Hi, I'm not sure if this is an R problem, a Debian problem, a GNU Emacs problem or an ESS problem. I get the following warning the first time I call help on a command in a session, for example: > ?sessionInfo Warning message: use of NULL environment is deprecated This only occurs in GNU Emacs, not when running R from bash, and not with Xemacs. It started happening when I updated R and a lot of packages to 2.3.1. I checked the archives and found this message: http://tolstoy.newcastle.edu.au/R/devel/06/05/5278.html. My packages are all up-to-date. I tried manually removing a package and re-installing it using install.packages. The install went OK, but it had no effect (the warning still appeared). Any help would be greatly appreciated. I am running the Quantian distro inside a VMware virtual machine, on a Windows XP Pro host. Thanks, Simon. > sessionInfo() Version 2.3.1 (2006-06-01) i386-pc-linux-gnu attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" -- Simon Blomberg, B.Sc.(Hons.), Ph.D, M.App.Stat. Centre for Resource and Environmental Studies The Australian National University Canberra ACT 0200 Australia T: +61 2 6125 7800 email: Simon.Blomberg_at_anu.edu.au F: +61 2 6125 0757 CRICOS Provider # 00120C
Hi again, After some fiddling around, I think that r-recommended is not getting updated properly. I have the following output from apt-get. It looks like there is a problem with file r-recommended_2.3.1-0sarge2_i386.deb Again, any help would be appreciated. Thanks, Simon. root at Quantian:apt-get -f install Reading package lists... 0% Reading package lists... 0% Reading package lists... 2% Reading package lists... Done Building dependency tree... 0% Building dependency tree... 0% Building dependency tree... 50% Building dependency tree... 50% Building dependency tree... 97% Building dependency tree... Done Correcting dependencies... Done The following extra packages will be installed: r-recommended The following packages will be upgraded: r-recommended 1 upgraded, 0 newly installed, 0 to remove and 102 not upgraded. 3 not fully installed or removed. Need to get 0B/6264kB of archives. After unpacking 24.6MB of additional disk space will be used. Do you want to continue [Y/n]? Y WARNING: The following packages cannot be authenticated! r-recommended Install these packages without verification [y/N]? Y W: Couldn't stat source package list http://ndiswrapper.sourceforge.net ./ Packages (/var/lib/apt/lists/ndiswrapper.sourceforge.net_debian_._Packages) - stat (2 No such file or directory) W: Couldn't stat source package list http://kanotix.com ./ Packages (/var/lib/apt/lists/kanotix.com_files_debian_._Packages) - stat (2 No such file or directory) (Reading database ... 325419 files and directories currently installed.) Preparing to replace r-recommended 2.3.0-1 (using .../r-recommended_2.3.1-0sarge2_i386.deb) ... Unpacking replacement r-recommended ... Replacing files in old package r-cran-vr ... Replacing files in old package r-cran-boot ... Replacing files in old package r-cran-cluster ... Replacing files in old package r-cran-foreign ... dpkg: error processing /var/cache/apt/archives/r-recommended_2.3.1-0sarge2_i386.deb (--unpack): trying to overwrite `/usr/lib/R/library/grid/html/00Index.html', which is also in package r-base-html dpkg-deb: subprocess paste killed by signal (Broken pipe) Errors were encountered while processing: /var/cache/apt/archives/r-recommended_2.3.1-0sarge2_i386.deb W: Couldn't stat source package list http://ndiswrapper.sourceforge.net ./ Packages (/var/lib/apt/lists/ndiswrapper.sourceforge.net_debian_._Packages) - stat (2 No such file or directory) W: Couldn't stat source package list http://kanotix.com ./ Packages (/var/lib/apt/lists/kanotix.com_files_debian_._Packages) - stat (2 No such file or directory) W: Couldn't stat source package list http://ndiswrapper.sourceforge.net ./ Packages (/var/lib/apt/lists/ndiswrapper.sourceforge.net_debian_._Packages) - stat (2 No such file or directory) W: Couldn't stat source package list http://kanotix.com ./ Packages (/var/lib/apt/lists/kanotix.com_files_debian_._Packages) - stat (2 No such file or directory) W: You may want to run apt-get update to correct these problems E: Sub-process /usr/bin/dpkg returned an error code (1) Simon Blomberg wrote:> Hi, > > I'm not sure if this is an R problem, a Debian problem, a GNU Emacs > problem or an ESS problem. I get the following warning the first time I > call help on a command in a