Hannes Mühleisen | 24 Feb 11:16 2013
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MonetDB.R connector

Hello everybody,

We would like to announce the immediate availability of the first native connector for the open source
database MonetDB [1] in R.  The connector is available on CRAN [2] and implements the R DBI [3]. MonetDB is
particularly suited to support statistics due to its column-oriented storage model that allows fast
bulk operations. 

We invite everybody to try this combination and are looking forward to your feedback.

Best,

Hannes Mühleisen

[1] http://www.monetdb.org
[2] http://cran.r-project.org/web/packages/MonetDB.R/index.html
[3] http://cran.r-project.org/web/packages/DBI/index.html
	[[alternative HTML version deleted]]

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McGehee, Robert | 12 Feb 16:05 2013

PostgreSQL killed on dbDisconnect (RPostgreSQL)

Hi,
Has anyone had an issue where a PostgreSQL connection was forcibly killed (SIGKILL) by RPostgreSQL,
causing a full database crash/recovery/restart? 

This seems to happen about twice a week when a RPostgreSQL connection is closed using dbDisconnect (or when
an R session ends) while other queries are running. The Linux OOM killer is not enabled on this server and I
can find no evidence of hardware problems or any evidence of problems with the PostgreSQL database. This
left me to wonder if there was a problem with the way RPostgreSQL (or R) disconnects that causes the
database crash.

I generally interface with RPostgreSQL inside a function like this:

FUN <- function() {
	conn <- dbConnect(dbDriver("PostgreSQL"), host="xx", user="xx", password="xx", dbname="xx")
	on.exit(dbDisconnect(conn), add=TRUE)
	dbGetQuery("SELECT 1;", conn=conn)
}

I found record of a similar problem with the RpgSQL package here (from 2009):
https://stat.ethz.ch/pipermail/r-help/2009-January/184707.html
which indicates that dbDisconnect() caused a crash under similar circumstances in RpgSQL. However, in
this case there was a crash in R; in my case there is a crash in PostgreSQL (and it's a different package).

Has anyone else had a problem like this with RPostgreSQL or know if it is even possible for RPostgreSQL to
send a SIGKILL signal to a PostgreSQL connection? I'm reluctant to remove dbDisconnect everywhere, as I
don't want zombie connections accumulating. Also, I'm not the only user of the database.

Thanks, Robert

_______________________________________________
(Continue reading)

Jim Porzak | 23 Jan 20:08 2013
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RpgSQL/RJDBC(?) on R15.2(64) Win7 throws can't find .verify.JDBC.result

All, I see:

> options(RpgSQL.user = "tableau", RpgSQL.password = "******",
+         RpgSQL.host = "10.8.0.1", RpgSQL.port = 5432,
+         RpgSQL.JAR = "C:/Drivers/JDBC")
>
> library(RpgSQL)                                  ## Version: 0.1-6
Loading required package: RJDBC           ## Version: 0.2-1
Loading required package: DBI                ## Version: 0.2-5
Loading required package: rJava              ## Version: 0.9-3

> con <- dbConnect(pgSQL(), dbname = "bidata_pg")
Error in .local(drv, ...) : could not find function ".verify.JDBC.result"

The above works just fine with R14.2 & prior versions of PpgSQL & RJDBC.

I noticed H2 user had a similar error which they worked around by
rolling back to RJDBC 0.2-0
I tried hacking a roll-back using files from my 14.2 install but that
didn't work.
I did not see any window binaries for RJDBC 0.2-0

Suggestions?

Jim Porzak
Minted.com
San Francisco, CA
www.linkedin.com/in/jimporzak
use R! Group SF: www.meetup.com/R-Users/

(Continue reading)

norbert hoeller | 3 Dec 13:02 2012
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Re: ROracle 1.1-5 and date fields?

Hi Don,

i ran into the same error.

