[BioC] REACTOME biomaRt not working in R 2.14, biomaRt 2.10.0

[Dan Tenenbaum]

Hi Kenny,

On Fri, Dec 9, 2011 at 8:09 AM, kenny daily <kmdaily at gmail.com> wrote:
> 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")

This command works for me, with a similar sessionInfo(). Can you try
again? I wonder if it was a transient failure to connect to biomart?

Dan


sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] 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      BiocInstaller_1.2.1

loaded via a namespace (and not attached):
[1] RCurl_1.8-0.1 tools_2.14.0  XML_3.6-2.1

> 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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