From Bernhard_Pfaff at fra.invesco.com  Wed Apr 26 09:28:34 2006
From: Bernhard_Pfaff at fra.invesco.com (Pfaff, Bernhard Dr.)
Date: Wed, 26 Apr 2006 08:28:34 +0100
Subject: [Rd] R 2.3.0: Use of NULL as an environment is deprecated
Message-ID: <E4A9111DA23BA048B9A46686BF727CF403908B@DEFRAXMB01.corp.amvescap.net>

Dear Andy, Uwe and remaining list subscribers,

now, coming closer to the evil's root. Yesterday, I source compiled on a
Linux box at home and the result is the same behaviour as pointed out
below. This is regardless of the package version of 'urca'. Aside of
'urca', other packages that have Imports/Depends entries in the
DESCRIPTION to packages that are shipped within the standard library of
R show the warning too, e.g. fMultivar, VLMC, to name but a few.
I do have set on both OS, i.e. Windows and Linux, a second library tree
in Renviron.site with R-LIBS. If I comment this out and do a reinstall
of the packages, i.e. the packages are now installed in the standard
library, the warning does not show up any longer. Has something changed
with regard to additional libraries that slipped my notice by upgrading
to version 2.3.0?

Is it possible that during startup the environment is handeld/passed
differently for standard and additional libraries? Would this odd
behaviour qualify as a bug?



Best,
Bernhard


From: Uwe Ligges
> 
> Pfaff, Bernhard Dr. wrote:
> 
> > Pfaff, Bernhard Dr. wrote:
> > 
> > 
> >>Pfaff, Bernhard Dr. wrote:
> >>
> >>
> >>
> >>>Dear R-Devel subscriber,
> >>>
> >>>first, let me express my thank to the R-Core team for the new 
> >>>release!
> >>
> >>I
> >>
> >>
> >>>appreciate their efforts and time spent to enhance R.
> >>>In accordance with the 'NEWS' file (see excerpt of it below),
> >>>
> >>>[...
> >>>o	Changed the environment tree to be rooted in an empty
> >>>	environment, available as emptyenv().  baseenv() has been
> >>>	modified to return an environment with emptyenv() as parent,
> >>>	rather than NULL.
> >>>
> >>>...
> >>>
> >>>o	Use of NULL as an environment is deprecated and gives a warning.
> >>>...]
> >>>
> >>>I detected the warning message as announced for a couple of
> >>
> >>contributed
> >>
> >>
> >>>packages, e.g.
> >>>
> >>>library(ape)
> >>>library(car)
> >>>library(chron)
> >>>library(urca)
> >>
> >>
> >>
> >>Not so for me. Are you sure you have reinstalled those 
> packages under
> >>R-2.3.0?
> >>
> >>Uwe Ligges
> >>
> >>
> >>Dear Uwe,
> >>
> >>thank you for your hint. That fixes the warnings for 
> packages 'ape', 
> >>'car' and 'chron' issued formerly. However, even after a 
> fresh install 
> >>the warnings still show up for the packages 'VLMC' and 
> 'urca', as an 
> >>example. Any further clues are most welcome.
> > 
> > 
> > 
> > OS? R release?
> > 
> > and please report the result of
> > 
> >    packageDescription("urca")
> >    packageDescription("VLMC")
> > 
> > Uwe Ligges
> > 
> > 
> > Hello Uwe,
> > 
> > here is the detailed information:
> > 
> > 
> > 
> >>R.version
> > 
> >                _                         
> > platform       i386-pc-mingw32           
> > arch           i386                      
> > os             mingw32                   
> > system         i386, mingw32             
> > status                                   
> > major          2                         
> > minor          3.0                       
> > year           2006                      
> > month          04                        
> > day            24                        
> > svn rev        37909                     
> > language       R                         
> > version.string Version 2.3.0 (2006-04-24)
> > 
> > 
> > Package: urca
> > Version: 0.9-2
>               ^^^
> > Date: 2006-02-25
> > Title: Unit root and cointegration tests for time series data
> > Author: Bernhard Pfaff <bernhard.pfaff at pfaffikus.de>
> > Maintainer: Bernhard Pfaff <bernhard at pfaffikus.de>
> > Depends: R (>= 2.0.0)
> > Imports: nlme, methods, graphics, stats
> > LazyLoad: yes
> > Description: Unit root and cointegration tests encountered 
> in applied
> >         econometric analysis are implemented.
> > License: GPL version 2 or newer
> > URL: http://www.r-project.org
> > Packaged: Sat Feb 25 19:34:29 2006; bp
> > Built: R 2.3.0; ; 2006-03-03 21:12:31; windows
>                           ^^^^^
> 
> Well, 0.9-3 is on CRAN, so you have *not* upgraded your *own* 
> package!!!
> 
> Please upgrade ALL your packages and re-install also ALL 
> those that are 
> from prior R releases.

