[APT] how to debug "Hash Sum mismatch"?

[Tom Roche]

I'm trying to update debian packages for R, for which the recommended
mirrors are listed @

http://cran.r-project.org/mirrors.html

My sources.list formerly contained

deb http://lib.stat.cmu.edu/R/CRAN/bin/linux/debian squeeze-cran/

with which I was able to keep up-to-date for many months. But tonight 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/

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

Given that CRAN is a fairly reliable organization, and I have just
failed with 3 recommended mirrors, I'm wondering if something is wrong
on my end. How to debug?

TIA, Tom Roche <Tom_...@pobox.com>


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[Chris Bannister]

On Fri, Jan 25, 2013 at 10:54:16PM -0500, Tom Roche wrote:
> 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

Without knowing all your details, I'd probably:

rm /var/lib/apt/lists/*

rm /var/lib/apt/lists/partial/*

then try updating again.

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who are being oppressed, and loving the people who are doing the
oppressing." --- Malcolm X

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[Tom Roche]

summary: trying to update R packages from recommended mirrors @

http://cran.r-project.org/mirrors.html

This has worked well for a long time, but now I keep getting errors like

Failed to fetch <mirror URI/>/squeeze-cran/<deb name/>: Hash Sum mismatch

No fix from either

sudo rm /var/lib/apt/lists/partial/*
sudo rm /var/lib/apt/lists/*
sudo aptitude update

or

sudo rm /var/lib/apt/lists/partial/*
sudo rm /var/lib/apt/lists/*
sudo apt-get update

details:

http://lists.debian.org/debian-user/2013/01/msg00995.html

>> 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/

>> 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

http://lists.debian.org/debian-user/2013/01/msg00997.html

> Without knowing all your details, I'd probably:

> rm /var/lib/apt/lists/*

> rm /var/lib/apt/lists/partial/*

> then try updating again.

Unfortunately, no fix:

me@it:~ $ sudo rm /var/lib/apt/lists/*
rm: cannot remove `/var/lib/apt/lists/partial': Is a directory
me@it:~ $ sudo rm /var/lib/apt/lists/partial/*
me@it:~ $ sudo emacs -nw -q /etc/apt/sources.list
me@it:~ $ sudo aptitude update
...
W: Failed to fetch bzip2:/var/lib/apt/lists/partial/lib.stat.cmu.edu_R_CRAN_bin_linux_debian_squeeze-cran_Packages: Hash Sum mismatch
E: Some index files failed to download. They have been ignored, or old ones used instead.
E: Couldn't rebuild package cache

me@it:~ $ sudo emacs -nw -q /etc/apt/sources.list
me@it:~ $ sudo rm /var/lib/apt/lists/partial/* ; sudo rm /var/lib/apt/lists/* ; sudo aptitude update
...

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

E: Some index files failed to download. They have been ignored, or old ones used instead.
E: Couldn't rebuild package cache

me@it:~ $ sudo emacs -nw -q /etc/apt/sources.list
me@it:~ $ sudo rm /var/lib/apt/lists/partial/* ; sudo rm /var/lib/apt/lists/* ; sudo aptitude update
...

W: Failed to fetch bzip2:/var/lib/apt/lists/partial/mirrors.nics.utk.edu_cran_bin_linux_debian_squeeze-cran_Packages: Hash Sum mismatch

E: Some index files failed to download. They have been ignored, or old ones used instead.
E: Couldn't rebuild package cache

For the helluvit, I also tried `apt-get`, which does not fail-fast
like `aptitude`:

me@it:~ $ sudo rm /var/lib/apt/lists/partial/* ; sudo rm /var/lib/apt/lists/* ; sudo apt-get update
...
Reading package lists... Done
me@it:~ $ sudo aptitude install r-base r-base-core r-recommended r-base-dev liblapack3 liblapack-dev
The following NEW packages will be installed:
r-base-dev
The following packages will be upgraded:
r-base r-base-core r-recommended
3 packages upgraded, 1 newly installed, 0 to remove and 1603 not upgraded.
Need to get 21.1 MB of archives. After unpacking 500 kB will be used.
Do you want to continue? [Y/n/?]
Get: 1 http://mirrors.nics.utk.edu/cran/bin/linux/debian/ squeeze-cran/ r-base-core 2.15.2-1~squeezecran.0 [21.0 MB]
Get: 2 http://mirrors.nics.utk.edu/cran/bin/linux/debian/ squeeze-cran/ r-base 2.15.2-1~squeezecran.0 [37.1 kB]
Get: 3 http://mirrors.nics.utk.edu/cran/bin/linux/debian/ squeeze-cran/ r-recommended 2.15.2-1~squeezecran.0 [2,688 B]
Get: 4 http://mirrors.nics.utk.edu/cran/bin/linux/debian/ squeeze-cran/ r-base-dev 2.15.2-1~squeezecran.0 [3,906 B]
Fetched 21.1 MB in 12s (1,650 kB/s)

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

What else to try?