A post on stackoverflow was inspiring:

http://stackoverflow.com/questions/7678485/oracle-ora-01805-on-oracle-11g-database

So I  upgraded the timezone-version, and now i, too, can read these
pretty dates when using "ROracle"...

In short, what i did, to the good old database [as SYS-user]:

select version from v$timezone_file;
/*
   VERSION
----------
        11
*/
--- so, i upgraded to (the latest) TZ-version 14:
--- You have to be in Migrate-mode to run  dbms_dst.begin_upgrade, so first

shutdown immediate
---- and then
startup migrate;

begin
 dbms_dst.begin_upgrade(new_version => 14);
end;
/
(Continue reading)

Muhammad Abuizzah | 1 Dec 18:54 2012
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RODBC drop work without Error Message

I have a large database on sql Server 2012 Developers edition, some tables are upto 10GB in size,  I have
been connecting fine to the database and extracting info.  
today was the first time I tried to pull 1/2 gb in one query, nothing fancy a query that always worked with
smaller size.

R dropped the work without providing an error message.  I got the "sand clock" running for a couple of
seconds, as if R had stared communication with the database, but 
then nothing. I looked at my windows task manger, and CPU utilization was at zero.

I ran memory.size() function to confirm availability of memory and it read 24 thousand I don't remember the
rest, I have 24GBs of ram on my computer.  the size of the other R objects in memory was around 2GB

Are there any known issues between RODBC and SQLServer?

thanks

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Marc Schwartz | 1 Dec 16:28 2012

Re: remote connection to an Oracle database - using RODBC

Hi Raff,

Based upon the reply from Actual Tech below, you should definitely remove the XML file name from the Setup
File entry in the driver configuration. 

I did not see an indication in your communication with them below that you specifically mentioned the need
for Kerberos based authentication, which would be a critical omission in the interaction with them, if
so. :-)

From a search this morning, if my read is correct, it would seem that the Kerberos authentication needs to be
supported in the ODBC driver, so that the authentication process is transparent to the calling program
(eg. R/RODBC). Looking through some sites that I found, there are options in the DSN configuration in ODBC
Manager that support Oracle Advanced Security. You may need to confirm the correct settings with your
SysAdmin/DBAdmin for Kerberos on your Oracle server.

1. Go into ODBC Manager and select the DSN configuration for your Oracle server. 

2. On the initial page ("Introduction"), select Continue. 

3. That will bring you to a page where you "Enter the data source name". Be sure that information is correct
and then press Continue.

4. On the next page ("Select the database"), select "Advanced Options".  That will bring up a dialog window
where you can select "Use Oracle Advanced Security". Once you select that, you can then enter the
additional parameters for Encryption and Checksum. Once you do that with the correct parameters, press OK.

5. That should then bring you to a "Conclusion" window. On the bottom of that window will be a Test button,
which you should press. You should then be prompted for  username and password information. Then press OK,
which should then bring up a test results window with information on success/failure. If successful,
then press OK and you will be returned to the Conclusion window and you are done.
(Continue reading)

sasidhar M | 30 Nov 11:40 2012
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oracle database connection issue from R in Linux

Hi,

This is sasi.
I installed R 64 bit and oracle client 64 bit in fedora 17. After R is
working fine. Oracle database also working fine. but problem is, If i try
to connect oracle from R its not connecting.
So, pls guide me how to connect from R to oracle.

how, i tried:--

odbcinst.ini file code is

[ORACLE2]
Description = oracle driver
Driver = /ibexis/app/oracle/product/11.2.0/db_1/lib/libsqora.so.11.1
DontDLClose = 1
FileUsage = 1
UsageCount = 1

I tried in R ...
>library(RODBC)
>con <- odbcConnect("data source name", uid="username", pwd="password")

after this line i got error,

> odbcConnect("india", uid="data_quality", pwd="data_quality")
[1] -1
Warning messages:
1: In odbcDriverConnect("DSN=india;UID=data_quality;PWD=data_quality") :
  [RODBC] ERROR: state 01000, code 0, message [unixODBC][Driver
(Continue reading)

Tomas Lanczos | 29 Nov 16:32 2012
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Problems with the RPostgreSQL package compilation


  Hello,

  I am trying to install RPostgreSQL, but without success at the moment,
getting an errormessage - see below.
  My OS is Fedora 17, R version 2.15.2, PostgreSQL 9.2.1 with Postgis
2.0.1 spatial extension. I installed libpqxx 4.0.0 and its devel
tools also.

