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10 Replies Latest reply: Oct 16, 2013 9:47 AM by Sherry LaMonica RSS

update documentation in regard to R-2.13.2

1003974 Newbie
Currently Being Moderated
Hi,

I have installed R-2.13.2 from source on Linux as per instruction on:

http://docs.oracle.com/cd/E27988_01/doc/doc.112/e26499/install.htm

After installing the client and support packages and running a first test, this is what I get:

++++

R version 2.13.2 (2011-09-30)
Copyright (C) 2011 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.
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
Warning messages:
1: package 'ORE' was built under R version 2.15.1
2: package 'OREbase' was built under R version 2.15.1
3: In .recacheSubclasses(def@className, def, doSubclasses, env) :
undefined subclass "className" of class "characterORNULL"; definition not updated
4: package 'OREstats' was built under R version 2.15.1
5: In eval(quote({ : bytecode version mismatch; using eval
6: package 'OREgraphics' was built under R version 2.15.1
7: package 'OREeda' was built under R version 2.15.1
8: package 'OREdm' was built under R version 2.15.1
9: package 'OREpredict' was built under R version 2.15.1
10: package 'ORExml' was built under R version 2.15.1
>
ore.connect(user = "rquser",
+ sid = "orcl",
+ host = "localhost",
+ password = "xxx",
+ port = 1521,
+ all = TRUE)
Loading required package: ROracle
Loading required package: DBI
Error: 'dbConnect' is not an exported object from 'namespace:ROracle'
In addition: Warning messages:
1: package 'ROracle' was built under R version 2.15.1
2: package 'DBI' was built under R version 2.15.1

++++

As the warnings clearly state the newest packages for download (ore-client-linux-x86-64-1.3.1.zip, ore-supporting-linux-x86-64-1.3.1.zip) are built under 2.15.1.

I hence suggest to update the documentation accordingly. I might be just looking at the wrong version of the installation docs, in which case I would welcome anyone pointing out the errors of my ways.

In regard to the namespace error: My working hypothesis is, that this a consequence of the version disparity. I'm compiling 2.15.1 as I write this to test it. I can call dbConnect() directly without any errors. If you have any further thoughts on this point please let me know.

Best,

Vincent

Edited by: 1000971 on Apr 23, 2013 9:51 AM
  • 1. Re: update documentation in regard to R-2.13.2
    Sherry LaMonica Journeyer
    Currently Being Moderated
    Vincent,

    Oracle R Enterprise 1.3 and 1.3.1 are certified with R 2.15.1.
    Oracle R Enterprise 1.0 and 1.1 are certified with R 2.13.2.
    Oracle R Distribution (for Linux, Solaris, and AIX) was created to work with Oracle R Enterprise

    The link to the latest Oracle R Enterprise Installation and Administration Guide is here:

    http://docs.oracle.com/cd/E36939_01/welcome.html

    The link that explains the R requirements is here:

    http://docs.oracle.com/cd/E36939_01/doc/doc.13/e36763/prereq.htm#autoId1

    Instructions for installing Oracle R Distribution on Linux are here:

    http://docs.oracle.com/cd/E36939_01/doc/doc.13/e36763/prereq.htm#autoId4

    Sherry
  • 2. Re: update documentation in regard to R-2.13.2
    FernandoGoncalves Newbie
    Currently Being Moderated

    Hi Sherry

     

    Im having the same problem and I suppose (also) that  the most up to date documentation is not up to date.

     

    I've read the docs of version ORE 1.3.1 here = http://docs.oracle.com/cd/E36939_01/doc/doc.13/e36763/prereq.htm#BABDIJAI

     

    Installed as per the manual the R language from the repository.

