
Hi all,

I get a hideous segfault when trying to connect to ensembl database via mysql.
The error message and sessionInfo follows.
Any help would be apprecited
Ariel./


>
> library(biomaRt)
Loading required package: XML
Loading required package: RCurl
> library(RMySQL)
Loading required package: DBI
> human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", mysql=TRUE)

 *** caught segfault ***
address 0x55, cause 'memory not mapped'

Traceback:
 1: .Call("RS_MySQL_newConnection", drvId, con.params, groups, default.file,           PACKAGE = .MySQLPkgName)
 2: mysqlNewConnection(drv, ...)
 3: .class1(object)
 4: .class1(object)
 5: is(object, Cl)
 6: .valueClassTest(standardGeneric("dbConnect"), "DBIConnection",     "dbConnec      t")
 7: dbConnect(driv, user = user[i], host = host[i], password = password[i])
 8: listMarts(mysql = TRUE)
 9: useMart("ensembl", dataset = "hsapiens_gene_ensembl", mysql = TRUE)

Possible actions:
1: abort (with core dump)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:


0000000000000000000000000000000000000000000000000000000000000


> sessionInfo()
R version 2.4.0 (2006-10-03)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
   RMySQL       DBI   biomaRt     RCurl       XML
 "0.5-10"  "0.1-11"   "1.8.0"   "0.7-0" "0.99-93"

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