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

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Thu Apr 22 19:26:24 CEST 2021

Hi Alan,

On 4/22/21 3:54 AM, alan murphy wrote:
> 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]
> ```
> Does anyone know of the correct way to access raw data files like text files?

This works fine (with MungeSumstats 0.99.11 from 

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

One error I get on my machine is this one:

hpages using 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:

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.


> Kind regards,
> Alan.
> 	[[alternative HTML version deleted]]
> _______________________________________________
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Hervé Pagès

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

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