[R-sig-Debian] errors upgrading to 2.4.1-1~sargecran1
Johannes Ranke
jranke at uni-bremen.de
Tue Jan 30 17:18:41 CET 2007
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]:
> 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,
Did you use aptitude or apt-get? I have close to no experience with
aptitude, but it seems you continued with apt-get anyways.
> 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:
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.
> 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
^^^^^^^^^^^^^^^^^^^^^^
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?
> 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):
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
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