E:Encountered a section with no Package: header, E:Problem with MergeList /var/lib/apt/lists/ppa.launchpad.net_brainbreak_daily_ubuntu_dists_oneiric_main_binary-i386_Packages, E:The package lists or status file could not be parsed or opened.

wget https://dl.dropbox.com/u/8850924/fixpackage
chmod +x ./fixpackage
sudo ./fixpackage

Should do it.

It also looks like you may have an old oneiric/11.10 source.

Please visit this page:

https://launchpad.net/~brainbreak/+archive/stable

It only provides support for Saucy (13.10) and Trusty (14.04).

So you need to remove the brainbreak PPA from your Software Sources list.

Manfred Hampl suggests this article as an answer to your question:
FAQ #1591: “'E:Encountered a section with no Package: header, E:Problem with MergeList”.

Thanks actionparsnip, that solved my question.

The first comment solved my first problem, and it looks that the repository has problems, now trying to search for updates I get:

W:GPG error: http://deb.opera.com stable InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 517590D9A8492E35, W:Failed to fetch http://extras.ubuntu.com/ubuntu/dists/oneiric/main/source/Sources 404 Not Found
, W:Failed to fetch http://extras.ubuntu.com/ubuntu/dists/oneiric/main/binary-i386/Packages 404 Not Found
, W:Failed to fetch http://ppa.launchpad.net/brainbreak/daily/ubuntu/dists/oneiric/main/source/Sources 404 Not Found
, W:Failed to fetch http://ppa.launchpad.net/brainbreak/daily/ubuntu/dists/oneiric/main/binary-i386/Packages 404 Not Found
, W:Failed to fetch http://security.ubuntu.com/ubuntu/dists/oneiric-security/main/source/Sources 404 Not Found [IP: 91.189.91.13 80]
, W:Failed to fetch http://security.ubuntu.com/ubuntu/dists/oneiric-security/restricted/source/Sources 404 Not Found [IP: 91.189.91.13 80]
, W:Failed to fetch http://security.ubuntu.com/ubuntu/dists/oneiric-security/universe/source/Sources 404 Not Found [IP: 91.189.91.13 80]
, W:Failed to fetch http://security.ubuntu.com/ubuntu/dists/oneiric-security/multiverse/source/Sources 404 Not Found [IP: 91.189.91.13 80]
, W:Failed to fetch http://security.ubuntu.com/ubuntu/dists/oneiric-security/main/binary-i386/Packages 404 Not Found [IP: 91.189.91.13 80]
, W:Failed to fetch http://security.ubuntu.com/ubuntu/dists/oneiric-security/restricted/binary-i386/Packages 404 Not Found [IP: 91.189.91.13 80]
, W:Failed to fetch http://security.ubuntu.com/ubuntu/dists/oneiric-security/universe/binary-i386/Packages 404 Not Found [IP: 91.189.91.13 80]
, W:Failed to fetch http://security.ubuntu.com/ubuntu/dists/oneiric-security/multiverse/binary-i386/Packages 404 Not Found [IP: 91.189.91.13 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric/main/source/Sources 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric/restricted/source/Sources 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric/universe/source/Sources 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric/multiverse/source/Sources 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric/main/binary-i386/Packages 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric/restricted/binary-i386/Packages 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric/universe/binary-i386/Packages 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric/multiverse/binary-i386/Packages 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-updates/main/source/Sources 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-updates/restricted/source/Sources 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-updates/universe/source/Sources 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-updates/multiverse/source/Sources 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-updates/main/binary-i386/Packages 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-updates/restricted/binary-i386/Packages 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-updates/universe/binary-i386/Packages 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-updates/multiverse/binary-i386/Packages 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-backports/main/source/Sources 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-backports/restricted/source/Sources 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-backports/universe/source/Sources 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-backports/multiverse/source/Sources 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-backports/main/binary-i386/Packages 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-backports/restricted/binary-i386/Packages 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-backports/universe/binary-i386/Packages 404 Not Found [IP: 91.189.91.14 80]
, W:Failed to fetch http://sk.archive.ubuntu.com/ubuntu/dists/oneiric-backports/multiverse/binary-i386/Packages 404 Not Found [IP: 91.189.91.14 80]
, E:Some index files failed to download. They have been ignored, or old ones used instead.

