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

alan murphy @|@nmurph94 @end|ng |rom hotm@||@com
Fri Apr 23 10:04:11 CEST 2021

Hey Herv�,

Thank you for very much for your input, I have updated the vignette builder as suggested.

To note, the original issue I was having was solved with the help of Spencer Nystrom.

Kind regards,

From: Herv� Pag�s <hpages.on.github using gmail.com>
Sent: Thursday 22 April 2021 18:26
To: alan murphy <alanmurph94 using hotmail.com>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Reference inst/extdata files in vignette

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.
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Herv� Pag�s

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

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