10 Replies Latest reply: Oct 16, 2013 11:47 AM by Sherry Lamonica-Oracle RSS

    update documentation in regard to R-2.13.2

    1003974
      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-Oracle
          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

            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-Oracle

              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

                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-Oracle

                  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

                    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-Oracle

                      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

                        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-Oracle

                          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