Michael Friendly
2007-Jan-30 15:09 UTC
[R-sig-Debian] errors upgrading to 2.4.1-1~sargecran1
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
Johannes Ranke
2007-Jan-30 16:18 UTC
[R-sig-Debian] errors upgrading to 2.4.1-1~sargecran1
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 > > _______________________________________________ > R-SIG-Debian mailing list > R-SIG-Debian at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian-- 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