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wvictor14 / planet

For inferring ancestry, gestational age, and cell type proportions from placental DNA methylation array data
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Fix install error #6

Closed wvictor14 closed 3 years ago

wvictor14 commented 3 years ago

This allows installation on linux without errors. At least on ubuntu18.04.2 LTS (Bionic Beaver), R version 3.6.3

However, the data is not exported properly. For example, data(pl_cell_cpgs_third) results in an "object not found" message. Other objects are also not exported properly.

Everything works fine on Windows and Mac though, AFAIK.

It seems that the problem has something to do with sysdata.rda. After removing nbeta object from sysdata.rda this works. I had to export nbeta as an external object, however, which is not ideal. It shouldn't be available to the user since it's only used internally for pl_infer_ethnicity.

I suspect the problem has something to do with nbeta being a list, containing three objects of class dgCMatrix. However, after converting these to normal matrices (which should still function properly with pl_infer_ethnicity), there still is an install error. I have absolutely no idea what's going on :(

So for now, this package is unusable on some linux installations.

wvictor14 commented 3 years ago

partially addresses #2

wvictor14 commented 3 years ago

Linux is case sensitive whereas windows/mac are case-insensitive. Changing Data/ to data/ fixed this. Thanks for jim for the help..

https://github.com/r-lib/remotes/issues/560#event-4079708112