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,
Alan.
From: Herv� Pag�s
Sent: Thursday 22 April 2021 18:26
To: alan murphy ; bioc-devel@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]
> 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@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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>
--
Herv� Pag�s
Bioconductor Core Team
hpages.on.git...@gmail.com
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