Re: [Rd] R 2.3.0: Use of NULL as an environment is deprecated

From: Pfaff, Bernhard Dr. <Bernhard_Pfaff_at_fra.invesco.com>
Date: Wed 26 Apr 2006 - 07:28:34 GMT


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@pfaffikus.de>
> > Maintainer: Bernhard Pfaff <bernhard@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@stat.math.ethz.ch>
> > Maintainer: Martin Maechler <maechler@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@fra.invesco.com
> >>>*****************************************************************
> >>>Confidentiality Note: The information contained in this
> >>
> >>mess...{{dropped}}
> >>
> >>
> >>>______________________________________________
> >>>R-devel@r-project.org mailing list
> >>>https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >>
> >
> > ______________________________________________
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
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>
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