How to include a Bioconductor package?

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by kban » Sat Feb 09, 2019 8:06 am

Hi,

I'm trying to write a module that uses a Bioconductor package (bioconductor.org). It uses a different way of installing packages and I'm not sure how to include it in the Jamovi module using the DESCRIPTION and NAMESPACE method as described in the tutorial.

Thanks in advance!

Kenneth
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by jonathon » Sat Feb 09, 2019 8:24 am

oh yeah. that is tricky.

probably the easiest way is to install a similar version of R to what jamovi uses (3.3 on macOS, 3.4 on windows, 3.5 on linux), install the R package using that version to wherever it wants to install it.

then copy the *installed* package to the build/R folder that jmvtools create inside the module source folder.

then it should work.

let us know if you get stuck

cheers

jonathon
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by kban » Sat Feb 09, 2019 8:51 am

Thanks Jonathon!

I was wondering if it's possible to use serRepositories() to include Bioconductor in the install.packages path?

I tried this in R and it seems to pull in the Bioconductor package I needed
> setRepositories(ind=c(1:8))
> install.packages("RNASeqPower")

Is this a possible option?

Cheers,
Kenenth
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by jonathon » Sat Feb 09, 2019 9:14 pm

yeah, you're right. that would make for a good option.

i'll see about adding something like that - but might take me a week or so, so the install and copy should work if you want to get up and running now.

cheers

jonathon
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