session, for example: > > > ?sessionInfo > Warning message: > use of NULL environment is deprecated > > This only occurs in GNU Emacs, not when running R from bash, and not > with Xemacs. It started happening when I updated R and a lot of packages > to 2.3.1. I checked the archives and found this message: > http://tolstoy.newcastle.edu.au/R/devel/06/05/5278.html. My packages are > all up-to-date. I tried manually removing a package and re-installing it > using install.packages. The install went OK, but it had no effect (the > warning still appeared). Any help would be greatly appreciated. > > I am running the Quantian distro inside a VMware virtual machine, on a > Windows XP Pro host. > > Thanks, > > Simon. > > > sessionInfo() > Version 2.3.1 (2006-06-01) > i386-pc-linux-gnu > > attached base packages: > [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" > [7] "base" > >-- Simon Blomberg, B.Sc.(Hons.), Ph.D, M.App.Stat. Centre for Resource and Environmental Studies The Australian National University Canberra ACT 0200 Australia T: +61 2 6125 7800 email: Simon.Blomberg_at_anu.edu.au F: +61 2 6125 0757 CRICOS Provider # 00120C
On 15 June 2006 at 14:51, Simon Blomberg wrote:
| Hi,
|
| I'm not sure if this is an R problem, a Debian problem, a GNU Emacs
| problem or an ESS problem. I get the following warning the first time I
| call help on a command in a session, for example:
|
| > ?sessionInfo
| Warning message:
| use of NULL environment is deprecated
Howdy from UseR. I think this has to do with a change in R 2.3.* and you may
be out of sync between ess and r-base-core.
| This only occurs in GNU Emacs, not when running R from bash, and not
| with Xemacs. It started happening when I updated R and a lot of packages
| to 2.3.1. I checked the archives and found this message:
ESS adds some initialization code. I can try to compare this when I get
home. An ess upgrade may cure it.
Dirk
| http://tolstoy.newcastle.edu.au/R/devel/06/05/5278.html. My packages are
| all up-to-date. I tried manually removing a package and re-installing it
| using install.packages. The install went OK, but it had no effect (the
| warning still appeared). Any help would be greatly appreciated.
|
| I am running the Quantian distro inside a VMware virtual machine, on a
| Windows XP Pro host.
Quantian,which I'll take about in 10 minutes, is in need of an R upgrade to
2.3.1. Hopefully in the next few weeks...
Dirk
|
| Thanks,
|
| Simon.
|
| > sessionInfo()
| Version 2.3.1 (2006-06-01)
| i386-pc-linux-gnu
|
| attached base packages:
| [1] "methods" "stats" "graphics"
"grDevices" "utils" "datasets"
| [7] "base"
|
| --
| Simon Blomberg, B.Sc.(Hons.), Ph.D, M.App.Stat.
| Centre for Resource and Environmental Studies
| The Australian National University
| Canberra ACT 0200
| Australia
| T: +61 2 6125 7800 email: Simon.Blomberg_at_anu.edu.au
| F: +61 2 6125 0757
| CRICOS Provider # 00120C
|
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian
--
Hell, there are no rules here - we're trying to accomplish something.
-- Thomas A. Edison
Simon Blomberg <blomsp at ozemail.com.au> wrote: [...]> This only occurs in GNU Emacs, not when running R from bash, and not > with Xemacs. It started happening when I updated R and a lot of packages > to 2.3.1. I checked the archives and found this message: > http://tolstoy.newcastle.edu.au/R/devel/06/05/5278.html.Currently, I'm getting the following at startup in my system, whether from Emacs/ESS or a console: ---<---------------cut here---------------start-------------->--- During startup - Warning message: use of NULL environment is deprecated R> if(!exists("baseenv", mode="function")) baseenv <- function() NULL options(STERM='iESS', editor='emacsclient') R> R> sessionInfo() Version 2.3.1 (2006-06-01) i486-pc-linux-gnu attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: chron gmodels lattice "2.3-3" "2.12.0" "0.13-8" ---<---------------cut here---------------end---------------->--- Of the packages showing as attached, only chron is installed in a local library. I've narrowed down the culprit of the warning at startup to gmodels, which I've gotten from r-cran-gmodels, from the unstable distribution. From reading this thread, and the one Simon refers to, is it right to say that there's not much we (as users) can do until the gmodels package maintainer replaces use of the NULL environment in the source? Likewise for other Debian R packages generating the warning when loading them? Cheers, -- Seb