  Thank You for any help, advice or hint in advance.

  Regards

  Tomas

 
  install.packages("RPostgreSQL", dependencies=TRUE)
  trying URL 'http://cran.fyxm.net/src/contrib/RPostgreSQL_0.3-3.tar.gz'
  Content type 'application/x-gzip' length 474570 bytes (463 Kb)
  opened URL
  ==================================================
  downloaded 463 Kb

  * installing *source* package ‘RPostgreSQL’ ...
  ** package ‘RPostgreSQL’ successfully unpacked and MD5 sums checked
  checking for gcc... gcc
  checking for C compiler default output file name... a.out
  checking whether the C compiler works... yes
  checking whether we are cross compiling... no
  checking for suffix of executables...
(Continue reading)

Paul Gilbert | 28 Nov 18:17 2012
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problems with RPostgreSQL compilation


(moved from R-help)

You should get better help with this on R-SIG-DB. It seems you need some 
additional hint to help the loader find pg.
Paul

On 12-11-28 06:00 AM, r-help-request@... wrote:
> Date: Thu, 22 Nov 2012 12:15:18 +0100
> From: Tomas Lanczos<lanczos@...>
> To:r-help@...
> Subject: Re: [R] problems with RPostgreSQL compilation
> Message-ID: <1353582918.3021.12.camel <at> freya>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank You for Your answer.I have installed libpqxx 4.0.0 and its devel
> tools also.
>
> Regards
>
> Tomas
>
>
> On Thu, 2012-11-22 at 19:32 +0900, Pascal Oettli wrote:
>> >Hello,
>> >
>> >Do you have the shared libraries required by PostgreSQL installed on
>> >your machine (libpq)?
>> >
>> >Regards,
(Continue reading)

MacQueen, Don | 16 Nov 20:11 2012

ROracle 1.1-5 and date fields?

I updated R and packages today, and am seeing some changes in ROracle
behavior that I want to ask about. I'll describe the problems first;
details follow.

1) dbListTables now lists only my personal tables
previously it listed global tables
(don't see any way to show an example of this)

2) simple queries to tables with date fields fail.
For example,

> dbGetQuery(con,"select * from wdrstats")
Error in .oci.GetQuery(conn, statement, ...) :
  Error in try({ : ORA-01805: possible error in date/time operation

The table in this example has, among others, two date fields.
That is, "describe wdrstats;" returns (among others)
EFFDATE             DATE
ENTERED   NOT NULL  DATE
By the way, I'm very happy to see that ROracle is being actively
maintained. Thank you!

Thanks
-Don

-------------------------------
This was a substantial upgrade; previously I had
  ROracle 0.5-12 with R 2.14.1
now I have
  ROracle 1.1-5 and R 2.15.2
(Continue reading)

Benjamin Tyner | 11 Nov 05:10 2012
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RJDBC: dbGetQuery works but fetch does not.

Hello,

When using fetch() with RJDBC, I get the error:

   Error in function (classes, fdef, mtable)  :
     unable to find an inherited method for function "fetch", for 
signature "JDBCResult", "missing"

However if I use dbGetQuery instead, it works splendidly. my driverClass 
is com.sybase.jdbc2.jdbc.SybDriver and I'm using:

   R version 2.14.1 (2011-12-22)
   Platform: x86_64-unknown-linux-gnu (64-bit)
   RJDBC_0.2-0
   rJava_0.9-3
   DBI_0.2-5

Any ideas?

Thanks
Ben
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