[R-sig-DB] Intermittent connectivity issues for RJDBC / Oracle

[Dirk Eddelbuettel]

Denis,

On 4 October 2012 at 14:07, Denis Mukhin wrote:
| David,
| 
| Have you considered using ROracle instead? It is also DBI based. ROracle uses native interfaces (OCI) so it should be much faster (although I have not run any comparisons). It is also actively maintained by Oracle so if you have any problems/concerns we should be able to address them fairly quickly.

This is the second time this week you are pulling this stunt, and I formally
object.  

If someone wants and need (R)Oracle, they will know where and how to get it,
provided they also find their six-figure check.

This is an open source mailing list, and I would like to ask you to stop your
salesmanship here.  The last post ("I don't know anything about RPostgreSQL,
but this is what ROracle does") was borderline amusing, but this one is very
clearly stepping over that line we all know.

Stop it now, please.

Dirk


| 
| Denis
| 
| -----Original Message-----
| From: David [mailto:david using serendipityscience.com] 
| Sent: Thursday, October 04, 2012 4:45 PM
| To: r-sig-db using r-project.org
| Subject: [R-sig-DB] Intermittent connectivity issues for RJDBC / Oracle
| 
| I will forward more details like versions of xyz when i can, but any thoughts on what I can focus on to debug the problem described below?
| 
| Thank you, David
| ---------- Forwarded message ----------
| From: "dh_ss" <david using serendipityscience.com>
| Date: Oct 4, 2012 1:29 AM
| Subject: [R] Intermittent connectivity issues for JDBC / Oracle
| To: <r-help using r-project.org>
| 
| 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 using ss-dev:~/scripts$ ./dbCheck.R
| Loading required package: methods
| Loading required package: DBI
| Loading required package: rJava
| NULL
| R using ss-dev:~/scripts$ ./dbCheck.R
| Loading required package: methods
| Loading required package: DBI
| Loading required package: rJava
| NULL
| R using ss-dev:~/scripts$ ./dbCheck.R
| Loading required package: methods
| Loading required package: DBI
| Loading required package: rJava
| NULL
| R using ss-dev:~/scripts$ ./dbCheck.R
| Loading required package: methods
| Loading required package: DBI
| Loading required package: rJava
| NULL
| R using ss-dev:~/scripts$ ./dbCheck.R
| Loading required package: methods
| Loading required package: DBI
| Loading required package: rJava
| NULL
| R using ss-dev:~/scripts$ ./dbCheck.R
| Loading required package: methods
| Loading required package: DBI
| Loading required package: rJava
| NULL
| R using 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 using 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 using ss-dev:~/scripts$ ./dbCheck.R
| Loading required package: methods
| Loading required package: DBI
| Loading required package: rJava
| NULL
| R using 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.
| 
| 
| 
| --
| View this message in context:
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| Sent from the R help mailing list archive at Nabble.com.
| 
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-- 
Dirk Eddelbuettel | edd using debian.org | http://dirk.eddelbuettel.com