Entering edit mode
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
