Re: [Rd] R 2.3.0: Use of NULL as an environment is deprecated
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
> > day24
> > svn rev37909
> > 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 <[EMAIL PROTECTED]>
> > Maintainer: Bernhard Pfaff <[EMAIL PROTECTED]>
> > 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 <[EMAIL PROTECTED]>
> > Maintainer: Martin Maechler <[EMAIL PROTECTED]>
> > 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
> >
Re: [Rd] R 2.3.0: Use of NULL as an environment is deprecated
> "BernPf" == Pfaff, Bernhard Dr <[EMAIL PROTECTED]> > on Wed, 26 Apr 2006 08:28:34 +0100 writes: BernPf> Dear Andy, Uwe and remaining list subscribers, BernPf> now, coming closer to the evil's root. Yesterday, I source compiled on a BernPf> Linux box at home and the result is the same behaviour as pointed out BernPf> below. This is regardless of the package version of 'urca'. Aside of BernPf> 'urca', other packages that have Imports/Depends entries in the BernPf> DESCRIPTION to packages that are shipped within the standard library of BernPf> R show the warning too, e.g. fMultivar, VLMC, to name but a few. BernPf> I do have set on both OS, i.e. Windows and Linux, a second library tree BernPf> in Renviron.site with R-LIBS. If I comment this out and do a reinstall BernPf> of the packages, i.e. the packages are now installed in the standard BernPf> library, the warning does not show up any longer. Has something changed BernPf> with regard to additional libraries that slipped my notice by upgrading BernPf> to version 2.3.0? I don't think so. I ***NEVER*** install a package into the standard library. We have all CRAN packages in a different library, (and Bioconductor too) and I typically use about 6 library (paths), and I don't have your problem. I only get your warning if I get a version of a package that was installed previous to 2.3.0 (or it's alpha / beta / rc ) versions. BernPf> Is it possible that during startup the environment is handeld/passed BernPf> differently for standard and additional libraries? Would this odd BernPf> behaviour qualify as a bug? If it was general, yes, but I think it's not. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 2.3.0: Use of NULL as an environment is deprecated
> "BernPf" == Pfaff, Bernhard Dr <[EMAIL PROTECTED]>
> on Wed, 26 Apr 2006 08:28:34 +0100 writes:
BernPf> Dear Andy, Uwe and remaining list subscribers,
BernPf> now, coming closer to the evil's root. Yesterday, I source
compiled on a
BernPf> Linux box at home and the result is the same behaviour as
pointed out
BernPf> below. This is regardless of the package version of 'urca'.
Aside of
BernPf> 'urca', other packages that have Imports/Depends entries in
the
BernPf> DESCRIPTION to packages that are shipped within the standard
library of
BernPf> R show the warning too, e.g. fMultivar, VLMC, to name but a
few.
BernPf> I do have set on both OS, i.e. Windows and Linux, a second
library tree
BernPf> in Renviron.site with R-LIBS. If I comment this out and do a
reinstall
BernPf> of the packages, i.e. the packages are now installed in the
standard
BernPf> library, the warning does not show up any longer. Has
something changed
BernPf> with regard to additional libraries that slipped my notice
by upgrading
BernPf> to version 2.3.0?
I don't think so.
I ***NEVER*** install a package into the standard library.
We have all CRAN packages in a different library,
(and Bioconductor too) and I typically use about 6 library (paths),
and I don't have your problem.
I only get your warning if I get a version of a package that was
installed previous to 2.3.0 (or it's alpha / beta / rc ) versions.
BernPf> Is it possible that during startup the environment is
handeld/passed
BernPf> differently for standard and additional libraries? Would
this odd
BernPf> behaviour qualify as a bug?
If it was general, yes, but I think it's not.
Hello Martin and all others involved in this thread,
thank you very much for your time and patience. After having updated the
packages in the standard library, too, the warning message does indeed
not show up any longer by issuing the command library(urca) and similar
with other packages. Just out of curiosity, I wonder what has changed in
these packages (i.e. nlme, foreign, cluster and VR got updated) from
downloading the '.exe' or the tarball in the official 2.3.0 release up
to now?
