How to include a Bioconductor package?

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kban
Posts: 2
Joined: Sat Feb 09, 2019 7:58 am

How to include a Bioconductor package?

Post by kban »

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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jonathon
Posts: 2613
Joined: Fri Jan 27, 2017 10:04 am

Re: How to include a Bioconductor package?

Post by jonathon »

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
kban
Posts: 2
Joined: Sat Feb 09, 2019 7:58 am

Re: How to include a Bioconductor package?

Post by kban »

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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jonathon
Posts: 2613
Joined: Fri Jan 27, 2017 10:04 am

Re: How to include a Bioconductor package?

Post by jonathon »

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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