The problem could be the mirror site:  Some sites are not as up-to-date
as
others.

Andy


 
> Uwe Ligges
> 
> 
> 
> 
> 
> 
> > -- File: C:/R/package/urca/DESCRIPTION
> > 
> > 
> > 
> > 
> >>packageDescription("VLMC")
> > 
> > Package: VLMC
> > Version: 1.3-9
> > Note: ===== vlmc.version in R/vlmc.R
> > Date: 2005-10-06
> > Author: Martin Maechler <maechler at stat.math.ethz.ch>
> > Maintainer: Martin Maechler <maechler at stat.math.ethz.ch>
> > Title: VLMC -- Variable Length Markov Chains
> > Description: Functions, Classes & Methods for estimation, 
> prediction,
> >         and simulation (bootstrap) of VLMC -- Variable Length Markov
> >         Chain -- Models
> > Depends: stats, MASS
> > License: GPL version 2 or later
> > Packaged: Thu Oct 6 15:00:09 2005; maechler
> > Built: R 2.3.0; i386-pc-mingw32; 2006-03-03 19:04:48; windows
> > 
> > -- File: C:/R/package/VLMC/DESCRIPTION
> > 
> > Both packages have Depends/Imports directives in their DESCRIPTION 
> > files. Now, I do get the following for VLMC if I do a 
> 'library(MASS)'
> > first:
> > 
> > 
> >>library(MASS)
> > 
> > Warning message:
> > Verwendung der NULL Umgebung ist veraltet
> > 
> >>library(VLMC)
> >>
> > 
> > 
> > and likewise for urca:
> > 
> > 
> >>library(nlme)
> > 
> > Warning message:
> > Verwendung der NULL Umgebung ist veraltet
> > 
> >>library(urca)
> >>
> > 
> > 
> > 
> > 
> > 
> >>Best,
> >>Bernhard
> >>
> >>
> >>
> >>>Now, I am wondering what would be a suitable/elegant way 
> to fix the 
> >>>packages' code such that the warning does not appear any 
> longer. I am 
> >>>adressing this question to R-devel, because this might also be of 
> >>>interest for other package mainatiners.
> >>>
> >>>Many thanks in advance for any hints and pointers.
> >>>
> >>>Regards,
> >>>Bernhard
> >>>
> >>>
> >>>
> >>>
> >>>Dr. Bernhard Pfaff
> >>>Global Structured Products Group
> >>>(Europe)
> >>>
> >>>Invesco Asset Management Deutschland GmbH
> >>>Bleichstrasse 60-62
> >>>D-60313 Frankfurt am Main
> >>>
> >>>Tel: +49(0)69 298 07230
> >>>Fax: +49(0)69 298 07178
> >>>Email: bernhard_pfaff at fra.invesco.com
> >>>*****************************************************************
> >>>Confidentiality Note: The information contained in this
> >>
> >>mess...{{dropped}}
> >>
> >>
> >>>______________________________________________
> >>>R-devel at r-project.org mailing list 
> >>>https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >>
> > 
> > ______________________________________________
> > R-devel at r-project.org mailing list 
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> ______________________________________________
> R-devel at r-project.org mailing list 
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> 


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[Rd] R 2.3.0: Use of NULL as an environment is deprecated
Pfaff, Bernhard Dr.