[R-sig-Debian] stable backport apt problem (solved)
Dirk Eddelbuettel
edd at debian.org
Tue May 2 22:19:09 CEST 2006
Robert,
Thanks for the follow-up. Hopefully someone (Christian ?) can pick it up from
here as I don't use or build these backported packages...
On 2 May 2006 at 11:50, Robert King wrote:
| Hi Dirk,
|
| This is my attempt to re-create the problem. I'm not so sure it is just
| a dependency problem now. I think there is possibly an apt problem on
| my machine, combined with a problem with the dependencies where
| r-recommended is wanting its old dependencies at the same time as trying
| to replace them.
|
| I removed all the r-\* packages, removed the backports line from
| /etc/apt/source.list, installed
| r-base-core r-recommended r-base-dev r-mathlib
| which went OK, then added the backport URL to sources.list again:
|
| tolstoy:/home/king# apt-get upgrade
| Reading Package Lists... Done
| Building Dependency Tree... Done
| The following packages have been kept back:
| kernel-image-2.6-686 r-base-dev
| 0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
A little suspicious that r-base-dev is still hanging around...
| tolstoy:/home/king# apt-get install r-base-dev
| Reading Package Lists... Done
| Building Dependency Tree... Done
| Some packages could not be installed. This may mean that you have
| requested an impossible situation or if you are using the unstable
| distribution that some required packages have not yet been created
| or been moved out of Incoming.
|
| Since you only requested a single operation it is extremely likely that
| the package is simply not installable and a bug report against
| that package should be filed.
| The following information may help to resolve the situation:
|
| The following packages have unmet dependencies:
| r-base-dev: Depends: r-base-core (= 2.3.0-0sarge1) but 2.1.0-1 is to
| be installed
| E: Broken packages
Could that be related.
| tolstoy:/home/king# apt-get install r-base-core=2.3.0-0sarge1
| Reading Package Lists... Done
| Building Dependency Tree... Done
| E: Version '2.3.0-0sarge1' for 'r-base-core' was not found
|
| tolstoy:/home/king# apt-cache show r-base-core
| shows the following versions of r-base-core available
|
| Version: 2.1.0-1
| Version: 2.2.1-6
|
| Even though
| /var/lib/apt/lists/cran.au.r-project.org_bin_linux_debian_stable_Packages
| shows version 2.3.0-0sarge1
| and I can download it with wget
Try 'apt-cache policy r-base-core' which will tell you what it knows about
the package and its distributions as well as how it is 'pinned' (ie which
preferences are expressed in terms of stable vs testing vs ..._
| tolstoy:/home/king# grep 'Package: r-base-core' /var/lib/apt/lists/*
| /var/lib/apt/lists/cran.au.r-project.org_bin_linux_debian_stable_Packages:Package:
| r-base-core
| (has Version: 2.3.0-0sarge1)
| /var/lib/apt/lists/ftp.au.debian.org_debian_dists_stable_main_binary-i386_Packages:Package:
| r-base-core
| (has Version: 2.1.0-1)
| /var/lib/apt/lists/ftp.au.debian.org_debian_dists_testing_main_binary-i386_Packages:Package:
| r-base-core
| (has Version: 2.2.1-6)
|
| Even if I remove the testing line from the sources.list, apt-cache and
| apt-get will only see the stable version
|
| Then to the manual-download solution:
|
| # dpkg -i r-base-core_2.3.0-0sarge1_i386.deb
| (Reading database ... 62319 files and directories currently installed.)
| Preparing to replace r-base-core 2.1.0-1 (using
| .../r-base-core_2.3.0-0sarge1_i386.deb) ...
| Unpacking replacement r-base-core ...
| Setting up r-base-core (2.3.0-0sarge1) ...
| Installing new version of config file /etc/R/Makeconf ...
|
| Configuration file `/etc/R/Renviron'
| ==> Modified (by you or by a script) since installation.
| ==> Package distributor has shipped an updated version.
| What would you like to do about it ? Your options are:
| Y or I : install the package maintainer's version
| N or O : keep your currently-installed version
| D : show the differences between the versions
| Z : background this process to examine the situation
| The default action is to keep your current version.
| *** Renviron (Y/I/N/O/D/Z) [default=N] ?
|
| # dpkg -i /nfs/r-mathlib_2.3.0-0sarge1_i386.deb
| (Reading database ... 62472 files and directories currently installed.)
| Preparing to replace r-mathlib 2.1.0-1 (using
| .../r-mathlib_2.3.0-0sarge1_i386.deb) ...
| Unpacking replacement r-mathlib ...
| Setting up r-mathlib (2.3.0-0sarge1) ...
