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leekgroup / phenopredict

Use gene expression to predict phenotype sample information
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Quickstart vignette not building #3

Open assaron opened 7 years ago

assaron commented 7 years ago

Hello, I can't build the phenopredict-quickstart vignette: it fails on the line: test_data<-extract_data(expression=cm_new, inputdata=inputdata, predictordata=predictor) with an error: Error in extract_data(expression = cm_new, inputdata = inputdata, predictordata = predictor) : unused arguments (expression = cm_new, inputdata = inputdata)

Can you, please, update it?

idontgetoutmuch commented 7 years ago

I followed the instructions in the vignette but got

> document("phenopredict")
Updating phenopredict documentation
Loading phenopredict
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Error: 'inputdata' is not an exported object from 'namespace:phenopredict'
ShanEllis commented 7 years ago

@idontgetoutmuch and @assaron, apologies for the mistakes here and delay in getting back to you.

I've updated the vignette. Please let me know how everything looks now if you get a change to take a look?

idontgetoutmuch commented 7 years ago

Thanks for the quick response :) I don't have access to a computer ATM but will try next week.