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

[Dirk Eddelbuettel]

On 19 June 2006 at 10:53, Simon Blomberg wrote:
| 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.

Try upgrading ESS -- here is what I get on my Debian testing system (with
ess-5.3.0-1, but still r-base-core-2.3.0-1) now that I am back at home:

   > if(!exists("baseenv", mode="function")) baseenv <- function() NULL
   options(STERM='iESS', editor='emacsclient')
   > > 

As you can see, ESS adds some code to catch the change in baseenv. That ought
to fix the issue for you. Let us know if that works.

Dirk


| 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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| > | R-SIG-Debian at r-project.org
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| >
| >   
| 

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