     

    #> R --version

    R --version
    Oracle Distribution of R version 3.0.1  (--) -- "Good Sport"
    Copyright (C)  The R Foundation for Statistical Computing
    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 the terms of the
    GNU General Public License versions 2 or 3.
    For more information about these matters see
    http://www.gnu.org/licenses/.


    installed the ORE packages as per the documentation executing ORE CMD INSTALL

     

    i can 'see' the packages from the R shell

    R> .libPaths("/u01/app/oracle/product/11.2.0.3/db_2/R/library/")

    R> .libPaths()

    .libPaths()
    [1] "/u01/app/oracle/product/11.2.0.3/db_2/R/library"
    [2] "/usr/lib64/R/library"                          
    [3] "/usr/share/R/library"


     

    R> installed.packages()

     

    [...] some content removed [...]

     

    NeedsCompilation Built  
    DBI         NA               "2.15.1"
    ORE         NA               "2.15.1"
    OREbase     NA               "2.15.1"
    OREdm       NA               "2.15.1"
    OREeda      NA               "2.15.1"
    OREgraphics NA               "2.15.1"
    OREpredict  NA               "2.15.1"
    OREstats    NA               "2.15.1"
    ORExml      NA               "2.15.1"
    png         NA               "2.15.1"
    ROracle     NA               "2.15.1"
    base        NA               "3.0.1"
    boot        NA               "3.0.1"
    class       "yes"            "3.0.1"
    cluster     "yes"            "3.0.1"


    [...] some content removed [...]

     

    I've followed the instructions till here = http://docs.oracle.com/cd/E36939_01/doc/doc.13/e36763/admin.htm#BAJGFEGE

    and after setting the libPath when executing at the R shell ,as per the Manual ,

    R> ORE

    ORE
    Error: object 'ORE' not found


    if instead I execute

     

    R> library(ORE)

    library(ORE)
    Error: package ‘ORE’ was built before R 3.0.0: please re-install it


    But i can load them at my workstation (ubuntu) ,after installing ore-supporting and ore-client:

     

    #> R --version
    R version 2.15.2 (2012-10-26) -- "Trick or Treat"
    Copyright (C) 2012 The R Foundation for Statistical Computing
    ISBN 3-900051-07-0
    Platform: x86_64-pc-linux-gnu (64-bit)

     

    R>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

     

     

     


    Can you clarify somehow ?

     

    Thank you very much.

     

     

    PS:

    (even though I bump into another error when trying to connect  :-P ... but that is another story ,though ...

    R> ore.connect(user = "rquser", sid = "V11", host = "v11", password = "ll", port = 1525, all = TRUE)
    Error in .oci.GetQuery(conn, statement, data = data, prefetch = prefetch,  :
      ORA-06520: PL/SQL: Error loading external library
    ORA-06522: /u01/app/oracle/product/11.2.0.3/db_2/lib/librqe.so: undefined symbol: R_Decode2Long
    ORA-06512: at "RQSYS.RQEVALIMPL", line 17
    ORA-06512: at "RQSYS.RQEVALIMPL", line 14
    ORA-06512: at line 4

    )

  • 3. Re: update documentation in regard to R-2.13.2
    Sherry LaMonica Journeyer
    Currently Being Moderated

    Fernando,

     

    Oracle R Distribution 3.0.1 will be compatible with a future release of Oracle R Enterprise. See this blog post for details:

    https://blogs.oracle.com/R/entry/updating_ord

     

    -The version of Oracle R Distribution on the server must match the R version on the client.

    -Oracle R Distribution 2.15.x is certified with with Oracle R Enterprise 1.3.x. 

    -You have R 2.15.2 installed on your client, so you will need to to uninstall R-3.0.1 on the server and install R-2.15.2. 

    Here are the steps, to be performed as root:


    1. Remove R-3.0.1

    rpm -e R-3.0.1-1.el5.x86_64

    rpm -e R-devel

    rpm -e R-core

     

    2.  Install R-2.15.2

    a. Install Oracle Linux 5 yum repository:

    cd /etc/yum.repos.d

    wget http://public-yum.oracle.com/public-yum-el5.repo

     

    Open public-yum-el5.repo in a text editor and set

    "enabled=1" for [el5_latest]

    and [el5_addons]


    b. Install R-2.15.2:

    yum install R-2.15.2

     

    You can avoid setting .libPaths() to point to $ORACLE_HOME/R/library by starting R with the ORE script from the Linux shell:

     

    %ORE

     

    Sherry


  • 4. Re: update documentation in regard to R-2.13.2
    FernandoGoncalves Newbie
    Currently Being Moderated

    Sherry

     

    Thank You .Ill give it a try and feed this back as soon as I can.

