The UCSC Genome browser have updated GENCODE track to v24 and track "GENCODE v22" is not longer supported. This affects makeTxDbFromUCSC() and makeTxDbPackageFromUCSC() that depend on supportedUCSCtables("hg38"). So using the current GenomicFeature v1.24.5 on R 3.3 or R3.4, we have

>  supportedUCSCtables(genome="hg38")

                                               track           subtrack

knownGene                                GENCODE v22               <NA>

knownGeneOld3                         Old UCSC Genes               <NA>

ccdsGene                                        CCDS               <NA>

refGene                                 RefSeq Genes               <NA>

xenoRefGene                             Other RefSeq               <NA>

vegaGene                                  Vega Genes Vega Protein Genes

vegaPseudoGene                            Vega Genes   Vega Pseudogenes

> TxDb <- makeTxDbFromUCSC(genome="hg38", tablename="knownGene")

Error in normArgTrack(track, trackids) : Unknown track: GENCODE v22

> sessionInfo()

R Under development (unstable) (2016-09-18 r71304)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu 14.04.3 LTS


locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              

 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    

 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   

 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 

 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       


attached base packages:

[1] stats4    parallel  stats     graphics  grDevices utils     datasets 

[8] methods   base     


other attached packages:

[1] GenomicFeatures_1.24.5 AnnotationDbi_1.34.4   Biobase_2.32.0        

[4] GenomicRanges_1.24.2   GenomeInfoDb_1.8.7     IRanges_2.6.1         

[7] S4Vectors_0.10.3       BiocGenerics_0.18.0    BiocInstaller_1.22.3  

I am able to get TxDb from UCSC gencode v24 track using the following code, but having GenomicFeatures functions to do the tedious work would be handy.  

library(GenomicFeatures)
library(rtracklayer)
ucsc_txtable <-
    getTable(ucscTableQuery(session, track="GENCODE v24", table="knownGene"))

tablename="knownGene"
track="GENCODE v24"
mapdef <- GenomicFeatures:::.howToGetTxName2GeneIdMapping("knownGene")
txname2geneid <- GenomicFeatures:::.fetchTxName2GeneIdMappingFromUCSC(session, 
           track, tablename, mapdef)
transcript_ids = NULL
txdb <- GenomicFeatures:::.makeTxDbFromUCSCTxTable(ucsc_txtable, txname2geneid$genes, 
        genome="hg38", tablename, track, txname2geneid$gene_id_type, 
        full_dataset = is.null(transcript_ids), circ_seqs = DEFAULT_CIRC_SEQS,
        taxonomyId = NA, miRBaseBuild = NA)

NOTE: I tried to use the devel version of GenomicFeature v1.25.16 download from https://bioconductor.org/packages/devel/bioc/html/GenomicFeatures.html, but the knownGene tablename is not available. Therefore, I cannot use MakeTxDbFromUCSC() to build the TxDb from Gencode track. I thought Herve has fixed it on v1.25.17, but I cannot see the updated version of package on the devel page. And I am not sure if Herve also has updated the track name to GENCODE v24 on the devel version v1.25.17.

Any update will be appreciated. 

Thanks,

Chao-Jen

Hi Chao-Jen,

Herve fixed this last week, looks like in version 1.25.18:

------------------------------------------------------------------------
r121527 | hpages@fhcrc.org | 2016-09-29 00:37:33 -0700 (Thu, 29 Sep 2016) | 3 lines

Update name of UCSC track associated to the knownGene table from "GENCODE v22"
to "GENCODE v24".

Valerie