
Hi Jim,

I think I have an out of the box (fedora core 5) mysql client, and this morning 
I installed the devel rpm.
I do not use yum (I did not succeed to solve some proxy/port issues). I downlad
the rpm and then local install. 

[ariel@LAB309-10 Downloads]$ rpm -qa |grep mysql
mysql-5.0.18-2.1
libdbi-dbd-mysql-0.8.1a-1.2.1
mysql-connector-odbc-3.51.12-1.2.1
mysql-devel-5.0.18-2.1


I noticed you have  5.0.27 version, I will try to update...

Thanks
Ariel./





-----Original Message-----
From: Jim [mailto:jmacdon@med.umich.edu]
Sent: Tue 11/28/2006 11:16 AM
To: Ariel Chernomoretz
Cc: bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] biomaRt. useMart with mysql=TRUE  gives segfault!
 
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@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"
>
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>
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