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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_U S.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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

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