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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Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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