[BioC] makeTranscriptDbFromUCSC() fails to download table

Burak Kutlu bkutlu at systemsbiology.org
Fri Dec 24 01:38:44 CET 2010


For some reason I started getting error for the following call
hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename =

The curious thing is that it was working this morning, it does not
seem to be a problem related to the goldenPath.

Thanks in advance

> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] GenomicFeatures_1.2.3 GenomicRanges_1.2.2   IRanges_1.8.7

loaded via a namespace (and not attached):
[1] Biobase_2.10.0     biomaRt_2.6.0      Biostrings_2.18.2
BSgenome_1.18.2    DBI_0.2-5
[6] RCurl_1.4-3        RSQLite_0.9-4      rtracklayer_1.10.6 XML_3.2-0

Burak Kutlu, PhD.
Research Scientist
Hood Lab
Institute for Systems Biology

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