[R] Strange Conflicts with Debian Repositories

Lorenzo Isella lorenzo.isella at gmail.com
Sun Nov 8 17:05:40 CET 2009


Dear All,
I have just installed a fresh Debian testing (squeeze) on my system
(amd64 architecture).
I am experiencing some really strange problems in updating my system
whenever I have both the R repository and the multimedia repository
available.
This is my source.list (when I disable the multimedia repository)

~$ cat /etc/apt/sources.list
deb http://ftp.ch.debian.org/debian/ testing main contrib non-free
deb-src http://ftp.ch.debian.org/debian/ testing main non-free contrib

deb http://security.debian.org/ testing/updates main contrib non-free
deb-src http://security.debian.org/ testing/updates main contrib non-free

#deb http://www.debian-multimedia.org testing main

#deb http://<favorite-cran-mirror>/bin/linux/debian lenny-cran/
#deb-src http://<favorite-cran-mirror>/bin/linux/debian lenny-cran/

# Add R-repository
deb http://cran.ch.r-project.org/bin/linux/debian lenny-cran/
deb-src http://cran.ch.r-project.org/debian/bin/linux/debian lenny-cran/

This way I have no trouble to update/upgrade my system (only, I do not
see the sources of the R packages, but this is really a minor issue
for now)

~$ sudo apt-get update
Get:1 http://security.debian.org testing/updates Release.gpg [835B]
Ign http://security.debian.org testing/updates/main Translation-en_US
Ign http://security.debian.org testing/updates/contrib Translation-en_US
Get:2 http://ftp.ch.debian.org testing Release.gpg [835B]
Ign http://ftp.ch.debian.org testing/main Translation-en_US
Ign http://ftp.ch.debian.org testing/contrib Translation-en_US
Ign http://security.debian.org testing/updates/non-free Translation-en_US
Hit http://security.debian.org testing/updates Release
Ign http://ftp.ch.debian.org testing/non-free Translation-en_US
Hit http://ftp.ch.debian.org testing Release
Ign http://security.debian.org testing/updates/main Packages/DiffIndex
Hit http://ftp.ch.debian.org testing/main Packages/DiffIndex
Ign http://security.debian.org testing/updates/contrib Packages/DiffIndex
Ign http://security.debian.org testing/updates/non-free Packages/DiffIndex
Ign http://security.debian.org testing/updates/main Sources/DiffIndex
Ign http://security.debian.org testing/updates/contrib Sources/DiffIndex
Ign http://security.debian.org testing/updates/non-free Sources/DiffIndex
Get:3 http://cran.ch.r-project.org lenny-cran/ Release.gpg [197B]
Ign http://cran.ch.r-project.org lenny-cran/ Translation-en_US
Ign http://cran.ch.r-project.org lenny-cran/ Release.gpg
Hit http://ftp.ch.debian.org testing/contrib Packages/DiffIndex
Ign http://ftp.ch.debian.org testing/non-free Packages/DiffIndex
Hit http://ftp.ch.debian.org testing/main Sources/DiffIndex
Ign http://ftp.ch.debian.org testing/non-free Sources/DiffIndex
Hit http://ftp.ch.debian.org testing/contrib Sources/DiffIndex
Hit http://security.debian.org testing/updates/main Packages
Hit http://security.debian.org testing/updates/contrib Packages
Hit http://security.debian.org testing/updates/non-free Packages
Hit http://security.debian.org testing/updates/main Sources
Hit http://security.debian.org testing/updates/contrib Sources
Get:4 http://cran.ch.r-project.org lenny-cran/ Release [1,288B]
Hit http://ftp.ch.debian.org testing/non-free Packages
Hit http://ftp.ch.debian.org testing/non-free Sources
Hit http://security.debian.org testing/updates/non-free Sources
Ign http://cran.ch.r-project.org lenny-cran/ Release
Ign http://cran.ch.r-project.org lenny-cran/ Packages
Ign http://cran.ch.r-project.org lenny-cran/ Sources
Ign http://cran.ch.r-project.org lenny-cran/ Packages
Ign http://cran.ch.r-project.org lenny-cran/ Sources
Get:5 http://cran.ch.r-project.org lenny-cran/ Packages [11.4kB]
Err http://cran.ch.r-project.org lenny-cran/ Sources
  404  Not Found
Fetched 14.5kB in 3s (3,851B/s)
W: Failed to fetch
http://cran.ch.r-project.org/debian/bin/linux/debian/lenny-cran/Sources.gz
 404  Not Found

E: Some index files failed to download, they have been ignored, or old
ones used instead.

