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$set(
collapse = TRUE,
comment = "#>"
)
```
# headline
```{r setup}
library(staduicc)
spieldatenpfad <- system.file("./inst/extdata/spieldaten.rda", package =
"staduicc")
message(spieldatenpfad)
load(spieldatenpfad)
```
<end of Rmd code>
The message which comes with running the code is as follows:
ℹ Installing staduicc in temporary library
ℹ Building vignettes for staduicc
--- re-building 'staduicc.Rmd' using rmarkdown
processing file: staduicc.Rmd
1/5
2/5 [unnamed-chunk-1]
3/5
4/5 [setup]
Quitting from staduicc.Rmd:19-24 [setup]
Error: processing vignette 'staduicc.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'staduicc.Rmd'
SUMMARY: processing the following file failed:
'staduicc.Rmd'
Error:
! in callr subprocess.
Caused by error:
! Vignette re-building failed.
ℹ See `$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 Hüsing
Epidemiologie
Landeskrebsregister NRW gGmbH
Gesundheitscampus 10
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