|
| # dpkg -i /nfs/r-recommended_2.3.0-0sarge1_i386.deb
| dpkg: considering removing r-cran-boot in favour of r-recommended ...
| dpkg: no, cannot remove r-cran-boot (--auto-deconfigure will help):
| r-recommended depends on r-cran-boot (>= 1.2.19)
| r-cran-boot is to be removed.
| dpkg: regarding .../r-recommended_2.3.0-0sarge1_i386.deb containing
| r-recommended:
| r-recommended conflicts with r-cran-boot
| r-cran-boot (version 1.2.22-1) is installed.
| dpkg: error processing /nfs/r-recommended_2.3.0-0sarge1_i386.deb
| (--install):
| conflicting packages - not installing r-recommended
| Errors were encountered while processing:
| /nfs/r-recommended_2.3.0-0sarge1_i386.deb
|
| Try auto-deconfigure as recommended:
|
| tolstoy:/home/king# dpkg -i --auto-deconfigure
| /nfs/r-recommended_2.3.0-0sarge1_i386.deb
| dpkg: considering removing r-cran-boot in favour of r-recommended ...
| dpkg: yes, will remove r-cran-boot in favour of r-recommended.
| (Reading database ... 62468 files and directories currently installed.)
| Preparing to replace r-recommended 2.1.0-1 (using
| .../r-recommended_2.3.0-0sarge1_i386.deb) ...
| De-configuring r-recommended, so that we can remove r-cran-boot ...
| Unpacking replacement r-recommended ...
| Replacing files in old package r-cran-kernsmooth ...
| Replacing files in old package r-cran-vr ...
| Replacing files in old package r-cran-cluster ...
| Replacing files in old package r-cran-foreign ...
| Replacing files in old package r-cran-lattice ...
| Replacing files in old package r-cran-mgcv ...
| Replacing files in old package r-cran-nlme ...
| Replacing files in old package r-cran-rpart ...
| Replacing files in old package r-cran-survival ...
| Ignoring deprecated call to build-help.pl from postinst or postrm script.
| More than one copy of package r-recommended has been unpacked
| in this run ! Only configuring it once.
| Setting up r-recommended (2.3.0-0sarge1) ...
|
| tolstoy:/home/king# apt-get -f install
| Reading Package Lists... Done
| Building Dependency Tree... Done
| Correcting dependencies... Done
| The following extra packages will be installed:
| r-base-dev
| The following packages will be REMOVED:
| 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-dev
| 1 upgraded, 0 newly installed, 9 to remove and 1 not upgraded.
| Need to get 0B/2208B of archives.
| After unpacking 19.0MB disk space will be freed.
| Do you want to continue? [Y/n]
| Removing r-cran-kernsmooth ...
| Ignoring deprecated call to build-help.pl from postinst or postrm script.
| Removing r-cran-mgcv ...
| Ignoring deprecated call to build-help.pl from postinst or postrm script.
| Removing r-cran-vr ...
| Ignoring deprecated call to build-help.pl from postinst or postrm script.
| Removing r-cran-nlme ...
| Ignoring deprecated call to build-help.pl from postinst or postrm script.
| Removing r-cran-lattice ...
| Ignoring deprecated call to build-help.pl from postinst or postrm script.
| Removing r-cran-rpart ...
| Ignoring deprecated call to build-help.pl from postinst or postrm script.
| Removing r-cran-survival ...
| Ignoring deprecated call to build-help.pl from postinst or postrm script.
| (Reading database ... 62787 files and directories currently installed.)
| Preparing to replace r-base-dev 2.1.0-1 (using
| .../r-base-dev_2.3.0-0sarge1_all.deb) ...
| Unpacking replacement r-base-dev ...
| Setting up r-base-dev (2.3.0-0sarge1) ...
| tolstoy:/home/king# apt-get install r-base
| Reading Package Lists... Done
| Building Dependency Tree... Done
| Suggested packages:
| ess r-doc-info r-doc-pdf r-doc-html
| Recommended packages:
| r-base-html r-base-latex
| The following NEW packages will be installed:
| r-base
| 0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
| Need to get 0B/22.8kB of archives.
| After unpacking 57.3kB of additional disk space will be used.
| Selecting previously deselected package r-base.
| (Reading database ... 62789 files and directories currently installed.)
| Unpacking r-base (from .../r-base_2.3.0-0sarge1_all.deb) ...
| Setting up r-base (2.3.0-0sarge1) ...
|
Yes, someone will have to work out how the r-recommended 'sumo' package that
Christian builds can safely remove/upgrade/... the individual packages from
an older Debian stable installation.