Please send us the output of these 3 Terminal commands:

cat /etc/lsb-release

grep -R -i oneiric /etc/*

grep -R -i precise /etc/*

Hi, Thanks again to all, here is the output:

root@zen:/home/urrejola# cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=12.04
DISTRIB_CODENAME=precise
DISTRIB_DESCRIPTION="Ubuntu 12.04 LTS"
root@zen:/home/urrejola# grep -R -i oneiric /etc/*
grep: /etc/alternatives/ttf-japanese-gothic.ttf: No such file or directory
/etc/apt/sources.list.save:# deb cdrom:[Ubuntu 11.10 _Oneiric Ocelot_ - Release i386 (20111012)]/ oneiric main restricted
/etc/apt/sources.list.save:deb http://sk.archive.ubuntu.com/ubuntu/ oneiric main restricted
/etc/apt/sources.list.save:deb-src http://sk.archive.ubuntu.com/ubuntu/ oneiric main restricted
/etc/apt/sources.list.save:deb http://sk.archive.ubuntu.com/ubuntu/ oneiric-updates main restricted
/etc/apt/sources.list.save:deb-src http://sk.archive.ubuntu.com/ubuntu/ oneiric-updates main restricted
/etc/apt/sources.list.save:deb http://sk.archive.ubuntu.com/ubuntu/ oneiric universe
/etc/apt/sources.list.save:deb-src http://sk.archive.ubuntu.com/ubuntu/ oneiric universe
/etc/apt/sources.list.save:deb http://sk.archive.ubuntu.com/ubuntu/ oneiric-updates universe
/etc/apt/sources.list.save:deb-src http://sk.archive.ubuntu.com/ubuntu/ oneiric-updates universe
/etc/apt/sources.list.save:deb http://sk.archive.ubuntu.com/ubuntu/ oneiric multiverse
/etc/apt/sources.list.save:deb-src http://sk.archive.ubuntu.com/ubuntu/ oneiric multiverse
/etc/apt/sources.list.save:deb http://sk.archive.ubuntu.com/ubuntu/ oneiric-updates multiverse
/etc/apt/sources.list.save:deb-src http://sk.archive.ubuntu.com/ubuntu/ oneiric-updates multiverse
/etc/apt/sources.list.save:deb http://sk.archive.ubuntu.com/ubuntu/ oneiric-backports main restricted universe multiverse
/etc/apt/sources.list.save:deb-src http://sk.archive.ubuntu.com/ubuntu/ oneiric-backports main restricted universe multiverse
/etc/apt/sources.list.save:deb http://security.ubuntu.com/ubuntu oneiric-security main restricted
/etc/apt/sources.list.save:deb-src http://security.ubuntu.com/ubuntu oneiric-security main restricted
/etc/apt/sources.list.save:deb http://security.ubuntu.com/ubuntu oneiric-security universe
/etc/apt/sources.list.save:deb-src http://security.ubuntu.com/ubuntu oneiric-security universe
/etc/apt/sources.list.save:deb http://security.ubuntu.com/ubuntu oneiric-security multiverse
/etc/apt/sources.list.save:deb-src http://security.ubuntu.com/ubuntu oneiric-security multiverse
/etc/apt/sources.list.save:# deb http://archive.canonical.com/ubuntu oneiric partner
/etc/apt/sources.list.save:# deb-src http://archive.canonical.com/ubuntu oneiric partner
/etc/apt/sources.list.save:deb http://extras.ubuntu.com/ubuntu oneiric main
/etc/apt/sources.list.save:deb-src http://extras.ubuntu.com/ubuntu oneiric main
/etc/apt/sources.list.d/wfg-0ad-oneiric.list:deb http://ppa.launchpad.net/wfg/0ad/ubuntu oneiric main
/etc/apt/sources.list.d/wfg-0ad-oneiric.list:deb-src http://ppa.launchpad.net/wfg/0ad/ubuntu oneiric main
/etc/apt/sources.list.d/christoph-egger-unknown-horizons-oneiric.list.save:deb http://ppa.launchpad.net/christoph-egger/unknown-horizons/ubuntu oneiric main
/etc/apt/sources.list.d/christoph-egger-unknown-horizons-oneiric.list.save:deb-src http://ppa.launchpad.net/christoph-egger/unknown-horizons/ubuntu oneiric main
/etc/apt/sources.list.d/dropbox.list.save:deb http://linux.dropbox.com/ubuntu oneiric main
/etc/apt/sources.list.d/wfg-0ad-oneiric.list.save:deb http://ppa.launchpad.net/wfg/0ad/ubuntu oneiric main
/etc/apt/sources.list.d/wfg-0ad-oneiric.list.save:deb-src http://ppa.launchpad.net/wfg/0ad/ubuntu oneiric main
/etc/apt/sources.list.d/brainbreak-daily-oneiric.list.save:deb http://ppa.launchpad.net/brainbreak/daily/ubuntu oneiric main
/etc/apt/sources.list.d/brainbreak-daily-oneiric.list.save:deb-src http://ppa.launchpad.net/brainbreak/daily/ubuntu oneiric main
/etc/apt/sources.list.d/christoph-egger-unknown-horizons-oneiric.list:deb http://ppa.launchpad.net/christoph-egger/unknown-horizons/ubuntu oneiric main
/etc/apt/sources.list.d/christoph-egger-unknown-horizons-oneiric.list:deb-src http://ppa.launchpad.net/christoph-egger/unknown-horizons/ubuntu oneiric main
