Issues when testing prepareAnnotation

[cying111]

I tested the function with this chunk of code:
#' library(TxDb.Hsapiens.UCSC.hg38.knownGene)
#' txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
#' prepareAnnotations(txdb)

It throws error message as:
'select()' returned many:many mapping between keys and columns
Error in .rowNamesDF<-(x, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning messages:
1: In .set_group_names(ans, use.names, x, "tx") :
some group names are NAs or duplicated
2: In .set_group_names(grl, use.names, txdb, by) :
some group names are NAs or duplicated
Error in .rowNamesDF<-(x, value = value) :
duplicate 'row.names' are not allowed

[cying111]

I am closing this now. The function now works with this library but there is still warning message as follows, which I guess is because multiple versions of transcripts or NA transcripts exist:
Warning message:
In .set_group_names(grl, use.names, txdb, by) :
some group names are NAs or duplicated

Example problem transcript:
GRangesList object of length 2:
$ENST00000431238.7
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | exon_rank exon_endRank
|
[1] chrX 253743-253846 + | 1 2
[2] chrX 254937-255091 + | 2 1

$ENST00000431238.7
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | exon_rank exon_endRank
[1] chrY 253743-253846 + | 1 2
[2] chrY 254937-255091 + | 2 1

---

seqinfo: 595 sequences (1 circular) from hg38 genome