TIA, Tom Roche <Tom_...@pobox.com>


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[Chris Bannister]

On Sat, Jan 26, 2013 at 12:45:30PM -0500, Tom Roche wrote:
> > Without knowing all your details, I'd probably:
>
> > rm /var/lib/apt/lists/*
>
> > rm /var/lib/apt/lists/partial/*
>
> > then try updating again.
>
> Unfortunately, no fix:
>
> me@it:~ $ sudo rm /var/lib/apt/lists/*
> rm: cannot remove `/var/lib/apt/lists/partial': Is a directory
> me@it:~ $ sudo rm /var/lib/apt/lists/partial/*
> me@it:~ $ sudo emacs -nw -q /etc/apt/sources.list
> me@it:~ $ sudo aptitude update
> ...
> W: Failed to fetch bzip2:/var/lib/apt/lists/partial/lib.stat.cmu.edu_R_CRAN_bin_linux_debian_squeeze-cran_Packages: Hash Sum mismatch
> E: Some index files failed to download. They have been ignored, or old ones used instead.
> E: Couldn't rebuild package cache

[...]

> me@it:~ $ sudo rm /var/lib/apt/lists/partial/* ; sudo rm /var/lib/apt/lists/* ; sudo apt-get update

> Reading package lists... Done

Now try apt-get upgrade.

> me@it:~ $ sudo aptitude install r-base r-base-core r-recommended r-base-dev liblapack3 liblapack-dev
> The following NEW packages will be installed:
> r-base-dev
> The following packages will be upgraded:
> r-base r-base-core r-recommended
> 3 packages upgraded, 1 newly installed, 0 to remove and 1603 not upgraded.

^^^^^^^^^^^^^^^^^
Is there a reason for not
upgrading all those
packages?

> Need to get 21.1 MB of archives. After unpacking 500 kB will be used.
> Do you want to continue? [Y/n/?]
> Get: 1 http://mirrors.nics.utk.edu/cran/bin/linux/debian/ squeeze-cran/ r-base-core 2.15.2-1~squeezecran.0 [21.0 MB]
> Get: 2 http://mirrors.nics.utk.edu/cran/bin/linux/debian/ squeeze-cran/ r-base 2.15.2-1~squeezecran.0 [37.1 kB]
> Get: 3 http://mirrors.nics.utk.edu/cran/bin/linux/debian/ squeeze-cran/ r-recommended 2.15.2-1~squeezecran.0 [2,688 B]
> Get: 4 http://mirrors.nics.utk.edu/cran/bin/linux/debian/ squeeze-cran/ r-base-dev 2.15.2-1~squeezecran.0 [3,906 B]
> Fetched 21.1 MB in 12s (1,650 kB/s)
>
> 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
>
> What else to try?

First, happens when you do "apt-get update && apt-get upgrade"

Just a wild stab in the dark, is bzip2 installed :)
(apt-cache policy bzip2)

There are also plenty of hits on google for:
W: Failed to fetch bzip2: Hash Sum mismatch

This link (https://answers.launchpad.net/ubuntu/+question/6841) suggests:
rm /var/cache/apt/pkgcache.bin
rm /var/cache/apt/srcpkgcache.bin

These should be regenerated with an apt-get update command.

And you are only having trouble with the CRAN repositories?

--
"If you're not careful, the newspapers will have you hating the people
who are being oppressed, and loving the people who are doing the
oppressing." --- Malcolm X

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[Tom Roche]

http://lists.debian.org/debian-user/2013/01/msg01054.html (rearranged)

> you are only having trouble with the CRAN repositories?

Correct. (And, yes, I do have bzip2 :-)

> > 3 packages upgraded, ... and 1603 not upgraded.

