[BioC] makeTranscriptDbFromUCSC

Georg Otto georg.otto at imm.ox.ac.uk
Wed Jan 15 13:09:13 CET 2014

Dear Bioconductors,

I am trying to use makeTranscriptDbFromUCSC() from the GenomicFeatures,
but it results in an error:

> txdb.ensgene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "knownGene")

Error in tableNames(ucscTableQuery(session, track = track)) : 
  error in evaluating the argument 'object' in selecting a method for
function 'tableNames': Error in scan(file, what, nmax, sep, dec, quote,
skip, nlines, na.strings,  : 
  line 1 did not have 2 elements

However a query for hg18 works fine:

> txdb.ensgene <- makeTranscriptDbFromUCSC(genome = "hg18", tablename = "ensGene")
Download the ensGene table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TranscriptDb object ... OK

Any idea what is going on?

Best wishes,


> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
 [1] Rsamtools_1.14.2        Biostrings_2.30.1       rtracklayer_1.22.0     
 [4] pamr_1.54.1             survival_2.37-4         cluster_1.14.4         
 [7] RColorBrewer_1.0-5      gplots_2.12.1           xtable_1.7-1           
[10] scatterplot3d_0.3-34    plyr_1.8                org.Hs.eg.db_2.10.1    
[13] goseq_1.14.0            geneLenDataBase_0.99.12 BiasedUrn_1.06.1       
[16] edgeR_3.4.2             limma_3.18.7            biomaRt_2.18.0         
[19] KEGG.db_2.10.1          RSQLite_0.11.4          DBI_0.2-7              
[22] GenomicFeatures_1.14.2  AnnotationDbi_1.24.0    GenomicRanges_1.14.4   
[25] XVector_0.2.0           IRanges_1.20.6          DESeq_1.14.0           
[28] lattice_0.20-24         locfit_1.5-9.1          Biobase_2.22.0         
[31] BiocGenerics_0.8.0      corrplot_0.73          

loaded via a namespace (and not attached):
 [1] annotate_1.40.0    bitops_1.0-6       BSgenome_1.30.0    caTools_1.16      
 [5] compiler_3.0.1     gdata_2.13.2       genefilter_1.44.0  geneplotter_1.40.0
 [9] grid_3.0.1         gtools_3.1.1       KernSmooth_2.23-10 Matrix_1.1-0      
[13] mgcv_1.7-27        nlme_3.1-113       RCurl_1.95-4.1     stats4_3.0.1      
[17] tcltk_3.0.1        tools_3.0.1        XML_3.98-1.1       zlibbioc_1.8.0

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