[Bioc-devel] Reference inst/extdata files in vignette

Hi Alan,

Hi all,

I'm working on the development of MungeSumstats(https://github.com/neurogenomics/MungeSumstats) and am trying to reference raw data files (txt and VCF) in my vignette. These files are stored in `inst/extdata` but when I try load then with the below it fails on Bioconductor checks but will pass local checks:

```
eduAttainOkbayPth <- system.file("extdata","eduAttainOkbay.txt", package="MungeSumstats")

reformatted <-   MungeSumstats::format_sumstats(path=eduAttainOkbayPth,ref_genome="GRCh37")
```
The error is caused by a validation check I have to ensure the path passed to `format_sumstats` is valid. Locally this works (see below) but I get an error on Bioconductor:

```

file.exists(eduAttainOkbayPth)[1]

TRUE
```

Does anyone know of the correct way to access raw data files like text files?

This works fine (with MungeSumstats 0.99.11 from 
https://git.bioconductor.org/packages/MungeSumstats).

What error do you see and where do you see it?

One error I get on my machine is this one:

hpages at spectre:~/sandbox$ bdevbuild MungeSumstats
* checking for file ?MungeSumstats/DESCRIPTION? ... OK
* preparing ?MungeSumstats?:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ?MungeSumstats.Rmd? using knitr
Error: processing vignette 'MungeSumstats.Rmd' failed with diagnostics:
It seems you should call rmarkdown::render() instead of 
knitr::knit2html() because MungeSumstats.Rmd appears to be an R Markdown 
v2 document.
--- failed re-building ?MungeSumstats.Rmd?

SUMMARY: processing the following file failed:
   ?MungeSumstats.Rmd?

Error: Vignette re-building failed.
Execution halted

Note that you won't necessarily get that error on our builders (because 
we use a more forgiving version of knitr there) but it still something 
that would need to be addressed.

Best,
H.

Kind regards,
Alan.


	[[alternative HTML version deleted]]

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Herv? Pag?s

Bioconductor Core Team
hpages.on.github at gmail.com