In your R script (create_regions_from_gencode.R) there is a small bug

[Alex-Nesta]

transcripts.data <- unlist(transcripts.data) ###ERROR
exons.data <- unlist(exons.data)
threeUTRs.data <- unlist(threeUTRs.data)
fiveUTRs.data <- unlist(fiveUTRs.data)
cds.data <- unlist(cds.data)
introns.data <- unlist(introns.data)
genes.data <- unlist(genes.data) ####ERROR

There error is:

Error in getListElement(x, i, ...) : 
  GRanges objects don't support [[, as.list(), lapply(), or unlist() at
  the moment
Calls: unlist ... FUN -> [[ -> [[ -> getListElement -> getListElement
Execution halted

I did not need those lines to work for my purposes, but just an FYI on the issue.

[xf78]

I have the same problem，Bioconductor 3.8 may not support the this，but I didn't solve it

[saketkc]

Thanks @Alex-Nesta and @xf78 for reporting the issue. I will try to have a fix soonish. In the meantime, can you check if the data you need is here: https://github.com/saketkc/gencode_regions/tree/master/data Happy to add if it's missing (which is very likely!)

[bug1303]

I had the same issue, using GenomicFeatures v 1.34.3 (not sure which other packages/versions might be relevant for this). It appears that genes(), transcripts(), and promoters() return a GRanges object ["The only exception being when genes is used with single.strand.genes.only=FALSE, in which case a GRangesList object is returned."], while threeUTRsByTranscript(), fiveUTRsByTranscript(), cdsBy(), exonsBy(), intronsByTranscript() return a GRangesList object, so for the latter ones the unlist is required, but not for the former ones.

By simply removing the lines as mentioned above transcripts.data <- unlist(transcripts.data) and genes.data <- unlist(genes.data)

as well as replacing promoters.data <- unlist(promoters(TxDb, upstream=len, downstream=len)) with promoters.data <- promoters(TxDb, upstream=len, downstream=len)

I managed to recreate the files as provided in data/GRCm38/vM14/

[longqh3]

I also encountered this issue currently, using conda hosted R-3.3.2 to install dependencies solved the issue. However, while conducting problem searching, I noticed that

The overall goal of all these changes is to bring more consitency between IRanges and GRanges objects
 (GRanges objects will also support [[, unlist(), as.list(), and lapply() in Bioconductor 3.8).

in unlist doesn't work for IRanges, so maybe downgrading to Bioconductor 3.8 version can also solve the issue (I'm not pretty sure, haven't tried yet).