Regards, Dirk
| Dirk Eddelbuettel wrote:
| > Hi Robert,
| >
| > On 2 May 2006 at 10:03, Robert King wrote:
| > | Hello,
| > |
| > | I started writing this email to describe a problem, then fixed it, so
| > | I'll display my ignorance anyway in case other people have a problem
| > | with it.
| > |
| > | What happened was that I could get apt-get to upgrade the documentation
| > | packages, but not the others.
| > |
| > | What I think was the problem was some remaining r-cran-* packages that
| > | are now in r-recommended. These seemed to be blocking the upgrade of
| > | r-recommended, and hence r-base-core and thus r-base.
| > |
| > | What I did was manually download r-base-core r-base-dev and
| > | r-recommended and install the .debs with dpkg.
| >
| > Hm, sounds like Christian's backported packages need some more finetuning on
| > the Depends/Provides/Conflicts.
| >
| > The more detail you could supply as to "what was blocked how" would
| > presumably help.
| >
| > Dirk
| >
| > | Once this was done apt-get was able to fix the mess.
| > |
| > | Here is some of the output I collected in the process.
| > |
| > | This is the result of dpkg -l r-\* after the apt-get upgrade, which kept
| > | back r-base r-base-dev r-base-core r-recommended
| > |
| > |
| > | +++-==============-==============-============================================
| > | ii r-base 2.1.0-1 GNU R statistical computing language
| > | and env
| > | ii r-base-core 2.1.0-1 GNU R core of statistical computing
| > | language
| > | ii r-base-dev 2.1.0-1 GNU R installation of auxiliary GNU R
| > | packag
| > | ii r-base-html 2.3.0-0sarge1 GNU R html docs for statistical
| > | computing sy
| > | ii r-base-latex 2.3.0-0sarge1 GNU R LaTeX docs for statistical
| > | computing s
| > |
| > | [ some r-cran-* packages deleted ]
| > |
| > | un r-doc-html <none> (no description available)
| > | un r-doc-info <none> (no description available)
| > | un r-doc-pdf <none> (no description available)
| > | ii r-mathlib 2.1.0-1 GNU R standalone mathematics library
| > | ii r-recommended 2.1.0-1 GNU R collection of recommended
| > |
| > | This is more sources.list
| > |
| > | tolstoy:/etc/apt# cat sources.list
| > | deb http://ftp.au.debian.org/debian/ stable main contrib non-free
| > | deb http://ftp.au.debian.org/debian/ testing main contrib non-free
| > | deb-src http://ftp.au.debian.org/debian/ stable main contrib non-free
| > |
| > | deb http://security.debian.org/ stable/updates main contrib non-free
| > |
| > | #cran backports
| > | deb http://cran.au.r-project.org/bin/linux/debian/ stable/
| > |
| > | tolstoy:/etc/apt# apt-get install r-base-core=2.3.0-0sarge1
| > | Reading Package Lists... Done
| > | Building Dependency Tree... Done
| > | E: Version '2.3.0-0sarge1' for 'r-base-core' was not found
| > |
| > | tolstoy:~# wget
| > | http://cran.au.r-project.org/bin/linux/debian/stable/r-base-core_2.3.0-0sarge1_i386.deb
| > | --02:19:54--
| > | http://cran.au.r-project.org/bin/linux/debian/stable/r-base-core_2.3.0-0sarge1_i386.deb
| > | => `r-base-core_2.3.0-0sarge1_i386.deb'
| > | Resolving proxy.newcastle.edu.au... 134.148.172.1, 134.148.20.65
| > | Connecting to proxy.newcastle.edu.au[134.148.172.1]:8080... connected.
| > | Proxy request sent, awaiting response... 200 OK
| > | Length: 8,315,512 [application/x-debian-package]
| > |
| > | 100%[====================================>] 8,315,512 1.03M/s
| > | ETA 00:00
| > |
| > | 02:20:02 (1.02 MB/s) - `r-base-core_2.3.0-0sarge1_i386.deb' saved
| > | [8315512/8315512]
| > |
| > | tolstoy:~# dpkg -i r-base-core_2.3.0-0sarge1_i386.deb
| > | (Reading database ... 64541 files and directories currently installed.)
| > | Preparing to replace r-base-core 2.1.0-1 (using
| > | r-base-core_2.3.0-0sarge1_i386.deb) ...
| > | Unpacking replacement r-base-core ...
| > | Setting up r-base-core (2.3.0-0sarge1) ...
| > |
| > | _______________________________________________
| > | R-SIG-Debian mailing list
| > | R-SIG-Debian at r-project.org
| > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| >
|
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