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

[Hervé Pagès]

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]
> 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 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:
   ‘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.
> 
> 
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> 
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-- 
Hervé Pagès

Bioconductor Core Team
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