When I run devtools::check() to build my package and the generate the html file of the rmarkdown vignette, I get an error that the data files can't be found. The html file can be built using any of these:
knitr::knit2html('vignettes/myvignette.Rmd') # works fine
devtools::build_vignettes() # works fine
devtools::build() # works fine
But when I run devtools:check() I get:
mydata <- read.csv("data/mycsv.csv")
Warning in file(file, "rt") :
cannot open file 'data/mycsv.csv': No such file or directory
When sourcing 'myvignette.R':
Error: cannot open the connection
Execution halted
How can I get devtools::check() to work? system.file may be relevant but I haven't been able to adapt it to solve my problem. I realise that using rda data files might be a workaround, but I want to use plain text files to store the data in this case.
Here's the myvignette.Rmd, in /vignettes
<!--
%\VignetteEngine{knitr::rmarkdown}
%\VignetteIndexEntry{Supplementary materials}
-->
```{r setup, message=FALSE, echo=FALSE}
library(knitr)
# This is necessary to direct knitr to find the
# 'data', and other directories that contain
# files needed to execute this document
# thanks to https://stackoverflow.com/a/24585750/1036500
opts_knit$set(root.dir=normalizePath('../'))
```
```{r}
library(mypackage)
myfunc()
```
```{r}
mydata <- read.csv("data/mycsv.csv", header = FALSE)
mydata
```
Here are the key bits of my example package (the rest is auto-generated by devtools::check and I haven't altered them):
DESCRIPTION
Package: mypackage
Title: What the package does (short line)
Version: 0.1
Authors@R: "First Last <first.last@example.com> [aut, cre]"
Description: What the package does (paragraph)
Depends:
R (>= 3.1.1)
License: MIT
LazyData: true
VignetteBuilder: knitr
Suggests:
knitr
R/myfunction.r
#' my function
#' An example function
#' @export
#'
my_func <- function() Sys.time()
R/docfordata.r
#' @title mycsv
#' @docType data
#' @keywords dataset
#' @format csv
#' @name mycsv
NULL
data/mycsv.csv
1,2,3
11,12,13
22,23,23
I'm working in RStudio 0.98.953, here's the session info
sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] mypackage_0.1
loaded via a namespace (and not attached):
[1] devtools_1.5 digest_0.6.4 evaluate_0.5.5
[4] httr_0.3 memoise_0.2.1 packrat_0.3.0.107
[7] parallel_3.1.1 Rcpp_0.11.2 RCurl_1.95-4.1
[10] roxygen2_4.0.1 stringr_0.6.2 tools_3.1.1
[13] whisker_0.3-2
UPDATE
Following Andrie's helpful comments I've moved my csv file to inst/extdata and put this line in the vignette read.csv(system.file("extdata/mycsv.csv", package="mypackage"), header = FALSE) and that allows my package to pass both devtools::check and devtools::build. But now it failsknitr::knit2html('vignettes/myvignette.Rmd') anddevtools::build_vignettes()` and at the console with the error messages:
For knit2html:
Quitting from lines 22-29 (vignettes/myvignette.Rmd)
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
For build_vignettes:
Building mypackage vignettes
Quitting from lines 22-29 (myvignette.Rmd)
Error: processing vignette 'myvignette.Rmd' failed with diagnostics:
no lines available in input
For read.csv(system.file("extdata/mycsv.csv", package = "mypackage"), header = FALSE)
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
In addition: Warning message:
In file(file, "rt") :
file("") only supports open = "w+" and open = "w+b": using the former
This must be something to do with the wandering inst/ directory that gets moved around when the package is built. So it's fair enough that knit2html and the console might not work, but surely build_vignettes should still work?
Also related: How do I refer to files in the inst directory of an R package from a script in the data directory?
To use a file in the vignette, you can add the file to the vignette folder.
An example of this is in the package tidyr at https://github.com/hadley/tidyr/blob/master/vignettes/tidy-data.Rmd
Try putting your csv file directly to the vignette folder