[Bioc-devel] Error in GenomicFeatures::makeTxDbFromUCSC()

[Arora, Sonali]

Hi ,

I get an error when creating a txdb object for hg19 from the refGene Table

 > txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene")
Error in tableNames(ucscTableQuery(session, track = track)) :
   error in evaluating the argument 'object' in selecting a method for 
function 'tableNames': Error in relist(ans_unlistData, ans_partitioning) :
   shape of 'skeleton' is not compatible with 'NROW(flesh)'

Is this because GenomicRanges() is broken in devel ? Please advise.


 > sessionInfo()
R Under development (unstable) (2015-10-15 r69519)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
[1] GenomicFeatures_1.23.1 AnnotationDbi_1.33.0 Biobase_2.31.0         
GenomicRanges_1.21.32  GenomeInfoDb_1.7.0
[6] IRanges_2.5.0          S4Vectors_0.9.0 BiocGenerics_0.17.0    
BiocInstaller_1.21.1

loaded via a namespace (and not attached):
  [1] XVector_0.11.0             zlibbioc_1.17.0 
GenomicAlignments_1.7.0    BiocParallel_1.5.0
  [5] tools_3.3.0                SummarizedExperiment_1.1.0 
DBI_0.3.1                  lambda.r_1.1.7
  [9] futile.logger_1.4.1        rtracklayer_1.31.0 
futile.options_1.0.0       bitops_1.0-6
[13] RCurl_1.95-4.7             biomaRt_2.27.0 
RSQLite_1.0.0              Biostrings_2.39.0
[17] Rsamtools_1.23.0           XML_3.98-1.3

-- 
Thanks and Regards,
Sonali