[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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