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

[kenny daily]

Hi Dan, thanks for checking. I can connect now, but get errors when
trying to pull data:

> reactome <- useMart("REACTOME", dataset="pathway")
> hsREAlist <- getBM(attributes=c("pathway_db_id", "_displayname", "referencedatabase_kegg_gene", "complex__dm__displayname"), filters=c("pathway_db_id_list", "species_selection"), values=list(pathway_db_id_list="15869", species_selection="Homo sapiens"), mart=reactome)

Error in getBM(attributes = c("pathway_db_id", "_displayname",
"referencedatabase_kegg_gene",  :
  Query ERROR: caught BioMart::Exception::Query: <pre>Query error
occurred at web service based data source!

Remote data source: http://reactome.oicr.on.ca:5555/biomart/martservice?

Query XML:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "default" limitStart = "" limitSize =
"200" count = "" softwareVersion = "0.6" requestId=
"biomart-client">
	<Dataset name = "pathway" interface = "default" >
				<Attribute name = "pathway_db_id" />
				<Attribute name = "_displayname" />
				<Attribute name = "referencedatabase_kegg_gene" />
				<Attribute name = "complex__dm__displayname" />
	     	<ValueFilter name = "pathway_db_id_list" value = "15869"/>
	     	<ValueFilter name = "species_selection" value = "Homo sapiens"/>
	  </Dataset>
</Query>

Please ensure the above query XML is well-formed and does not contain
illegal characters.

Error message from remote server as below


Also:

> hsREAlist <- getBM(attributes=c("pathway_db_id", "_displayname"), mart=reactome)
Error in getBM(attributes = c("pathway_db_id", "_displayname"), mart =
reactome) :
  Query ERROR: caught BioMart::Exception::Query: <pre>Query error
occurred at web service based data source!

Remote data source: http://reactome.oicr.on.ca:5555/biomart/martservice?

Query XML:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "default" limitStart = "" limitSize =
"200" count = "" softwareVersion = "0.6" requestId=
"biomart-client">
	<Dataset name = "pathway" interface = "default" >
				<Attribute name = "pathway_db_id" />
				<Attribute name = "_displayname" />
	  </Dataset>
</Query>

Please ensure the above query XML is well-formed and does not contain
illegal characters.

Error message from remote server as below:
Query ERROR: caught BioMart::Exception::Database: Could not connect to
mysql database test_reactome_mart: DBI
connect('database=test_reactome_mart;host=localhost;port=8087','',...)
failed: Can't connect to local MySQL server through socket
'/usr/local/gkb_prod/BioMar

On Fri, Dec 9, 2011 at 3:51 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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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-- 
Kenny Daily
http://www.kennydaily.net/

--- Prediction is very difficult, especially about the future. (Niels Bohr) ---