errors upgrading to 2.4.1-1~sargecran1

Tue, Jan 30, 2007 8:18 AM

Hi Michael,

I don't exactly understand the sequence of actions that you have taken,
but I am commenting on what I can understand from the output you
supplied:

* Michael Friendly <friendly at yorku.ca> [070130 16:30]:

Did you use aptitude or apt-get? I have close to no experience with
aptitude, but it seems you continued with apt-get anyways.

Why are so many packages kept back? If you only have a source for Debian
stable in your /etc/apt/sources.list it would be safe to do an apt-get
dist-upgrade, which will also upgrade packages that require additional
dependencies to be removed or installed.

^^^^^^^^^^^^^^^^^^^^^^
Maybe this is a source of troubles, that these old packages are being
held back. I assume you were already running the 2.4.0 backports from
CRAN?

Somehow the process is trying to install r-cran-survival from stable.
This makes me wonder if you added the CRAN repository to your
/etc/apt/sources.list as described in the Debian README

	http://probability.ca/bin/linux/debian/README

In your case you could use

	deb http://probability.ca/bin/linux/debian	sarge/

to use one of the Canadian mirrors. It would be helpful to see 
your /etc/apt/sources.list for further diagnosis, if required.

Best regards,

Johannes Ranke

trying to overwrite `/usr/lib/R/library/survival/NAMESPACE', which is 
also in package r-recommended
dpkg-deb: subprocess paste killed by signal (Broken pipe)
Selecting previously deselected package r-cran-boot.
Unpacking r-cran-boot (from .../r-cran-boot_1.2.22-1_all.deb) ...
dpkg: error processing 
/var/cache/apt/archives/r-cran-boot_1.2.22-1_all.deb (--unpack):
  ... [snipped] ...

But, now I'm trying to upgrade other packages with install.packages(), 
as root, in R, and I get other errors I don't know how to solve:

#> R
R version 2.4.1 (2006-12-18)
Copyright (C) 2006 The R Foundation for Statistical Computing
 ...
 install.packages("vcd")
Warning in install.packages("vcd") : argument 'lib' is missing: using 
/usr/local/lib/R/site-library
--- Please select a CRAN mirror for use in this session ---
 ...
trying URL 'http://probability.ca/cran/src/contrib/vcd_1.0-2.tar.gz'
Content type 'application/x-tar' length 1068008 bytes
opened URL
==================================================
downloaded 1042Kb

* Installing *source* package 'vcd' ...
** R
** data
**  moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
Loading required package: MASS
Error in `parent.env<-`(`*tmp*`, value = NULL) :
        use of NULL environment is defunct
Error: package 'MASS' could not be loaded
Execution halted
ERROR: lazy loading failed for package 'vcd'
** Removing '/usr/local/lib/R/site-library/vcd'
** Restoring previous '/usr/local/lib/R/site-library/vcd'

The downloaded packages are in
        /tmp/RtmpvsdZyG/downloaded_packages
Warning message:
installation of package 'vcd' had non-zero exit status in: 
install.packages("vcd")

Can someone help?

thanks,
-Michael

-- 
Michael Friendly     Email: friendly at yorku.ca 
Professor, Psychology Dept.
York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street    http://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT  M3J 1P3 CANADA

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Dr. Johannes Ranke                 jranke at uni-bremen.de     Key ID: F649AF90
UFT Bremen, Leobenerstr. 1         +49 421 218 8971
D-28359 Bremen                     http://www.uft.uni-bremen.de/chemie/ranke

errors upgrading to 2.4.1-1~sargecran1

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