R SIG Debian - Nov 2009 - Conflict Between R and multimedia repositories

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

Thank you for posting here rather than on r-help as I suggested. Now, please
re-read what I wrote in response to your first post on the r-help list as 

On 8 November 2009 at 18:16, Lorenzo Isella wrote:
| 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/
[...]
| W: Failed to fetch
| http://cran.ch.r-project.org/debian/bin/linux/debian/lenny-cran/Sources.gz
|  404  Not Found

these are _still an invalid URLs that cannot get resolved_. 404s are the
error code that.

One of the niceties of the http protocol is that you can test the URL in your
browser. This one does not work, so you need to correct it.

In deb-src URL you have a double debian, and the for the other one the
cran.ch may be at fault -- but the direct ethz.ch address you get works as I
wrote in my email.

Dirk

-- 
Three out of two people have difficulties with fractions.

Hello,
I got another suggestion. With a source list like

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

# CRAN
deb http://debian.cran.r-project.org/cran2deb/debian-amd64/ testing/

I updated the R packages without any trouble. But if I re-enable the
multimedia repository, I have again the same problems.
Am I doing something wrong again?
Cheers

Lorenzo

?
>
> Let me recap
>
> ? ? ?i) ? without Debian multimedia it works
> ? ? ?ii) ?with Debian multimedia it does not work
>
> and you think the R site is to blame? Why?
No, it is not this simple
iii) without the R repositories, the multimedia repositories (and
everything else) works fine.

> Notice how you miss the trailing / at the multimedia URL. ?I haven't
used
> that site in a while -- maybe you need a / ? ?My laptop has the following

Allegedly not, at least if I follow http://debian-multimedia.org/ where I read


For squeeze (testing) alpha, amd64, armel, hppa, i386, ia64, mipsel,
powerpc and sparc packages
add in your /etc/apt/sources.list
deb http://www.debian-multimedia.org squeeze main
or
deb ftp://ftp.debian-multimedia.org squeeze main
or
deb http://www.debian-multimedia.org testing main or
deb ftp://ftp.debian-multimedia.org testing main


Unless there is something really broken in my apt, but I cannot understand how.

Lorenzo
>
> # CRAN
> # deb http://cran.us.r-project.org/bin/linux/debian/ lenny-cran/
>
>
> Notice, though, that two (harmless) messages are triggered by the
> emacs.orebokech.com and debian-multimedia about missing Releases files. ?I
> guess both sites use older repository layouts. ?But package info comes
> through.
>
> Hope this helps.
>
> Dirk
>
> --
> Three out of two people have difficulties with fractions.
>