[R-sig-Debian] annoying warnings in ESS/Emacs

[Simon Blomberg]

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