Connection to Oracle DB failing from R

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Connection to Oracle DB failing from R

Bogaso
Hi,

I am trying to establish a connection to a Oracle DB from R and used below
code which is failing every time I try -

> library(RJDBC)
Loading required package: DBI
> jdbcDriver =JDBC("oracle.jdbc.OracleDriver",classPath="ojdbc5.jar")

 *** caught segfault ***
address 0x854961, cause 'memory not mapped'

Traceback:
 1: .jinit(classPath)
 2: JDBC("oracle.jdbc.OracleDriver", classPath = "ojdbc5.jar")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:


Below is my session info -

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6

Matrix products: default
BLAS:
 /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] C/UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] RJDBC_0.2-8  DBI_1.1.0    rJava_0.9-13

loaded via a namespace (and not attached):
[1] compiler_4.0.2

I downloaded the JAR file from
https://www.oracle.com/database/technologies/jdbcdriver-ucp-downloads.html

Can you please help me to understand why it is failing?

        [[alternative HTML version deleted]]

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Re: Connection to Oracle DB failing from R

R help mailing list-2
> On Aug 31, 2020, at 6:55 AM, Christofer Bogaso <[hidden email]> wrote:
>
> Hi,
>
> I am trying to establish a connection to a Oracle DB from R and used below
> code which is failing every time I try -
>
>> library(RJDBC)
> Loading required package: DBI
>> jdbcDriver =JDBC("oracle.jdbc.OracleDriver",classPath="ojdbc5.jar")
>
> *** caught segfault ***
> address 0x854961, cause 'memory not mapped'
>
> Traceback:
> 1: .jinit(classPath)
> 2: JDBC("oracle.jdbc.OracleDriver", classPath = "ojdbc5.jar")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
>
> Below is my session info -
>
>> sessionInfo()
> R version 4.0.2 (2020-06-22)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS Catalina 10.15.6
>
> Matrix products: default
> BLAS:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
> LAPACK:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>
> locale:
> [1] C/UTF-8/C/C/C/C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] RJDBC_0.2-8  DBI_1.1.0    rJava_0.9-13
>
> loaded via a namespace (and not attached):
> [1] compiler_4.0.2
>
> I downloaded the JAR file from
> https://www.oracle.com/database/technologies/jdbcdriver-ucp-downloads.html
>
> Can you please help me to understand why it is failing?


Hi,

I am copying Simon here, as he is the package author/maintainer for RJDBC.

Typically, segfault's can indicate some kind of version mismatch in the components that have been installed.

Since there are multiple pieces to this installation, between the packages and the underlying Java installation on your Mac, I would defer to Simon's more intimate knowledge here.

In searching for related issues, I noted some other posts on multiple OSs, and some issues raised on Simon's Github repo for the package.

Also, I am torn between suggesting that this be re-posted to r-sig-db, which is specific to R and database interfaces, and r-sig-mac, which is specific to R on macOS.

However, I will defer to Simon on how he might prefer to handle follow up discussion on your issue.

Regards,

Marc Schwartz

______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: Connection to Oracle DB failing from R

R help mailing list-2
In reply to this post by Bogaso
Which version of java do you have installed?  Oracle's web site says
ojdbc5.jar is for Java 1.5 and ojdbc6.jar is for more recent versions.

Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Mon, Aug 31, 2020 at 3:56 AM Christofer Bogaso
<[hidden email]> wrote:

>
> Hi,
>
> I am trying to establish a connection to a Oracle DB from R and used below
> code which is failing every time I try -
>
> > library(RJDBC)
> Loading required package: DBI
> > jdbcDriver =JDBC("oracle.jdbc.OracleDriver",classPath="ojdbc5.jar")
>
>  *** caught segfault ***
> address 0x854961, cause 'memory not mapped'
>
> Traceback:
>  1: .jinit(classPath)
>  2: JDBC("oracle.jdbc.OracleDriver", classPath = "ojdbc5.jar")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
>
> Below is my session info -
>
> > sessionInfo()
> R version 4.0.2 (2020-06-22)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS Catalina 10.15.6
>
> Matrix products: default
> BLAS:
>  /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
> LAPACK:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>
> locale:
> [1] C/UTF-8/C/C/C/C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] RJDBC_0.2-8  DBI_1.1.0    rJava_0.9-13
>
> loaded via a namespace (and not attached):
> [1] compiler_4.0.2
>
> I downloaded the JAR file from
> https://www.oracle.com/database/technologies/jdbcdriver-ucp-downloads.html
>
> Can you please help me to understand why it is failing?
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: Connection to Oracle DB failing from R

Bogaso
Hi,

The Java version below. Let me know if any other information is
required. Thanks,

java -version
java version "1.8.0_201"
Java(TM) SE Runtime Environment (build 1.8.0_201-b09)
Java HotSpot(TM) 64-Bit Server VM (build 25.201-b09, mixed mode)


On Mon, Aug 31, 2020 at 8:21 PM William Dunlap <[hidden email]> wrote:

>
> Which version of java do you have installed?  Oracle's web site says
> ojdbc5.jar is for Java 1.5 and ojdbc6.jar is for more recent versions.
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Mon, Aug 31, 2020 at 3:56 AM Christofer Bogaso
> <[hidden email]> wrote:
> >
> > Hi,
> >
> > I am trying to establish a connection to a Oracle DB from R and used below
> > code which is failing every time I try -
> >
> > > library(RJDBC)
> > Loading required package: DBI
> > > jdbcDriver =JDBC("oracle.jdbc.OracleDriver",classPath="ojdbc5.jar")
> >
> >  *** caught segfault ***
> > address 0x854961, cause 'memory not mapped'
> >
> > Traceback:
> >  1: .jinit(classPath)
> >  2: JDBC("oracle.jdbc.OracleDriver", classPath = "ojdbc5.jar")
> >
> > Possible actions:
> > 1: abort (with core dump, if enabled)
> > 2: normal R exit
> > 3: exit R without saving workspace
> > 4: exit R saving workspace
> > Selection:
> >
> >
> > Below is my session info -
> >
> > > sessionInfo()
> > R version 4.0.2 (2020-06-22)
> > Platform: x86_64-apple-darwin17.0 (64-bit)
> > Running under: macOS Catalina 10.15.6
> >
> > Matrix products: default
> > BLAS:
> >  /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
> > LAPACK:
> > /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
> >
> > locale:
> > [1] C/UTF-8/C/C/C/C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] RJDBC_0.2-8  DBI_1.1.0    rJava_0.9-13
> >
> > loaded via a namespace (and not attached):
> > [1] compiler_4.0.2
> >
> > I downloaded the JAR file from
> > https://www.oracle.com/database/technologies/jdbcdriver-ucp-downloads.html
> >
> > Can you please help me to understand why it is failing?
> >
> >         [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.