CRAN repos broken?

[David Valentine]

I believe the Ubuntu CRAN mirrors are broken, and yesterday I sent the following e-mail to CRAN@r-project.org. I have not received a response, and the repos appear still to be broken. Does anyone have any insight on this?:confused:

Greetings:

I am using Ubuntu 6.10 (edgy), and previously have been successful using the CRAN mirrors as a repository to maintain R via apt-get. However, I am now getting the following error in response to "apt-get update": W: Conflicting distribution: http://cran.fhcrc.org (http://cran.fhcrc.org/) edgy/ Release (expected edgy but got ) This suggests to me that the Release file in the mirror download area does not specify edgy, and indeed its header reads as follows: Date: Wed, 17 Jan 2007 15:00:11 UTC
MD5Sum:Whereas a typical Ubuntu Release file header reads (from http://us.archive.ubuntu.com/ubuntu/dists/edgy/) Origin: Ubuntu
Label: Ubuntu
Suite: edgy
Version: 6.10
Codename: edgy
Date: Wed, 25 Oct 2006 17:07:09 UTC
Architectures: amd64 hppa i386 ia64 powerpc sparc
Components: main restricted universe multiverse
Description: Ubuntu Edgy 6.10
MD5Sum:The abbreviated header is also in the Ubuntu dapper Release file, whereas the Release file for Debian etch contains full headers like those above.

I have checked this on 3 mirrors.

Thus I believe that the CRAN Ubuntu Release files are currently incorrect and are causing apt-get to fail for all Ubuntu users.

If I should have sent this e-mail elsewhere, please let me know where, and accept my apology. Thank you for the contributions you have been making to academic data analysis.

[akniss]

I'm using the following mirror as a repo to keep my R up to date, and have had no issues. maybe give it a try.

## CRAN mirrors as repos to get latest R version
deb http://rh-mirror.linux.iastate.edu/CRAN/bin/linux/ubuntu/ edgy/

[David Valentine]

I get the same error using that repo, also on a different machine than I reported earlier. $sudo apt-get update yields Failed to fetch http://rh-mirror.linux.iastate.edu/CRAN/bin/linux/ubuntu/edgy/Release Unable to find expected entry Packages in Meta-index file (malformed Release file?)
Reading package lists... Done
W: Conflicting distribution: http://rh-mirror.linux.iastate.edu edgy/ Release (expected edgy but got )If I'm doing something wrong, I'm doing it consistently across multiple machines. Is no one else experiencing this?

[akniss]

I get a GPG error, but nothing that interferes with installation or updates... do you get the same error if you go through synaptic?

[David Valentine]

I get a GPG error, but nothing that interferes with installation or updates... do you get the same error if you go through synaptic?Synaptic (actually, adept in my case) does not give me that error, or other errors that I need to know about. I doubt that you're getting the actual CRAN updates, then, unless they're also going to the official Ubuntu repos. The GPG error comes from not supplying the GPG key (see the README file here (http://rh-mirror.linux.iastate.edu/CRAN/bin/linux/ubuntu/)), which I think is pretty much a show-stopper as far as getting updates is concerned. I think they only recently (January) started using secure repos.

[akniss]

R version 2.4.1 (2006-12-18)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

I successfully used the repo to get the latest version, and its difficult to tell if I'm getting updates since there haven't been any for a couple months.

[David Valentine]

I have that version as well. While all of the package files in the repos are dated 2007.01.01, all of the files having to do with managing them (Packages.gz, Release, Sources.gz) are dated 2007.01.17, and Release.gpg is dated 2007.03.06. This suggests to me that some reorganizing of the repos occurred after the most recent update, and those changes are generating the error(s). I suppose the test will be when they do release an update, unless they also change the Release file.

[David Valentine]

Received 2007.03.10 from the package maintainer:Thanks to Johannes' scripts and config files, the Release files for Ubuntu Dapper and Edgy should now be fixed. The updated files will start propagating to CRAN in about half an hour. I confirmed that apt-get no longer returns errors.