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3 Replies Latest reply: Aug 1, 2013 12:04 PM by Sherry LaMonica RSS

Rstudio crashes loading ORE 1.3 packages

Sean S. Han Newbie
Currently Being Moderated
Hi,

Happy New Year, All There!!

Recently I am testing a newly released ORE 1.3 packages on Exadata X3-2 QR machine.
Under Linux shell there's no problem to run it. Looks very good..

But, when I try loading ORE packages under RStudio, the session crashes showing the following error:
======================================================
The previous R session was abnormally terminated
due to an unexpected crash.

You may have lost workspace data as a result of
this crash.
======================================================

The error message pops up just after executing the following script:
======================================================
library(ORE)
Loading required package: OREbase

Attaching package: ‘OREbase’

The following object(s) are masked from ‘package:base’:

cbind, data.frame, eval, interaction, order, paste, pmax, pmin,
rbind, table

Loading required package: OREstats
Loading required package: MASS
Loading required package: OREgraphics
Loading required package: OREeda
Loading required package: OREdm
Loading required package: lattice
Loading required package: OREpredict
Loading required package: ORExml
ore.connect(user = 'rquser',
+ password = 'rquser',
+ host = '10.xxx.xxx.xxx',
+ service_name = 'DW',
+ type = 'ORACLE',
+ all = TRUE)
Loading required package: ROracle
Loading required package: DBI
======================================================

Anybody has same problem and how to divert?

Thanks all in advance.

Sean

Edited by: 950400 on Jan 2, 2013 5:50 PM
  • 1. Re: Rstudio crashes loading ORE 1.3 packages
    Sherry LaMonica Journeyer
    Currently Being Moderated
    Sean,

    Please verify the RStudio Server installation:

    cd /usr/sbin
    sudo rstudio-server verify-installation

    and restart the server:

    sudo rstudio-server restart

    Do you still have the problem?

    Thanks,

    Sherry
  • 2. Re: Rstudio crashes loading ORE 1.3 packages
    5c39a862-72a6-4abd-9070-8d09f274453e Newbie
    Currently Being Moderated

    Hi.

     

    May be, The R Session Error was "The previous R session was abnormally terminated due to an unexpected crash ...".

    I could not test R studio on Exadata... but I just hope this tips help you.

     

    ----------------------------------------------------------------------------------------------------------------------------------------------------------------

     

    My Installation environments are as followings.  (--> Please refer to Oracle R Enterprise Installation guide.)

    - Oracle Enterprise Linux 6.4 or CentOS 6.3

    - ORE (Oracle R Enterprise) 1.3.1 for Linux x86_64

    - Oracle R Distrubution (R 2.15.1)

    - Oracle Database 11g (11.2.0.3.0) or 11.2.0.1 and Bug 11678127 PSU --> Please refer to Oracle R Enterprise Installation guide and must apply the proper

      Oracle database patches for ORE

    - RStudio version : rstudio-server-0.97.551-i686.rpm (from RStudio)

    * Note :  Document --> Oracle R Enterprise Installation and Administration Guide Release 1.3 for Windows, Linux, Solaris, and AIX E36763-11

     

    I got the same error, but I solved the problem as followings.

    1) http://your_server_ip:8787

    2) login as oracle

    3) Setup like this on your browser, without belows Sys.setenv, you will get the error. Of course improper Oracle database setting also show you ...

        Modify this according to your environments.

     

    4) Please refer to the following logs on Chrome browser

     

    Oracle Distribution of R version 2.15.1 (--) -- "Roasted Marshmallows"

    Copyright (C) The R Foundation for Statistical Computing

    ISBN 3-900051-07-0

    Platform: x86_64-unknown-linux-gnu (64-bit)

     

    R is free software and comes with ABSOLUTELY NO WARRANTY.

    You are welcome to redistribute it under certain conditions.

    Type 'license()' or 'licence()' for distribution details.

     

      Natural language support but running in an English locale

     

    R is a collaborative project with many contributors.

    Type 'contributors()' for more information and

    'citation()' on how to cite R or R packages in publications.

