Greetings,
I've been trying to upgrade R packages on my Debian Etch
(whose other upgrades I have been cheerfully going along
with as they occur).
When I did, just now:
sudo apt-get dist-upgrade
I got:
Reading package lists... Done
Building dependency tree... Done
Calculating upgrade... Done
The following packages have been kept back:
r-base-core r-cran-boot r-cran-cluster r-cran-codetools
r-cran-kernsmooth r-cran-lattice r-cran-matrix r-cran-mgcv
r-cran-nlme r-cran-rpart r-cran-survival r-cran-vr
r-recommended
0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.
And the same failure to install these R packages occurs when I
try it from the update-manager or from synaptic.
In short, it's not going to upgrade any of those!
I can't find any indication of a reason why it won't upgrade
these, beyond the following message from update-manager:
Some updates require the removal of further software.
Use the function "Mark All Upgrades" of the package manager
"Synaptic" or run "sudo apt-get dist-upgrade" in a
terminal
to update your system completely.
The following upgrades will be skipped:
[Same list as above]
The "Mark All Upgrades" suggestion for synaptic didn't seem
to do anything.
So I'm stuck. Any advice/information/suggestions?
PS: I am *very reluctant* to attempt replacing my Debian Etch
with Debian Lenny (the latest). This system works as it is!
Also, I am not an in-depth expert on how Debian's package
management works.
With thanks,
Ted.
--------------------------------------------------------------------
E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk>
Fax-to-email: +44 (0)870 094 0861
Date: 10-Nov-09 Time: 08:39:56
------------------------------ XFMail ------------------------------
At 08:39 10/11/2009, Ted Harding wrote:>Greetings, >I've been trying to upgrade R packages on my Debian Etch >(whose other upgrades I have been cheerfully going along >with as they occur).I am not sure this is going to be helpful but I only ever upgrade R itself on my etch system on my netbook and have not had any problems so far. I upgraded to R 2.10.0 earlier today and have a working system. I do not do the complete upgrade because it asks for more disc space than I have on the netbook.>When I did, just now: > > sudo apt-get dist-upgrade > >I got: > > Reading package lists... Done > Building dependency tree... Done > Calculating upgrade... Done > The following packages have been kept back: > r-base-core r-cran-boot r-cran-cluster r-cran-codetools > r-cran-kernsmooth r-cran-lattice r-cran-matrix r-cran-mgcv > r-cran-nlme r-cran-rpart r-cran-survival r-cran-vr > r-recommended > 0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded. > >And the same failure to install these R packages occurs when I >try it from the update-manager or from synaptic. > >In short, it's not going to upgrade any of those! > >I can't find any indication of a reason why it won't upgrade >these, beyond the following message from update-manager: > > Some updates require the removal of further software. > Use the function "Mark All Upgrades" of the package manager > "Synaptic" or run "sudo apt-get dist-upgrade" in a terminal > to update your system completely. > > The following upgrades will be skipped: > [Same list as above] > >The "Mark All Upgrades" suggestion for synaptic didn't seem >to do anything. > >So I'm stuck. Any advice/information/suggestions? > >PS: I am *very reluctant* to attempt replacing my Debian Etch >with Debian Lenny (the latest). This system works as it is! >Also, I am not an in-depth expert on how Debian's package >management works. > >With thanks, >Ted. > >-------------------------------------------------------------------- >E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk> >Fax-to-email: +44 (0)870 094 0861 >Date: 10-Nov-09 Time: 08:39:56 >------------------------------ XFMail ------------------------------ > >_______________________________________________ >R-SIG-Debian mailing list >R-SIG-Debian at r-project.org >https://stat.ethz.ch/mailman/listinfo/r-sig-debianMichael Dewey http://www.aghmed.fsnet.co.uk
On Tue, Nov 10, 2009 at 2:39 AM, Ted Harding <Ted.Harding at manchester.ac.uk> wrote:> Greetings, > I've been trying to upgrade R packages on my Debian Etch > (whose other upgrades I have been cheerfully going along > with as they occur).[snip]> > ?The following upgrades will be skipped: > ?