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 <hpages.on.git...@gmail.com> Sent: Thursday 22 April 2021 18:26 To: alan murphy <alanmurp...@hotmail.com>; bioc-devel@r-project.org <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. > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Herv� Pag�s Bioconductor Core Team hpages.on.git...@gmail.com [[alternative HTML version deleted]]
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