[BioC] biomaRt. useMart with mysql=TRUE gives segfault!

[Jim]

Hi Ariel,

How did you install the MySQL headers? Did you use Yum, or just install 
the sources in your home directory? What version of MySQL are you using?

I don't have a problem connecting:

 > mart <- useMart("ensembl", "hsapiens_gene_ensembl", mysql=T)
Loading required package: RMySQL
Loading required package: DBI
connected to:  ensembl
Reading database configuration of: hsapiens_gene_ensembl
Checking main tables ... ok
Checking attributes and filters ... ok
Warning message:
NAs introduced by coercion
 > sessionInfo()
R version 2.4.0 alpha (2006-09-13 r39286)
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"  "0.8-0"  "1.2-0"

[jmacdon at backup_box ~]$ rpm -qa | grep -i mysql
mysql-devel-5.0.27-1.fc5
mysql-5.0.27-1.fc5

Is it possible you have mis-matched MySQL base and devel versions?

Best,

Jim

Ariel Chernomoretz wrote:
> 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"
>
> 	[[alternative HTML version deleted]]
>
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