[BioC] GenomicFeatures Transcripts Retrieval Fails

Dario Strbenac D.Strbenac at garvan.org.au
Mon Oct 22 02:00:15 CEST 2012


makeTranscriptDbFromUCSC isn't working for me. I can download R packages from CRAN and Bioconductor using install.packages or biocLite, so it's not a proxy issue. I can also paste the URL http://hgdownload.cse.ucsc.edu/goldenPath into a web browser and I get to the website fine.

> tx19 <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "refGene")
Error in function (type, msg, asError = TRUE)  : couldn't connect to host

R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

[1] LC_COLLATE=English_Australia.1252 
[2] LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

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

other attached packages:
[1] GenomicFeatures_1.10.0 AnnotationDbi_1.20.2  
[3] Biobase_2.18.0         GenomicRanges_1.10.1  
[5] IRanges_1.16.2         BiocGenerics_0.4.0    

loaded via a namespace (and not attached):
 [1] biomaRt_2.12.0     Biostrings_2.26.1 
 [3] bitops_1.0-4.1     BSgenome_1.24.0   
 [5] DBI_0.2-5          parallel_2.15.1   
 [7] RCurl_1.95-1.1     Rsamtools_1.10.1  
 [9] RSQLite_0.11.1     rtracklayer_1.18.0
[11] stats4_2.15.1      tools_2.15.1      
[13] XML_3.9-4.1        zlibbioc_1.2.0

Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050

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