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

[Simon Blomberg]

Dirk Eddelbuettel wrote:
> On 15 June 2006 at 15:26, Simon Blomberg wrote:
> | 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.
>
> r-recommended is 'virtual'. It will not pull newer version of the underlying
> things in.
>  
> apt-get dist-upgrade, on the other hand, should.
>   
Thanks Dirk. I tried that, but still the same error messages, and the 
same problem. I also tried updating ESS, but still no luck. I am using 
ESS 5.2.10.

Thanks,

Simon.
> Hth, Dirk
>
> | 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
> | 
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