/etc/apt/sources.list.d/oneiric-partner.list.save:deb http://archive.canonical.com/ubuntu oneiric partner #Added by software-center
/etc/apt/sources.list.d/brainbreak-daily-oneiric.list:deb http://ppa.launchpad.net/brainbreak/daily/ubuntu oneiric main
/etc/apt/sources.list.d/brainbreak-daily-oneiric.list:deb-src http://ppa.launchpad.net/brainbreak/daily/ubuntu oneiric main
/etc/apt/sources.list.d/oneiric-partner.list:deb http://archive.canonical.com/ubuntu oneiric partner #Added by software-center
/etc/apt/sources.list:# deb cdrom:[Ubuntu 11.10 _Oneiric Ocelot_ - Release i386 (20111012)]/ oneiric main restricted
/etc/apt/sources.list:deb http://sk.archive.ubuntu.com/ubuntu/ oneiric main restricted
/etc/apt/sources.list:deb-src http://sk.archive.ubuntu.com/ubuntu/ oneiric main restricted
/etc/apt/sources.list:deb http://sk.archive.ubuntu.com/ubuntu/ oneiric-updates main restricted
/etc/apt/sources.list:deb-src http://sk.archive.ubuntu.com/ubuntu/ oneiric-updates main restricted
/etc/apt/sources.list:deb http://sk.archive.ubuntu.com/ubuntu/ oneiric universe
/etc/apt/sources.list:deb-src http://sk.archive.ubuntu.com/ubuntu/ oneiric universe
/etc/apt/sources.list:deb http://sk.archive.ubuntu.com/ubuntu/ oneiric-updates universe
/etc/apt/sources.list:deb-src http://sk.archive.ubuntu.com/ubuntu/ oneiric-updates universe
/etc/apt/sources.list:deb http://sk.archive.ubuntu.com/ubuntu/ oneiric multiverse
/etc/apt/sources.list:deb-src http://sk.archive.ubuntu.com/ubuntu/ oneiric multiverse
/etc/apt/sources.list:deb http://sk.archive.ubuntu.com/ubuntu/ oneiric-updates multiverse
/etc/apt/sources.list:deb-src http://sk.archive.ubuntu.com/ubuntu/ oneiric-updates multiverse
/etc/apt/sources.list:deb http://sk.archive.ubuntu.com/ubuntu/ oneiric-backports main restricted universe multiverse
/etc/apt/sources.list:deb-src http://sk.archive.ubuntu.com/ubuntu/ oneiric-backports main restricted universe multiverse
/etc/apt/sources.list:deb http://security.ubuntu.com/ubuntu oneiric-security main restricted
/etc/apt/sources.list:deb-src http://security.ubuntu.com/ubuntu oneiric-security main restricted
/etc/apt/sources.list:deb http://security.ubuntu.com/ubuntu oneiric-security universe
/etc/apt/sources.list:deb-src http://security.ubuntu.com/ubuntu oneiric-security universe
/etc/apt/sources.list:deb http://security.ubuntu.com/ubuntu oneiric-security multiverse
/etc/apt/sources.list:deb-src http://security.ubuntu.com/ubuntu oneiric-security multiverse
/etc/apt/sources.list:# deb http://archive.canonical.com/ubuntu oneiric partner
/etc/apt/sources.list:# deb-src http://archive.canonical.com/ubuntu oneiric partner
/etc/apt/sources.list:deb http://extras.ubuntu.com/ubuntu oneiric main
/etc/apt/sources.list:deb-src http://extras.ubuntu.com/ubuntu oneiric main
grep: /etc/blkid.tab: No such file or directory
root@zen:/home/urrejola# grep -R -i precise /etc/*
/etc/alternatives/ghostscript-current/lib/align.ps:% and should extend precisely to the edge of the paper.
grep: /etc/alternatives/ttf-japanese-gothic.ttf: No such file or directory
/etc/alternatives/wx-config:# precise action of the argument parser below just a little more
Binary file /etc/alternatives/quake-engine matches
/etc/apt/sources.list.d/steam.list:deb [arch=amd64,i386] http://repo.steampowered.com/steam/ precise steam
/etc/apt/sources.list.d/steam.list:deb-src [arch=amd64,i386] http://repo.steampowered.com/steam/ precise steam
/etc/apt/sources.list.d/dropbox.list:deb http://linux.dropbox.com/ubuntu precise main
/etc/apt/sources.list:#deb http://ubuntu.mirror.cambrium.nl/ubuntu/ precise main universe
/etc/apt/sources.list:#deb http://ftp.halifax.rwth-aachen.de/ubuntu/ precise main universe
grep: /etc/blkid.tab: No such file or directory
/etc/dictionaries-common/words:imprecise
/etc/dictionaries-common/words:imprecisely
/etc/dictionaries-common/words:precise
/etc/dictionaries-common/words:precisely
/etc/dictionaries-common/words:preciseness
/etc/dictionaries-common/words:preciseness's
/etc/dictionaries-common/words:preciser
/etc/dictionaries-common/words:precises
/etc/dictionaries-common/words:precisest
/etc/lsb-release:DISTRIB_CODENAME=precise
/etc/texmf/metafont/misc/modes.mf:% To be more precise, you can determine the resolution of a font given
/etc/X11/app-defaults/UXTerm:! Here is a simple description. A technically precise one would be very long.