However (and this is really odd...) if I uncomment the multimedia
repository this is what happens

$ sudo apt-get update
Err http://www.debian-multimedia.org testing Release.gpg
  Could not resolve 'www.debian-multimedia.org'
Err http://security.debian.org testing/updates Release.gpg
  Could not resolve 'security.debian.org'
Err http://security.debian.org testing/updates/main Translation-en_US
  Could not resolve 'security.debian.org'
Err http://www.debian-multimedia.org testing/main Translation-en_US
  Could not resolve 'www.debian-multimedia.org'
Err http://security.debian.org testing/updates/contrib
Translation-en_US
  Could not resolve 'security.debian.org'
Err http://security.debian.org testing/updates/non-free Translation-en_US
  Could not resolve 'security.debian.org'
Err http://cran.ch.r-project.org lenny-cran/ Release.gpg
  Could not resolve 'cran.ch.r-project.org'
Err http://cran.ch.r-project.org lenny-cran/ Translation-en_US
  Could not resolve 'cran.ch.r-project.org'
Err http://cran.ch.r-project.org lenny-cran/ Release.gpg
  Could not resolve 'cran.ch.r-project.org'
Err http://ftp.ch.debian.org testing Release.gpg
  Could not resolve 'ftp.ch.debian.org'
Err http://ftp.ch.debian.org testing/main Translation-en_US
  Could not resolve 'ftp.ch.debian.org'
Err http://ftp.ch.debian.org testing/contrib Translation-en_US
  Could not resolve 'ftp.ch.debian.org'
Err http://ftp.ch.debian.org testing/non-free Translation-en_US
  Could not resolve 'ftp.ch.debian.org'
Reading package lists... Done
W: Failed to fetch
http://ftp.ch.debian.org/debian/dists/testing/Release.gpg  Could not
resolve 'ftp.ch.debian.org'

W: Failed to fetch
http://ftp.ch.debian.org/debian/dists/testing/main/i18n/Translation-en_US.bz2
 Could not resolve 'ftp.ch.debian.org'

W: Failed to fetch
http://ftp.ch.debian.org/debian/dists/testing/contrib/i18n/Translation-en_US.bz2
 Could not resolve 'ftp.ch.debian.org'

W: Failed to fetch
http://ftp.ch.debian.org/debian/dists/testing/non-free/i18n/Translation-en_US.bz2
 Could not resolve 'ftp.ch.debian.org'

W: Failed to fetch
http://security.debian.org/dists/testing/updates/Release.gpg  Could
not resolve 'security.debian.org'

W: Failed to fetch
http://security.debian.org/dists/testing/updates/main/i18n/Translation-en_US.bz2
 Could not resolve 'security.debian.org'

W: Failed to fetch
http://security.debian.org/dists/testing/updates/contrib/i18n/Translation-en_US.bz2
 Could not resolve 'security.debian.org'

W: Failed to fetch
http://security.debian.org/dists/testing/updates/non-free/i18n/Translation-en_US.bz2
 Could not resolve 'security.debian.org'

W: Failed to fetch
http://www.debian-multimedia.org/dists/testing/Release.gpg  Could not
resolve 'www.debian-multimedia.org'

W: Failed to fetch
http://www.debian-multimedia.org/dists/testing/main/i18n/Translation-en_US.bz2
 Could not resolve 'www.debian-multimedia.org'

W: Failed to fetch
http://cran.ch.r-project.org/bin/linux/debian/lenny-cran/Release.gpg
Could not resolve 'cran.ch.r-project.org'

W: Failed to fetch
http://cran.ch.r-project.org/bin/linux/debian/lenny-cran/en_US.bz2
Could not resolve 'cran.ch.r-project.org'

W: Failed to fetch
http://cran.ch.r-project.org/debian/bin/linux/debian/lenny-cran/Release.gpg
 Could not resolve 'cran.ch.r-project.org'

W: Some index files failed to download, they have been ignored, or old
ones used instead.

So, now nothing works...
If I uncomment the R cran repositories and leave the multimedia
repository, then everything works fine.
Bottom line: apt-get (on my system) does not like to have both the
multimedia and the R cran repositories available simultaneously, but I
cannot see why there should be any conflict. I am puzzled also because
I do not get any warnings e.g. about wrong signatures etc...
Any help is really appreciated.

Lorenzo



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