[R] dot - comma problem

Mon May 21 02:18:42 CEST 2012

Thanks for the replies and sorry for the missing information.

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System information:

R version 2.15.0 (2012-03-30)
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-suse-linux-gnu (64-bit)

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Package informations

ODB

>packageDescription("ODB")
Package: ODB
Type: Package
Title: Open Document Databases (.odb) management
Version: 1.0.0
Date: 2011-06-15
Author: Sylvain Mareschal
Maintainer: Sylvain Mareschal <maressyl at gmail.com>
URL: http://www.ovsa.fr/R
Description: This package provides functions to create, connect, update
        and query HSQL databases embedded in Open Document Databases
        (.odb) files, as OpenOffice and LibreOffice do.
License: GPL (>= 3)
LazyLoad: yes
Depends: methods, DBI, RJDBC, XML
SystemRequirements: zip
Packaged: 2011-06-15 19:12:53 UTC; Sylvain
Repository: CRAN
Date/Publication: 2011-06-17 06:44:34
Built: R 2.15.0; ; 2012-04-14 01:59:04 UTC; unix

DBI

> packageDescription("DBI")
Package: DBI
Version: 0.2-5
Title: R Database Interface
Author: R Special Interest Group on Databases (R-SIG-DB)
Maintainer: David A. James <daj025 at gmail.com>
Depends: R (>= 2.3.0), methods
Imports: methods
Description: A database interface (DBI) definition for communication
        between R and relational database management systems.  All
        classes in this package are virtual and need to be extended by
        the various R/DBMS implementations.
LazyLoad: yes
License: LGPL (>= 2)
Collate: DBI.R Util.R zzz.R
Packaged: 2009-12-21 19:58:17 UTC; sfalcon
Repository: CRAN
Date/Publication: 2009-12-22 07:54:43
Built: R 2.15.0; ; 2012-04-14 01:02:50 UTC; unix

RJDBC

> packageDescription("RJDBC")
Package: RJDBC
Version: 0.2-0
Title: Provides access to databases through the JDBC interface
Author: Simon Urbanek <Simon.Urbanek at r-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek at r-project.org>
Depends: methods, DBI, rJava (>= 0.4-15), R (>= 2.4.0)
Description: RJDBC is an implementation of R's DBI interface using JDBC
        as a back-end. This allows R to connect to any DBMS that has a
        JDBC driver.
License: GPL-2
URL: http://www.rforge.net/RJDBC/
Repository: CRAN
Date/Publication: 2011-05-17 04:39:36
Built: R 2.15.0; ; 2012-05-20 22:48:53 UTC; unix

XML

> packageDescription("XML")
Package: XML
Version: 3.8-0
Date: 2012/01/12
Author: Duncan Temple Lang (duncan at wald.ucdavis.edu)
Maintainer: Duncan Temple Lang <duncan at wald.ucdavis.edu>
Title: Tools for parsing and generating XML within R and S-Plus.
Depends: R (>= 1.2.0), methods, utils
Imports: methods
Suggests: bitops
SystemRequirements: libxml2 (>= 2.6.3)
LazyLoad: yes
Description: This package provides many approaches for both reading and
        creating XML (and HTML) documents (including DTDs), both local
        and accessible via HTTP or FTP.  It also offers access to an
        XPath "interpreter".
Note: The versions numbers 1.0 and 2.0 do not have any special
        significance, but are merely the result of incrementing the
        minor count by 1 for each release. Specifically, there is no
        change in the interface.
URL: http://www.omegahat.org/RSXML
License: BSD
Collate: AAA.R DTD.R DTDClasses.R DTDRef.R SAXMethods.S XMLClasses.R
        applyDOM.R assignChild.R catalog.R createNode.R dynSupports.R
        error.R flatTree.R htmlParse.R nodeAccessors.R parseDTD.R
        schema.S summary.R tangle.R toString.S tree.R version.R
        xmlErrorEnums.R xmlEventHandler.R xmlEventParse.R xmlHandler.R
        xmlInternalSource.R xmlOutputDOM.R xmlNodes.R xmlOutputBuffer.R
        xmlTree.R xmlTreeParse.R hashTree.R zzz.R supports.R parser.R
        libxmlFeatures.R xmlString.R saveXML.R namespaces.R
        readHTMLTable.R reflection.R xmlToDataFrame.R bitList.R
        compare.R encoding.R fixNS.R xmlRoot.R serialize.R
        xmlMemoryMgmt.R keyValueDB.R solrDocs.R
Repository: CRAN
Date/Publication: 2012-01-14 09:36:02
Built: R 2.14.1; x86_64-suse-linux-gnu; 2012-01-18 02:23:50 UTC; unix