Best,
Bernhard
*
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Re: [Rd] Daily package check and --install=no
> Jeff Enos writes: > R-devel, > There has been some confusion on the MatchIt package mailing list on > the meaning of [--install=no] in the comment column of CRAN's > automated package check. > It's my understanding that, at the very least, a package marked like > this will not have its test cases run each night. Are there other > checks that are omitted? > How, if at all, are such install flags related to the parameters one > can pass R CMD check, such as --no-install, --no-test, etc.? '--install=no' indicates that the checks are run with this flag, which is the same as '--no-install': $ R CMD check --help 2>&1 | grep no-install --no-install skip installation and associated tests [This is necessary because MatchIt depends on Zelig which suggests VGAM which is not in any of the standard repositories ...] -k __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 2.3.0: Use of NULL as an environment is deprecated
Pfaff, Bernhard Dr. wrote: >>"BernPf" == Pfaff, Bernhard Dr <[EMAIL PROTECTED]> >>on Wed, 26 Apr 2006 08:28:34 +0100 writes: > > > BernPf> Dear Andy, Uwe and remaining list subscribers, > BernPf> now, coming closer to the evil's root. Yesterday, I source > compiled on a > BernPf> Linux box at home and the result is the same behaviour as > pointed out > BernPf> below. This is regardless of the package version of 'urca'. > Aside of > BernPf> 'urca', other packages that have Imports/Depends entries in > the > BernPf> DESCRIPTION to packages that are shipped within the standard > library of > BernPf> R show the warning too, e.g. fMultivar, VLMC, to name but a > few. > BernPf> I do have set on both OS, i.e. Windows and Linux, a second > library tree > BernPf> in Renviron.site with R-LIBS. If I comment this out and do a > reinstall > BernPf> of the packages, i.e. the packages are now installed in the > standard > BernPf> library, the warning does not show up any longer. Has > something changed > BernPf> with regard to additional libraries that slipped my notice > by upgrading > BernPf> to version 2.3.0? > > I don't think so. > I ***NEVER*** install a package into the standard library. > We have all CRAN packages in a different library, > (and Bioconductor too) and I typically use about 6 library (paths), > and I don't have your problem. > > I only get your warning if I get a version of a package that was > installed previous to 2.3.0 (or it's alpha / beta / rc ) versions. > > BernPf> Is it possible that during startup the environment is > handeld/passed > BernPf> differently for standard and additional libraries? Would > this odd > BernPf> behaviour qualify as a bug? > > If it was general, yes, but I think it's not. > > > Hello Martin and all others involved in this thread, > > thank you very much for your time and patience. After having updated the > packages in the standard library, too, the warning message does indeed > not show up any longer by issuing the command library(urca) and similar > with other packages. Just out of curiosity, I wonder what has changed in > these packages (i.e. nlme, foreign, cluster and VR got updated) from > downloading the '.exe' or the tarball in the official 2.3.0 release up > to now? For sure you got (or still had in front of your R_LIBS path) packages that were compiled for R < 2.3.0! That's it. Very simple. Uwe Ligges > Best, > Bernhard > * > Confidentiality Note: The information contained in this message, > and any attachments, may contain confidential and/or privileged > material. It is intended solely for the person(s) or entity to > which it is addressed. Any review, retransmission, dissemination, > or taking of any action in reliance upon this information by > persons or entities other than the intended recipient(s) is > prohibited. If you received this in error, please contact the > sender and delete the material from any computer. > * __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 2.3.0: Use of NULL as an environment is deprecated
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)
>
> 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.
If you are a maintainer of a package getting this warning, then you
should replace all uses of NULL as an environment by baseenv() (to get
the previous behaviour), or emptyenv() (if you thought env=NULL gave you
an empty environment).
There's really not much a non-maintainer can do about this warning.
Duncan Murdoch
>
> 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: [EMAIL PROTECTED]
> *
> Confidentiality Note: The information contained in this mess...{{dropped}}
>
> __
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[Rd] Large number of linked environments makes save() crash R
Hi,
first, this not a problem originating from me, but it was observed
trying to do similar things with my R.oo package, so I troubleshooted
it and found the following.