[Same list as above] > > The "Mark All Upgrades" suggestion for synaptic didn't seem > to do anything. > > So I'm stuck. Any advice/information/suggestions? >I suppose the easiest first step is to run apt-get with the --verbose option. Here is what I would do (old school approach). Download the deb files in question. they may already be downloaded, in /var/cache/apt somewhere then try to manually install them with "dpkg -i *.deb" The errors you get will be much more informative. My old man opinion has always been that apt-get tries to make this too simple. It is virtually certain that those R debs were built with different shared libraries than you have, and for your system there are no appropriate updates for those shared libraries. So the r packages are held back, but they don't say why. If you don't want to upgrade your system's shared libraries, it may be you can build your own R with the libraries you have. The way to try is to do "apt-get source r" (or whatever the R package is called) to get the source code and debian packaging, and see if you can build packages for your system by running "dpkg-buildpackage -rfakeroot" in the directory where it has downloaded the code. apt-get source will grab the original tarball, the diff file, open the code, patch it, so it is literally waiting there for you to try to build it. And the errors you get there will be very informative. -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas
Ted, On 10 November 2009 at 08:39, (Ted Harding) wrote: | Greetings, | I've been trying to upgrade R packages on my Debian Etch | (whose other upgrades I have been cheerfully going along | with as they occur). | | When I did, just now: | | sudo apt-get dist-upgrade | | I got: | | Reading package lists... Done | Building dependency tree... Done | Calculating upgrade... Done | The following packages have been kept back: | r-base-core r-cran-boot r-cran-cluster r-cran-codetools | r-cran-kernsmooth r-cran-lattice r-cran-matrix r-cran-mgcv | r-cran-nlme r-cran-rpart r-cran-survival r-cran-vr | r-recommended | 0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded. | | And the same failure to install these R packages occurs when I | try it from the update-manager or from synaptic. | | In short, it's not going to upgrade any of those! | | I can't find any indication of a reason why it won't upgrade | these, beyond the following message from update-manager: | | Some updates require the removal of further software. | Use the function "Mark All Upgrades" of the package manager | "Synaptic" or run "sudo apt-get dist-upgrade" in a terminal | to update your system completely. | | The following upgrades will be skipped: | [Same list as above] | | The "Mark All Upgrades" suggestion for synaptic didn't seem | to do anything. | | So I'm stuck. Any advice/information/suggestions? Use a different command if the one you currently use hides information from you, so try 'sudo apt-get install r-base-core'. That _will_ show the cause, and you _still_ have a chance to back out by saying 'No' to the 'do you really want to do this' question. | PS: I am *very reluctant* to attempt replacing my Debian Etch | with Debian Lenny (the latest). This system works as it is! | Also, I am not an in-depth expert on how Debian's package | management works. You are of course entitled to your very own paranoia. Some people are afraid of the dark, others are afraid of spiders etc pp. Do we consider any of those fears to be reasonable? More seriously, the point of the CRAN backports is _precisely_ to give you current R versions without scaring you and the little children standing behind you as it won't require lenny. Deal? Dirk, who upgrades his Debian testing system daily -- Three out of two people have difficulties with fractions.
On Tue, Nov 10, 2009 at 2:39 AM, Ted Harding <Ted.Harding at manchester.ac.uk> wrote:> Greetings, > I've been trying to upgrade R packages on my Debian Etch > (whose other upgrades I have been cheerfully going along > with as they occur). > > When I did, just now: > > ?sudo apt-get dist-upgrade > > I got: > > ?Reading package lists... Done > ?Building dependency tree... Done > ?Calculating upgrade... Done > ?The following packages have been kept back: > ? ?r-base-core r-cran-boot r-cran-cluster r-cran-codetools > ? ?r-cran-kernsmooth r-cran-lattice r-cran-matrix r-cran-mgcv > ? ?r-cran-nlme r-cran-rpart r-cran-survival r-cran-vr > ? ?r-recommended > ?0 upgraded, 0 newly installed, 0 to remove and 13 not upgraded.Hey, Ted: Did you get to the bottom of this? I got an email responding to my post in this thread that said it seemed I was criticizing the people who make the packages. I didn't mean that at all and I'm sorry. I mean that if there is a mismatch between the libraries you happen to have on your particular system and the "standard" system that the packager is using (and aiming at, doing things correctly), then it can cause the exact problem you are seeing. I also agree with the post which says that you will get more information about the possible library mismatch if you do apt-get upgrade r-base-core Also, as he says, there's a good chance that if you enable the backports repository, there will be a version of the new R for the libraries that might exist in the older Linux. To me, the big uncertainty is whether your system is still in a "standard" state, so that the repository packages will work. If not, you may need to rebuild the packages custom for your system. -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas