R Markdown can't find a file but executing the chunks works

Question

I have a strange behaviour with r markdown and reading a txt file... only on a windows 7 machine. No problems on my Mac and haven't checked it on windows 8 yet.

I have a basic r markdown document

---
title: "Untitled"
output: html_document
---
```{r global_options, message=FALSE}
setwd('E:/Falk')
list.files(pattern='test')
```

```{r global variable settings, eval=TRUE}
pg_filename <- 'test.txt' 
pg <- read.delim (pg_filename)
```

If i set the eval=FALSE in the last chunk, the html gets created and I get the list with my test.txt file. If I set eval=TRUE I get an error message, that the file can not be found:

Quitting from lines 11-13 (Preview-2b2464944991.Rmd) 
Error in file(file, "rt") : cannot open the connection
Calls: <Anonymous> ... withVisible -> eval -> eval -> read.delim -> read.table -> file

Execution halted

If I put everything in one chunk the html gets created.

Has any one an idea what the problem is?

EDIT: Maybe I was not clear enough. I know the difference between eval=TRUE and FALSE but I don't know a way of testing the something in markdown, if there are error messages, but everything works fine in the chunks.

So, to make it more clear:

WORKS:

---
title: "Untitled"
output: html_document
---
```{r}
setwd('E:/Falk')
list.files(pattern='test')
pg_filename <- 'test.txt' 
pg <- read.delim (pg_filename)
```

DOES NOT WORK:

---
title: "Untitled"
output: html_document
---
```{r}
setwd('E:/Falk')
list.files(pattern='test')
```

```{r}
pg_filename <- 'test.txt' 
pg <- read.delim (pg_filename)
```

You should read the documentation: `eval=FALSE` means the chunk is just copied as-is into the output and not _evaluated_ or _executed_ using R. — Marco Torchiano, Feb 18 '15 at 10:13
Right, I know that... This was just mz test, that setwd works and list.files can find my test.txt file... Otherwise I get the message, that test.txt does not exist, but it exists. The script runs as chunks, but not as knit with eval TRUE even the file is there... Don't know a way to test this... The script also runs if I put everything in one chunk! — drmariod, Feb 18 '15 at 10:16

Konrad Rudolph · Accepted Answer · 2019-02-27T09:03:22.393

1

You cannot use setwd in knitr, and you shouldn’t use it in your R code anyway. You need to exclusively use relative paths instead.

In particular, setwd has no effect outside of its current chunk – the other chunks are going to be evaluated in the document’s path, not in the set path.

In general, setwd should only be used by the user in an interactive session, or in your project configuration file (local .Rprofile file) to set up a project directory. It has no place in scripts.

The most direct equivalent of setwd is to use the knitr option root.dir:

opts_knit$set(root.dir = 'some/dir')

edited Feb 27 '19 at 09:03

answered Feb 18 '15 at 10:43

Konrad Rudolph

530,221
131
937
1,214

1

Thanks for pointing this out. I don't use ssetwd() in scripts I provide to others users, exactly because of that reason and I hated to use this solution in markdown documents. But this was the only solution I found. Thanks to your Answer I just realised, that the Rmd has to be in the same folder and then the relative path will work. Didn't figured this out before. On my MAC it worked with the setwd() trick. – drmariod Feb 18 '15 at 11:34

R Markdown can't find a file but executing the chunks works

1 Answers1