goolam.R does not run without error

[benearnthof]

When running goolam.R to convert the data into a SingleCellExperiment line 17
sceset <- create_sce_from_counts(d, ann)
causes the following error:
Error in .calculate_cpm(assay(x, exprs_values), ...) : unused argument (use.size.factors = FALSE)
Traceback information:
`Error in .calculate_cpm(assay(x, exprs_values), ...) :
unused argument (use.size.factors = FALSE)
9. .local(x, ...)
8. .nextMethod(x = x, size_factors = size_factors, ...)
7. eval(call, callEnv)
6. eval(call, callEnv)
5. callNextMethod(x = x, size_factors = size_factors, ...)
4. .local(x, ...)
3. calculateCPM(sceset, use.size.factors = FALSE)
2. calculateCPM(sceset, use.size.factors = FALSE) at create_sce_mirror.R#14

1. create_sce_from_counts(d, ann)
   `
   R version 3.6.1; This happenes under both Windows 10 and Ubuntu 18.04

[lry199010]

into this function: sceset <- create_sce_from_counts(d, ann)
change: exprs(sceset) <- log2(calculateCPM(sceset, use.size.factors = FALSE) + 1)
correct:
exprs(sceset) <- log2(calculateCPM(sceset) + 1)