Hi,

I am trying to get gene list using geneList function from refGenome. However, I got the following error. 

best,

ilyas.

>library("refGenome")
Loading required package: doBy
Loading required package: RSQLite
Loading required package: DBI
> ens <-  ensemblGenome()
> cdir <- getwd()
> basedir(ens) <- cdir
> ens_gtf <- "Danio_rerio.GRCz10.85.gtf"
> read.gtf(ens, ens_gtf)
[read.gtf.refGenome] Reading file 'Danio_rerio.GRCz10.85.gtf'.

[GTF]   100000 lines processed.
[GTF]   200000 lines processed.
[GTF]   300000 lines processed.
[GTF]   400000 lines processed.
[GTF]   500000 lines processed.
[GTF]   600000 lines processed.
[GTF]   700000 lines processed.
[GTF]   800000 lines processed.
[GTF]   900000 lines processed.
[GTF]  1000000 lines processed.
[GTF]  1100000 lines processed.
[GTF]  1142762 lines processed.
[read.gtf.refGenome] Extracting genes table.
[read.gtf.refGenome] Found 32,105 gene records.
[read.gtf.refGenome] Finished.
> gt <- getGeneTable(ens)
> gl <- geneList(ens, gt$gene_id)
Error in `row.names<-.data.frame`(`*tmp*`, value = value) :
  duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names':  

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8.1 x64 (build 9600)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] refGenome_1.7.0 RSQLite_1.0.0   DBI_0.4-1       doBy_4.5-15    

loaded via a namespace (and not attached):
[1] MASS_7.3-45     Matrix_1.2-6    grid_3.3.1      lattice_0.20-33