> ^^^^^^^^^^^^^^^^^
> Is there a reason for not
> upgrading all those packages?

Yes: I'm currently on LMDE UP5, those packages are LMDE UP6, I
don't want to upgrade this box until I get my spare box updated.

> [ https://answers.launchpad.net/ubuntu/+question/6841) suggests]
> rm /var/cache/apt/pkgcache.bin
> rm /var/cache/apt/srcpkgcache.bin

alas, no fix:

$ sudo rm /var/cache/apt/pkgcache.bin /var/cache/apt/srcpkgcache.bin /var/lib/apt/lists/partial/* /var/lib/apt/lists/* ; sudo apt-get update
...

$ 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

> There are also plenty of hits on google for:
> W: Failed to fetch bzip2: Hash Sum mismatch

I'll try that.

thanks anyway, Tom Roche <Tom_...@pobox.com>

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[Chris Bannister]

On Sun, Jan 27, 2013 at 12:25:22PM -0500, Tom Roche wrote:
>
> > [ https://answers.launchpad.net/ubuntu/+question/6841) suggests]

Just as an aside, I don't remember putting square brackets "[" and "]"
around the url. I consider it unethical/bad practice to alter the quoted
text but make it look like that is what they wrote.

> > rm /var/cache/apt/pkgcache.bin
> > rm /var/cache/apt/srcpkgcache.bin
>
> alas, no fix:
>
> $ sudo rm /var/cache/apt/pkgcache.bin /var/cache/apt/srcpkgcache.bin /var/lib/apt/lists/partial/* /var/lib/apt/lists/* ; sudo apt-get update
> ...
> $ 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

Since your box is in somewhat disarrary, you could
"wget r-base-core_2.15.2-1~squeezecran.0_amd64.deb" then
"dpkg -i r-base-core_2.15.2-1~squeezecran.0_amd64.deb" although you may
run into conflicts and/or dependency problems.

Also, the apt-get update output seems to be snipped, is the CRAN
repository the only one in your sources.list?

Finally, from what I've read on some of those Google hits, the "Hash Sum
mismatch" error indicates you have packages which don't agree with APT
and the mirror, although I don't know how APT works this out. If you can
figure it could you please post the solution?

TTBOMK, and someone please correct me if I'm wrong, your troubles are
somehow due to you not doing an apt-get upgrade.

--
"If you're not careful, the newspapers will have you hating the people
who are being oppressed, and loving the people who are doing the
oppressing." --- Malcolm X

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[sp113438]

On Mon, 28 Jan 2013 15:08:54 +1300
Chris Bannister <cbann...@slingshot.co.nz> wrote:

> On Sun, Jan 27, 2013 at 12:25:22PM -0500, Tom Roche wrote:
> >
> > > [ https://answers.launchpad.net/ubuntu/+question/6841) suggests]
>
> Just as an aside, I don't remember putting square brackets "[" and "]"
> around the url. I consider it unethical/bad practice to alter the

> is but make it look like that is what they wrote.

>
> > > rm /var/cache/apt/pkgcache.bin
> > > rm /var/cache/apt/srcpkgcache.bin
> >
> > alas, no fix:
> >
> > $ sudo
> > rm /var/cache/apt/pkgcache.bin /var/cache/apt/srcpkgcache.bin /var/lib/apt/lists/partial/* /var/lib/apt/lists/* ;
> > sudo apt-get update ... $ 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
>
> Since your box is in somewhat disarrary, you could
> "wget r-base-core_2.15.2-1~squeezecran.0_amd64.deb" then
> "dpkg -i r-base-core_2.15.2-1~squeezecran.0_amd64.deb" although you
> may run into conflicts and/or dependency problems.
>
> Also, the apt-get update output seems to be snipped, is the CRAN
> repository the only one in your sources.list?
>
> Finally, from what I've read on some of those Google hits, the "Hash
> Sum mismatch" error indicates you have packages which don't agree
> with APT and the mirror, although I don't know how APT works this
> out. If you can figure it could you please post the solution?
>
> TTBOMK, and someone please correct me if I'm wrong, your troubles are
> somehow due to you not doing an apt-get upgrade.
>

Agreed, alter a quoted text is almost (?) a crime. At least a very bad
habit.
Punishment: write 100 lines, without copy/paste:
I shall not alter quoted text.
LOL

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