I have trouble getting the goseq package to work.

I am using R-3.3.0; and have installed goseq version 3.5; as well as the "org.Hs.eg.db" package.

Unfortunately I don't get goseq functions to work:

Example:

ensgenes<-c("ENSG00000130303","ENSG00000124785","ENSG00000134138")
getgo(ensgenes,"hg19","ensgene",fetch.cats="GO:BP")

gives:

Error in getgo(ensgenes, "hg19", "ensgene", fetch.cats = "GO:BP") :
  Couldn't grab GO categories automatically.  Please manually specify.

any advice??

thanks

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.4 LTS)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=C             
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
 [1] rtracklayer_1.32.2    GenomicRanges_1.24.3  GenomeInfoDb_1.8.7   
 [4] org.Hs.eg.db_3.3.0    AnnotationDbi_1.34.4  IRanges_2.6.1        
 [7] S4Vectors_0.10.3      Biobase_2.32.0        BiocGenerics_0.18.0  
[10] goseq_1.24.0          geneLenDataBase_1.8.0 BiasedUrn_1.07       
[13] edgeR_3.14.0          limma_3.28.21         ape_4.1              
[16] BiocInstaller_1.22.3

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9                XVector_0.12.1            
 [3] zlibbioc_1.18.0            GenomicAlignments_1.8.4   
 [5] BiocParallel_1.6.6         lattice_0.20-34           
 [7] tools_3.3.0                SummarizedExperiment_1.2.3
 [9] grid_3.3.0                 nlme_3.1-131              
[11] mgcv_1.8-17                DBI_0.6-1                 
[13] digest_0.6.12              Matrix_1.2-10             
[15] bitops_1.0-6               biomaRt_2.28.0            
[17] RCurl_1.95-4.8             memoise_1.1.0             
[19] RSQLite_1.1-2              GO.db_3.3.0               
[21] GenomicFeatures_1.24.5     Biostrings_2.40.2         
[23] Rsamtools_1.24.0           XML_3.98-1.7     

Do note that R is case sensitive, so you cannot pass 'ensgene' as an argument when the function expects 'ensGene':

> supportedGeneIDs()
    tablename         track           subtrack               GeneID
1   knownGene    UCSC Genes               <NA>       Entrez Gene ID
10   vegaGene    Vega Genes Vega Protein Genes HAVANA Pseudogene ID
12    ensGene Ensembl Genes               <NA>      Ensembl gene ID
21 geneSymbol       refGene            refFlat          Gene Symbol