rJava

> packageDescription("rJava")
Package: rJava
Version: 0.9-3
Title: Low-level R to Java interface
Author: Simon Urbanek <simon.urbanek at r-project.org>
Maintainer: Simon Urbanek <simon.urbanek at r-project.org>
Depends: R (>= 2.5.0), methods
Description: Low-level interface to Java VM very much like .C/.Call and
        friends. Allows creation of objects, calling methods and
        accessing fields.
License: GPL-2
URL: http://www.rforge.net/rJava/
SystemRequirements: java
Repository: CRAN
Date/Publication: 2011-12-11 10:41:33
Built: R 2.15.0; x86_64-suse-linux-gnu; 2012-04-14 01:58:28 UTC; unix

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hints Brain Ripley: "?Sys.setlocale will explain how to undo the damage."

I checked the content of Sys.getlocale() during various stages. Here is the 
result:

1. Stage: Starting R

R version 2.15.0 (2012-03-30)
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-suse-linux-gnu (64-bit)

> > assignInNamespace(".help.ESS",help, ns = asNamespace("base"))
> options(STERM='iESS', str.dendrogram.last ="'", editor='emacsclient')
> a <- Sys.getlocale()
> a
[1] 
"LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C"

2. Stage: Loading package "ODB" and all its dependecies

> library(ODB)
Lade nötiges Paket: DBI
Lade nötiges Paket: RJDBC
Lade nötiges Paket: rJava
Lade nötiges Paket: XML
Warnmeldung:
vorhergehender Import ‘show’ während des Ladens von ‘rJava’ ersetzt 
> b <- Sys.getlocale()
> b
[1] 
"LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8;LC_IDENTIFICATION=C"
> a==b
[1] TRUE

3. Stage: Loading the particular data base:

> db <- odb.open("Test.odb")
> c <- Sys.getlocale()
> c
[1] "de_DE.UTF-8"
> 

Thus, not just loading packages, but loading the data base overwrites the 
setting.

Then

> a <- 1.3
> a
[1] 1,3

with

> Sys.setlocale(category="LC_NUMERIC",locale="C")
[1] "C"
Warnmeldung:
In Sys.setlocale(category = "LC_NUMERIC", locale = "C") :
  das Setzen von 'LC_NUMERIC' kann bewirken, dass R sich komisch benimmt
> a
[1] 1.3

the issue could be solved.

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Hints Milan Bouchet-Valat:

"I recently experienced this with a totally unrelated package. The
culprit turned out to be RWeka (which depends on rJava, like ODB) when
used with Java 7 (on Fedora Linux 17). Can you simply try loading RJDBC
and print a decimal number? Please also check your Java version, and
give us system information as requested by Brian Ripley."

As you see below, simply loading RJDBC did not cause the problem:

R version 2.15.0 (2012-03-30)
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-suse-linux-gnu (64-bit)

> a <- 1.3
> a
[1] 1.3
> library(RJDBC)
Lade nötiges Paket: DBI
Lade nötiges Paket: rJava
Warnmeldung:
vorhergehender Import ‘show’ während des Ladens von ‘rJava’ ersetzt 
> a
[1] 1.3
> 

The java version is

java -version
java version "1.7.0_b147-icedtea"
OpenJDK Runtime Environment (suse-12.2-x86_64)
OpenJDK 64-Bit Server VM (build 22.0-b10, mixed mode)

When I changed to 1.6, the problem stayed the same

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However, the problem did NOT occur on the following machine

System: kubuntu 12.04 64 bit
java: 1.6.0_24
R: 2.14.1
ODB-package: 1.0.0 (as above)
DBI-package: 0.2-5 (as above)
RJDBC-package: 0.2-0 (as above)
XML-package: 3.93-0 (different to above)
rJava-package: 0.9-3 (as above)

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Note that after updating package "XML" to version 3.9-4 under R 2.15 on the 
suse machine, the problem did not disappear

Thanks so far