On R v2.3.0 (patched), the following will crash R on WinXP sooner or later:
troubleLimit <- 20435;
linkedList <- list(head=new.env());
currEnv <- linkedList$head;
for (kk in 1:(2*troubleLimit)) {
if (kk %% 100 == 0)
print(kk);
nextEnv <- new.env();
assign("nxt", nextEnv, envir=currEnv);
currEnv <- nextEnv;
if (kk > troubleLimit) {
cat("Saving linked list of length ", kk, "...", sep="");
save(linkedList, file="linkedList.RData");
cat("ok\n");
}
}
This gives:
...
[1] 20300
[1] 20400
Saving linked list of length 20436...ok
Saving linked list of length 20437...ok
Saving linked list of length 20438...
and then R crashes/terminates. On my WinXP machine it always happens
at the same number of environments.
I tried the same on R v2.2.0 (sic!) on Unix and there it gave a
segfault a bit after 1 environments. ...and, the purpose of the
example is not to implement linked lists, it to show that you can
torture R to crash.
Cheers
Henrik
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[Rd] Problems after lm(..., qr=FALSE)
The documentation for lm() indicates that the 'qr' component of an lm object is optional. But some functions do not behave well when this component is absent: summary() gives an error and predict() returns all zeroes. Example: > x <- 1:10; y <- x^2 > mm <- lm(y~x, qr=FALSE) > summary(mm) Error in summary.lm(mm) : invalid 'lm' object: no 'terms' nor 'qr' component > predict(mm, newdata=data.frame(x=11:15)) 1 2 3 4 5 0 0 0 0 0 > predict(mm, newdata=data.frame(x=11:15), se=TRUE) Error in qr.R(object$qr) : argument is not a QR decomposition > R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 3.0 year 2006 month 04 day24 svn rev37909 language R version.string Version 2.3.0 (2006-04-24) J. R. M. Hosking __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Large number of linked environments makes save() crash R
I think this is a C stack overflow problem. Probably needs a test added
internally to save().
I could not reproduce this on Linux: I got a C stack overflow that was
caught.
On Wed, 26 Apr 2006, Henrik Bengtsson (max 7Mb) wrote:
> Hi,
>
> first, this not a problem originating from me, but it was observed
> trying to do similar things with my R.oo package, so I troubleshooted
> it and found the following.
>
> On R v2.3.0 (patched), the following will crash R on WinXP sooner or later:
>
> troubleLimit <- 20435;
>
> linkedList <- list(head=new.env());
>
> currEnv <- linkedList$head;
> for (kk in 1:(2*troubleLimit)) {
> if (kk %% 100 == 0)
>print(kk);
> nextEnv <- new.env();
> assign("nxt", nextEnv, envir=currEnv);
> currEnv <- nextEnv;
> if (kk > troubleLimit) {
>cat("Saving linked list of length ", kk, "...", sep="");
>save(linkedList, file="linkedList.RData");
>cat("ok\n");
> }
> }
>
> This gives:
> ...
> [1] 20300
> [1] 20400
> Saving linked list of length 20436...ok
> Saving linked list of length 20437...ok
> Saving linked list of length 20438...
>
> and then R crashes/terminates. On my WinXP machine it always happens
> at the same number of environments.
>
> I tried the same on R v2.2.0 (sic!) on Unix and there it gave a
> segfault a bit after 1 environments. ...and, the purpose of the
> example is not to implement linked lists, it to show that you can
> torture R to crash.
>
> Cheers
>
> Henrik
>
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>
>
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University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [Rd] R, Rcmdr crash on WinXP PRO laptop (PR#8583)
Having the same behaviour with 2.2.1 and 2.2.1 patched, even if R Cmdr is not loaded. It does not appear to be strictly a data import problem. For me the issue appears when trying to open any scripts, although not always. For example, last week it occurred only a couple of times (had R running more or less 24/7), yesterday at least 10 times. The computer is Dell D610, graphics card Ati Mobility Radeon x300, win xp pro sp2. It appears that Rgui is still running, but its not just visible. I suspect it is not the the antivirus or firewall (I am having symantec) because I have not experienced the same with my HP laptop with the same antivirus/firewall installed. Jani Erola [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R, Rcmdr crash on WinXP PRO laptop (PR#8583)
.and the same issue occurs in version 2.3.0 JE __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Minor issue building 2.3.0 under Red Hat Linux 9
Building R 2.3.0 fails under Red Hat 9.0 because ssize_t is not defined in src/modules/internet/sock.h. Inserting #include at the top of this file fixes the problem. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