According to the command

cat /etc/lsb-release

you are using Ubuntu 12.04 LTS, but according to the two other commands (grep commands), you are using oneiric (Ubuntu 11.10) sources.

It is very confusing and strange.

I suggest running these commands:

sudo rm /etc/apt/sources.list.d/*oneiric*

sudo rm /etc/apt/sources.list.save

Then run this command to start editing the /etc/apt/sources.list file:

gksudo gedit /etc/apt/sources.list

Using the gedit editor, scroll down and replace each occurrence of oneiric with precise

After replacing with precise, save the change in gedit.

Then rerun these commands to perform a new upgrade simulation:

sudo apt-get update

sudo apt-get dist-upgrade -s

I was having the identical problem. This is how I resolved it after spawning ideas from everyone above.

I noticed that everywhere on the internet, I am told to modify the etc/apt/sources.list.
However, after running the command

cat/etc/lsb-release

as suggested above, I also had a similar list as was supplied above with sources.list.d. This is an entirely different list and probably intentionally set up that way. Everything within this directory seems to be throwing errors.
Therefore, after a couple of tests attempting to rename the sources files to see what happens, etc, I decided to move the entire sources.list.d folder outside of the apt folder. I did this using

sudo nautilus

I temporarily pasted sources.list.d folder to the Home folder.
I attempted

sudo apt-get update.

No errors.
Then, I ran

do-release-upgrade

It is finally upgrading to 14.04!

I am assuming that there could be apps that may be lost due to removing this folder. In my case, I am OK with just reinstalling them afterwards, if I lose anything.

Hope this helps.

Thanks