On Thu, Oct 4, 2012 at 4:29 AM, dh_ss <da...@serendipityscience.com> wrote: > I have been experiencing issues with an R script hanging when connecting to > an Oracle database. To help debug, I found a function here in the nabble > forum and made a small test script: > > #!/usr/bin/Rscript --no-restore --no-save --no-init-file > library("RJDBC") > drv<-JDBC("oracle.jdbc.OracleDriver","/home/oracle/lib/ojdbc6.jar", "'") > > dbCheck = function(url, user='', pwd='') { > j = .jcall("java/sql/DriverManager", "Ljava/sql/Connection;", > "getConnection", url, user, pwd, check=FALSE) > x = .jgetEx() > .jcheck() > x > } > dbCheck("jdbc:oracle:thin:@192.168.3.10:1521:psrndpt1","myuser","mypass") > > > When I run the file - sometimes it works, returning NULL, and sometimes it > hangs for between 1 and 2.5 minutes before throwing an error. The database > is new and stable, on the same network - with no connection issues from any > other clients. This machine isn't currently doing anything else except for > running this script. Output from running it several times looks like this: > > R@ss-dev:~/scripts$ ./dbCheck.R > Loading required package: methods > Loading required package: DBI > Loading required package: rJava > NULL > R@ss-dev:~/scripts$ ./dbCheck.R > Loading required package: methods > Loading required package: DBI > Loading required package: rJava > NULL > R@ss-dev:~/scripts$ ./dbCheck.R > Loading required package: methods > Loading required package: DBI > Loading required package: rJava > NULL > R@ss-dev:~/scripts$ ./dbCheck.R > Loading required package: methods > Loading required package: DBI > Loading required package: rJava > NULL > R@ss-dev:~/scripts$ ./dbCheck.R > Loading required package: methods > Loading required package: DBI > Loading required package: rJava > NULL > R@ss-dev:~/scripts$ ./dbCheck.R > Loading required package: methods > Loading required package: DBI > Loading required package: rJava > NULL > R@ss-dev:~/scripts$ ./dbCheck.R > Loading required package: methods > Loading required package: DBI > Loading required package: rJava > Error in .jcall("java/sql/DriverManager", "Ljava/sql/Connection;", > "getConnection", : > ignoring SIGPIPE signal > Calls: dbCheck -> .jcall -> .External > Execution halted > R@ss-dev:~/scripts$ ./dbCheck.R > Loading required package: methods > Loading required package: DBI > Loading required package: rJava > Error in .jcall("java/sql/DriverManager", "Ljava/sql/Connection;", > "getConnection", : > ignoring SIGPIPE signal > Calls: dbCheck -> .jcall -> .External > Execution halted > R@ss-dev:~/scripts$ ./dbCheck.R > Loading required package: methods > Loading required package: DBI > Loading required package: rJava > NULL > R@ss-dev:~/scripts$ ./dbCheck.R > Loading required package: methods > Loading required package: DBI > Loading required package: rJava > Error in .jcall("java/sql/DriverManager", "Ljava/sql/Connection;", > "getConnection", : > ignoring SIGPIPE signal > Calls: dbCheck -> .jcall -> .External > Execution halted > > > The times that it returns NULL, it returns immediately. When it throws the > error, it is a varying amount of time between roughly 1 and 2.5 minutes. > Both machines are not busy at all. > > Any ideas would greatly appreciated. Thanks. >
I'd suggest you take this to the R-SIG-DB (Databases) mailing list instead. I don't think it's mirrored on the abomination that is Nabble, so you'll have to subscribe and post there: https://stat.ethz.ch/mailman/listinfo/r-sig-db Note that they'll most certainly want your OS, rJava version, JVM version, R version, and relevant info about the Oracle DB as well. Cheers, Michael ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.