[BioC] makeTranscriptDbFromUCSC() error

Chris Cabanski ccabansk at genome.wustl.edu
Wed Jan 15 18:37:19 CET 2014

I am encountering an error when running makeTranscriptDbFromUCSC() that
was not occurring yesterday.  I have tried on 2 separate computers/R
versions and get similar errors. Playing around, it seems like the
function works for other genomes but not for hg19, which is what I am
looking for.  Any ideas on what is going wrong?

> library("TxDb.Hsapiens.UCSC.hg19.knownGene")

> tx <- makeTranscriptDbFromUCSC(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 scan(file, what, nmax, sep, dec, quote,
skip, nlines, na.strings,  :
  line 1 did not have 2 elements

> traceback()
2: tableNames(ucscTableQuery(session, track = track))
1: makeTranscriptDbFromUCSC(genome = "hg19", tablename = "refGene")

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1
[2] GenomicFeatures_1.14.2
[3] AnnotationDbi_1.24.0
[4] Biobase_2.22.0
[5] GenomicRanges_1.14.4
[6] XVector_0.2.0
[7] IRanges_1.20.6
[8] BiocGenerics_0.8.0

loaded via a namespace (and not attached):
 [1] biomaRt_2.18.0     Biostrings_2.30.1  bitops_1.0-6       BSgenome_1.30.0
 [5] DBI_0.2-7          RCurl_1.95-4.1     Rsamtools_1.14.2   RSQLite_0.11.4
 [9] rtracklayer_1.22.0 stats4_3.0.2       tools_3.0.2        XML_3.98-1.1
[13] zlibbioc_1.8.0

Christopher Cabanski, PhD
Postdoctoral Research Associate
Department of Medicine, Oncology Division / The Genome Institute
Washington University in St. Louis

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