I am trying to puild a package including a vignette. The focus of this package is the generation of linkage tables connecting cancer diagnoses.
The following code is processed into a HTML document when invoked with rmarkdown::render(), but fails to be processed with devtools::build_vignettes():
---
title: "staduicc"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{staduicc}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
# headline
```{r setup}
library(staduicc)
spieldatenpfad <- system.file("./inst/extdata/spieldaten.rda", package = "staduicc")
message(spieldatenpfad)
load(spieldatenpfad)
```
<end of Rmd code>
The message which comes with running the code is as follows:
? Installing staduicc in temporary library
? Building vignettes for staduicc
--- re-building 'staduicc.Rmd' using rmarkdown
processing file: staduicc.Rmd
1/5
2/5 [unnamed-chunk-1]
3/5
4/5 [setup]
Quitting from staduicc.Rmd:19-24 [setup]
Error: processing vignette 'staduicc.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'staduicc.Rmd'
SUMMARY: processing the following file failed:
'staduicc.Rmd'
Error:
! in callr subprocess.
Caused by error:
! Vignette re-building failed.
? See `$stdout` and `$stderr` for standard output and error.
Type .Last.error to see the more details.
<end of error messages>
I am suspecting it may have something to do which how system.path() is processed. But I?ll gladly take any hint that is more specific than my musings.
Dr. Johannes H?sing
Epidemiologie
Landeskrebsregister NRW gGmbH
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[R-pkg-devel] error message when trying to knit a vignette involving data import
2 messages · Hüsing, Johannes, Sebastian Meyer
Am 11.02.26 um 08:39 schrieb H?sing, Johannes via R-package-devel:
spieldatenpfad <- system.file("./inst/extdata/spieldaten.rda", package = "staduicc")
system.file() finds files in an _installed_ package, which is what you
want to access in a vignette. However, './inst/' only exists in your
source package. At installation, the _contents_ of that subdirectory are
copied recursively to the installation directory, so that will have
'./extdata' at the root. I recommend installing the package and checking
out its installation directory to see for yourself:
(instdir <- find.package("staduicc"))
browseURL(instdir)
(Browsing the directory should work via 'xdg-open' on Linux; I'm not
sure about Windows, but you will know the path.)
Sebastian Meyer