     

    Can you please shed some light on the problem mentioned on PS on point me to a solution ?

     

    I think I need to set LD_LIBRARY_PATH on exproc.ora so that the lib on $ORACLE_HOME/R/library gets loaded instead of the one in $ORACLE_HOME/lib (which is my case now)

     

    Can you confirm this ?

  • 5. Re: update documentation in regard to R-2.13.2
    Sherry LaMonica Journeyer
    Currently Being Moderated

    Regarding the eerror you are seeing after executing ore.connect():

     

    R> ore.connect(user = "rquser", sid = "V11", host = "v11", password = "ll", port = 1525, all = TRUE)
    Error in .oci.GetQuery(conn, statement, data = data, prefetch = prefetch,  :
      ORA-06520: PL/SQL: Error loading external library
    ORA-06522: /u01/app/oracle/product/11.2.0.3/db_2/lib/librqe.so: undefined symbol: R_Decode2Long
    ORA-06512: at "RQSYS.RQEVALIMPL", line 17
    ORA-06512: at "RQSYS.RQEVALIMPL", line 14
    ORA-06512: at line 4

    )

     

    This is a side effect of running ORE 1.3.x with ORD 3.0.1. Downgrading ORD as I explained previously will resolve the problem.

  • 6. Re: update documentation in regard to R-2.13.2
    FernandoGoncalves Newbie
    Currently Being Moderated

    Sherry

     

    Thank You very much both your answers solved my problems.

     

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

     

    I just would like to confirm if the documentation,here ,is accurate = 
    http://docs.oracle.com/cd/E36939_01/doc/
    doc.13/e36763/admin.htm#BAJGFEGE

    @ Validate Oracle R Enterprise Installation

    2) Start R on a client. Load the Oracle R Enterprise Packages:

    • R> ORE
      

    is correct ?

     

    because the onlye way I get to to load the libs is executgin :

     

    R> library(ORE)


    thank you.


     

  • 7. Re: update documentation in regard to R-2.13.2
    Sherry LaMonica Journeyer
    Currently Being Moderated

    The correct command to load the ORE packages is:

     

    R> library(ORE)

     

    This will be updated in a future Oracle R Enterprise Installation and Administration Guide release.

  • 9. Re: update documentation in regard to R-2.13.2
    User194454 Newbie
    Currently Being Moderated

    Hi Sherry,

     

    I'm working in a research center as ORACLE DBA, analysts and modelers they want to test Oracle R enterprise for their purposes and so I'm trying to install ORACLE R enterprise on one of our server where they are installed OEL 6.1 Santiago and Oracle Database enterprise 11.2.0.0 with patchset 11.2.0.3.

     

    Ok I did the mistake to install before R 3.0.1 and after Oracle R server, support and client packages.

     

    Of course it doesn't work how I understood after reading what you said so I removed R 3.0.1 and I installed R-2.15.3 and I reinstalled supporting and client packages with R CMD INSTALL.

     

    In oracle environment I invoked ORE and loaded comand library(ORE) without problems but when I tried to connect to DB with ore.connect I received this error:

     

    ORA-06522: /opt/oracle/app/oracle/product/11.2.0/db01/lib/librqe.so: undefined symbol: R_Decode2Long

     

    Any idea how to solve ?

     

    Thanks,

     

    Tony

  • 10. Re: update documentation in regard to R-2.13.2
    Sherry LaMonica Journeyer
    Currently Being Moderated

    Hi Tony,

     

    In addition to removing R-3.0.1, installing R-2.15.3 and reinstalling the ORE packages, you will also need to reinstall ORE server on the database server using the install.sh script.  This will resolve the error you are seeing.

     

    Sherry

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