[BioC] REACTOME biomaRt not working in R 2.14, biomaRt 2.10.0
kenny daily
kmdaily at gmail.com
Fri Dec 9 17:09:09 CET 2011
Hello,
I'm having trouble connecting to the REACTOME mart. The
output/traceback/sessionInfo follows. The connection to reactome works
when using an older version of R (2.13.2 and 2.9.0) and an older
version of biomaRt (2.8.1 and 2.0.0).
### Begin
> library(biomaRt)
# This works ok!
> human <- useMart("ensembl", dataset="hsapiens_gene_ensembl")
# This does not
> reactome <- useMart("REACTOME", dataset="pathway")
Error in read.table(con, sep = "\t", header = FALSE, quote = "",
comment.char = "", :
no lines available in input
> traceback()
4: stop("no lines available in input")
3: read.table(con, sep = "\t", header = FALSE, quote = "", comment.char = "",
as.is = TRUE)
2: bmVersion(mart, verbose = verbose)
1: useMart("REACTOME", dataset = "pathway")
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United
States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.10.0
loaded via a namespace (and not attached):
[1] RCurl_1.8-0.1 tools_2.14.0 XML_3.6-1.1
### End
Thank you!
--
Kenny Daily
http://www.kennydaily.net/
--- Prediction is very difficult, especially about the future. (Niels Bohr) ---
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