     

    Type 'demo()' for some demos, 'help()' for on-line help, or

    'help.start()' for an HTML browser interface to help.

    Type 'q()' to quit R.

     

    You are using Oracle's distribution of R. Please contact

    Oracle Support for any problems you encounter with this

    distribution.

     

    > Sys.setenv(ORACLE_SID="dwdb")
    > Sys.setenv(ORACLE_HOME="/u01/app/oracle/product/11.2.0/db")
    > Sys.setenv(LD_LIBRARY_PATH="/u01/app/oracle/product/11.2.0/db/lib")
    > Sys.setenv(PATH="/u01/app/oracle/product/11.2.0/db/bin:/usr/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/oracle/bin")
    >
    library(ORE)
    Loading required package: OREbase

    Attaching package: ‘OREbase’

    The following object(s) are masked from ‘package:base’:

      cbind, data.frame, eval, interaction, order, paste, pmax,
      pmin, rbind, table

    Loading required package: OREstats
    Loading required package: MASS
    Loading required package: OREgraphics
    Loading required package: OREeda
    Loading required package: OREdm
    Loading required package: lattice
    Loading required package: OREpredict
    Loading required package: ORExml
    > ore.connect(user="rquser",sid="dwdb", host="dwdb.localdomain", password="xxxx", port=1521, all=TRUE)
    Loading required package: ROracle
    Loading required package: DBI
    >
    > demo(table_apply, package="ORE")

     

    demo(table_apply)

    ---- ~~~~~~~~~~~


    Type <Return> to start :

    > #

    > # O R A C L E R E N T E R P R I S E S A M P L E L I B R A R Y

    > #

    > # Name: table_apply.R

    > # Description: Execute R code on all rows of a table

    > # passed in at once

    > #

    > #

    >

    > ## Set page width

    > options(width = 80)

     

    > # Push the built-in iris data frame to the database

    > IRIS_TABLE <- ore.push(iris)

     

    > # Display the class of IRIS_TABLE

    > class(IRIS_TABLE)

    [1] "ore.frame"

    attr(,"package")

    [1] "OREbase"

     

    > # Build a regression model using in memory data

    > mod = lm(Sepal.Length ~ . - Species, data = iris)

     

    > # Use tableApply to predict using the model on all rows of IRIS_TABLE

    > ore.tableApply(IRIS_TABLE,

    + function(dat, mod)

    + {

    + cbind(dat, PRED = predict(mod, newdata = dat))

    + },

    + mod = mod)

      Sepal.Length Sepal.Width Petal.Length Petal.Width Species PRED

    1 5.1 3.5 1.4 0.2 setosa 5.015416

    2 4.9 3.0 1.4 0.2 setosa 4.689997

    3 4.7 3.2 1.3 0.2 setosa 4.749251

    4 4.6 3.1 1.5 0.2 setosa 4.825994

    5 5.0 3.6 1.4 0.2 setosa 5.080499

    6 5.4 3.9 1.7 0.4 setosa 5.377194

    26 5.0 3.0 1.6 0.2 setosa 4.831824

    ....<omit> ....

     

     

    4. you can also test R studio like this.

       4.1) select R menu -> Tools --> shells ....

       4.2) at prompt, $ . ./bash_profile    <-- without this, you also get the crash messages.

       4.3) run R

       4.4) > library(ORE)

              > ore.connect(user="rquser",sid="dwdb", host="dwdb.localdomain", password="xxxx", port=1521, all=TRUE)

              > demo(table_apply, package="ORE")


    Thanks,

    Jin Young Song, TSC

  • 3. Re: Rstudio crashes loading ORE 1.3 packages
    Sherry LaMonica Journeyer
    Currently Being Moderated

    Jin,

     

    Thank you for sharing these steps.  I noticed you are running the 32-bit RStudio: rstudio-server-0.97.551-i686.rpm.  Oracle R Enterprise is supported for 64-bit Linux, so you'd want to use the 64-bit RStudio: http://download2.rstudio.org/rstudio-server-0.97.551-x86_64.rpm

     

    Sherry

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