[BioC] makeTranscriptDbFromUCSC() error

[Chris Cabanski]

You can disregard my previous message.  makeTranscriptDbFromUCSC() is
working correctly again.

-Chris

> Hi,
> 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)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [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
>
>



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