

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

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

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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Disclaimer<https://www.inbo.be/nl/disclaimer-mailberichten-van-het-inbo>

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:
>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
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

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

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