[R-sig-Debian] CRAN-only "Hash Sum mismatch"

[Johannes Ranke]

Hi Tom,

On Sun, Jan 27, 2013 at 12:47:56PM -0500, Tom Roche wrote:
> 
> summary: updating R .deb's from recommended mirrors @
> 
> http://cran.r-project.org/mirrors.html
> 
> has allowed me to keep my R version up-to-date for many months. But

That's nice to know. Please, the next time you ask for help on a Debian
mailing list, mention from the beginning that you are using a derivative
(Linux Mint). 

> since Friday (25 Jan) I get errors like
> 
> Failed to fetch <mirror URI/>/squeeze-cran/<deb name/>: Hash Sum mismatch
> 
> but can install .deb's from non-CRAN sources. No fix from
> 
> sudo rm /var/cache/apt/pkgcache.bin
> sudo rm /var/cache/apt/srcpkgcache.bin 
> sudo rm /var/lib/apt/lists/*
> sudo rm /var/lib/apt/lists/partial/*
> 
> and either
> 
> sudo aptitude update
> or
> sudo apt-get update
> 
> details:
> 
> http://lists.debian.org/debian-user/2013/01/msg00995.html

Meanwhile you got some more hints on this thread on debian-user.

> > I'm getting
> 
> > > E: Failed to fetch http://lib.stat.cmu.edu/R/CRAN/bin/linux/debian/squeeze-cran/r-base-core_2.15.2-1~squeezecran.0_amd64.deb: Hash Sum mismatch
> 
> > So I changed my sources.list
> 
> > - deb http://lib.stat.cmu.edu/R/CRAN/bin/linux/debian squeeze-cran/
> > + deb http://watson.nci.nih.gov/cran_mirror/bin/linux/debian squeeze-cran/

I just tried the latter entry on squeeze, and the indices download fine
after doing aptitude update:

....

Get:4 http://mirrors.nics.utk.edu squeeze-cran/ Release.gpg [198 B]                       
Ign http://mirrors.nics.utk.edu/cran/bin/linux/debian/ squeeze-cran/
Translation-de                                        
Ign http://mirrors.nics.utk.edu/cran/bin/linux/debian/ squeeze-cran/
Translation-en                                        
Get:5 http://mirrors.nics.utk.edu squeeze-cran/ Release [3651 B]                                                           
Get:6 http://mirrors.nics.utk.edu squeeze-cran/ Packages [16.9 kB]                               
Fetched 392 kB in 1s (206 kB/s)

so the problem may be an incomplete upgrade at your end (just guessing,
based on the thread on debian-user). Maybe try removing the CRAN
sources, complete the upgrade, and try again. However, please bear in
mind that you are using a repository for Debian squeeze, and I have no
idea in what way the Linux Mint release you are using deviates from
Debian stable.

Regards,

Johannes

> > did `sudo aptitude update`, and got
> 
> > > W: Failed to fetch bzip2:/var/lib/apt/lists/partial/watson.nci.nih.gov_cran%5fmirror_bin_linux_debian_squeeze-cran_Packages: Hash Sum mismatch

> 
> > So I changed my sources.list
> 
> > - deb http://lib.stat.cmu.edu/R/CRAN/bin/linux/debian squeeze-cran/
> > - deb http://watson.nci.nih.gov/cran_mirror/bin/linux/debian squeeze-cran/
> > + deb http://mirrors.nics.utk.edu/cran/bin/linux/debian squeeze-cran/
> 
> > did `sudo aptitude update`, and got
> 
> > > W: Failed to fetch bzip2:/var/lib/apt/lists/partial/mirrors.nics.utk.edu_cran_bin_linux_debian_squeeze-cran_Packages: Hash Sum mismatch
> 
> Note that
> 
> * I'm only using mirror hosts from
> 
> http://cran.r-project.org/mirrors.html
> 
> * I'm only having problems getting/installing .deb's from CRAN:
>   all other debian packages install normally
> 
> I got suggestions to try removing/recreating
> 
> /var/cache/apt/pkgcache.bin
> /var/cache/apt/srcpkgcache.bin 
> /var/lib/apt/lists/*
> /var/lib/apt/lists/partial/*
> 
> but no fix:
> 
> me at it:~ $ sudo rm /var/cache/apt/pkgcache.bin /var/cache/apt/srcpkgcache.bin /var/lib/apt/lists/partial/* /var/lib/apt/lists/* ; sudo aptitude update
> ...
> Reading package lists... Done
> me at it:~ $ sudo aptitude install r-base r-base-core r-recommended r-base-dev
> ...
> E: Failed to fetch http://mirrors.nics.utk.edu/cran/bin/linux/debian/squeeze-cran/r-base-core_2.15.2-1~squeezecran.0_amd64.deb: Hash Sum mismatch
> 
> me at it:~ $ sudo emacs -nw -q /etc/apt/sources.list
> me at it:~ $ sudo rm /var/cache/apt/pkgcache.bin /var/cache/apt/srcpkgcache.bin /var/lib/apt/lists/partial/* /var/lib/apt/lists/* ; sudo aptitude update
> ...
> Reading package lists... Done
> me at it:~ $ sudo aptitude install r-base r-base-core r-recommended r-base-dev
> ...
> E: Failed to fetch http://lib.stat.cmu.edu/R/CRAN/bin/linux/debian/squeeze-cran/r-base-core_2.15.2-1~squeezecran.0_amd64.deb: Hash Sum mismatch
> 
> How to fix, or further debug?
> TIA, Tom Roche <Tom_Roche at pobox.com>
> 
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-- 
Dr. Johannes Ranke                 jranke at uni-bremen.de