[BioC] makeTranscriptDbFromUCSC

[Georg Otto]

Please ignore this message, it works again.

Cheers,

Georg


Georg Otto <georg.otto at imm.ox.ac.uk> writes:

> 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,
>
> Georg
>
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
>  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
>  [7] LC_PAPER=C                 LC_NAME=C                 
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=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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