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

[Dirk Eddelbuettel]

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.

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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