[R-sig-Debian] errors upgrading to 2.4.1-1~sargecran1

[Michael Friendly]

I needed to upgrade to R 2.4.1 from debian stable maintained at 
http://cran.r-project.org/bin/linux/debian/.
and tried to upgrade with apt-get install r-base.  It installed R 2.4.1 
successfully,
but ran into errors while also upgrading r-recommended packages.  I was 
able to
fix that using apt-get install -f

euclid:~# aptitude install r-base
Reading Package Lists... Done
Building Dependency Tree
Reading extended state information
Initializing package states... Done
Reading task descriptions... Done
The following NEW packages will be automatically installed:
r-cran-boot r-cran-cluster r-cran-foreign r-cran-kernsmooth
r-cran-lattice r-cran-mgcv r-cran-nlme r-cran-rpart r-cran-survival
r-cran-vr
The following packages have been kept back:
bind9-host dnsutils ftpd gcc-3.4-base gnupg gv imagemagick info
libapache-mod-php4 libc6 libc6-dev libdns16 libdps1 libg2c0 libgcc1
libgsf-1 libgsf-gnome-1 libice6 libisc7 liblwres1 libmagick6 libncurses5
libncurses5-dev libnspr4 libnss3 libpaper-utils libqt3c102-mt
libreadline5 libsm6 libsoup2.2-7 libx11-6 libxaw7 libxext6 libxft1 libxi6
libxine1 libxmu6 libxmuu1 libxp6 libxpm4 libxrandr2 libxt6 libxtrap6
libxtst6 libxv1 locales mozilla-browser mozilla-firefox mozilla-psm
mozilla-thunderbird openoffice.org openoffice.org-bin
openoffice.org-l10n-en openoffice.org-mimelnk perlmagick php4 php4-common
python2.3 r-base-latex r-doc-pdf readline-common ssh tar texinfo
ttf-opensymbol x-window-system-core xbase-clients xfonts-100dpi
xfonts-75dpi xfonts-base xfonts-scalable xfree86-common xlibmesa-dri
xlibmesa-gl xlibmesa-glu xlibs xlibs-data xserver-common xserver-xfree86
xterm xutils
The following NEW packages will be installed:
r-cran-boot r-cran-cluster r-cran-foreign r-cran-kernsmooth
r-cran-lattice r-cran-mgcv r-cran-nlme r-cran-rpart r-cran-survival
r-cran-vr
The following packages will be upgraded:
r-base r-base-core r-recommended
The following packages are RECOMMENDED but will NOT be installed:
r-base-dev r-base-html
3 packages upgraded, 10 newly installed, 0 to remove and 81 not upgraded.
Need to get 10.0MB/14.8MB of archives. After unpacking 1106kB will be 
freed.
Do you want to continue? [Y/n/?] y
Writing extended state information... Done
Get:1 http://cran.R-project.org stable/ r-base 2.4.1-1~sargecran1 [23.9kB]
Get:2 http://cran.R-project.org stable/ r-recommended 2.4.1-1~sargecran1 
[1948B]
Get:3 http://cran.R-project.org stable/ r-base-core 2.4.1-1~sargecran1 
[9981kB]
Fetched 10.0MB in 2m28s (67.6kB/s)
Selecting previously deselected package r-cran-survival.
(Reading database ... 131466 files and directories currently installed.)
Unpacking r-cran-survival (from .../r-cran-survival_2.17-1_i386.deb) ...
dpkg: error processing 
/var/cache/apt/archives/r-cran-survival_2.17-1_i386.deb (--unpack):
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