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dh_ss

2012-Oct-04 03:29 UTC

[R] Intermittent connectivity issues for JDBC / Oracle

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 at ss-dev:~/scripts$ ./dbCheck.R
Loading required package: methods
Loading required package: DBI
Loading required package: rJava
NULL
R at ss-dev:~/scripts$ ./dbCheck.R
Loading required package: methods
Loading required package: DBI
Loading required package: rJava
NULL
R at ss-dev:~/scripts$ ./dbCheck.R
Loading required package: methods
Loading required package: DBI
Loading required package: rJava
NULL
R at ss-dev:~/scripts$ ./dbCheck.R
Loading required package: methods
Loading required package: DBI
Loading required package: rJava
NULL
R at ss-dev:~/scripts$ ./dbCheck.R
Loading required package: methods
Loading required package: DBI
Loading required package: rJava
NULL
R at ss-dev:~/scripts$ ./dbCheck.R
Loading required package: methods
Loading required package: DBI
Loading required package: rJava
NULL
R at 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 at 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 at ss-dev:~/scripts$ ./dbCheck.R
Loading required package: methods
Loading required package: DBI
Loading required package: rJava
NULL
R at 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.



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Sent from the R help mailing list archive at Nabble.com.

R. Michael Weylandt

2012-Oct-04 10:20 UTC

head link

[R] Intermittent connectivity issues for JDBC / Oracle

On Thu, Oct 4, 2012 at 4:29 AM, dh_ss <david at 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 at ss-dev:~/scripts$ ./dbCheck.R
> Loading required package: methods
> Loading required package: DBI
> Loading required package: rJava
> NULL
> R at ss-dev:~/scripts$ ./dbCheck.R
> Loading required package: methods
> Loading required package: DBI
> Loading required package: rJava
> NULL
> R at ss-dev:~/scripts$ ./dbCheck.R
> Loading required package: methods
> Loading required package: DBI
> Loading required package: rJava
> NULL
> R at ss-dev:~/scripts$ ./dbCheck.R
> Loading required package: methods
> Loading required package: DBI
> Loading required package: rJava
> NULL
> R at ss-dev:~/scripts$ ./dbCheck.R
> Loading required package: methods
> Loading required package: DBI
> Loading required package: rJava
> NULL
> R at ss-dev:~/scripts$ ./dbCheck.R
> Loading required package: methods
> Loading required package: DBI
> Loading required package: rJava
> NULL
> R at 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 at 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 at ss-dev:~/scripts$ ./dbCheck.R
> Loading required package: methods
> Loading required package: DBI
> Loading required package: rJava
> NULL
> R at 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

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