error: "install packages 'R.utils' required"

[gledauio]

[github-actions]

Hello @gledauio , thank you for submitting an issue!

[espenhgn]

Hi @gledauio. Can you post a list of libraries you require from your script(s) if we should rebuild this container? Looks like this one contains a fairly minimalist R environment.

[gledauio]

Hi Espen, the problem is that when you call unziped files LAVA is running ok when you call gz files then I got this error. Maybe it requires this package that is related to gz files. So I don't think it will require more other libraries because they already are called since the script is working ok while avoiding calling gz files.

[gledauio]

A list of required libraries for LAVA is represented here: https://github.com/josefin-werme/LAVA

[espenhgn]

Yes, I could see from the above that R.utils is missing as it is merely a suggested dependency for data.table.
I'll make a PR with a rebuilt container that includes R.utils. As far as I can tell, everything else is included. The quickfix I'm sure you figured out; just unzip the sumstats file ;-)

[espenhgn]

Hi @gledauio. I've opened #2 with a fix. Can you test it? The corresponding .sif file is this one: https://github.com/comorment/magma/blob/fix-1/containers/magma.sif

[gledauio]

Hi @gledauio. I've opened #2 with a fix. Can you test it? The corresponding .sif file is this one: https://github.com/comorment/magma/blob/fix-1/containers/magma.sif

Thanks Espen.