Ubuntu 14.04 upgrade from 13.10: Using unofficial software packages not provided by ubuntu

I am having an issues upgrading to 14.04 (Trusty Tahr) from 13.10 (Saucy Salamander), where I get a message Could not calculate the upgrade, and I believe it is due to my unofficial software packages. Can someone please suggest which packages I should resolve, and how to resolve these packages? My question is similar to this one here, but I need help in implementing the solution that resolves the packages.

I already unchecked all packages under "other" in the Software and Updates menu while trying to upgrade through Software Updater.

Running a grep Broken /var/log/dist-upgrade/apt.log showed me multiple packages, but I'm not sure which ones are broken and how to resolve them before upgrading. I suspect my configuration with Bumblebee and Nvidia Optimus has added some PPA's and other non-supported software.

Here is my grep Broken /var/log/dist-upgrade/apt.log output:

Broken libqt5core5a:amd64 Breaks on libqt5core5 [ amd64 ] < 5.0.2+dfsg1-7ubuntu11.1 > ( libs ) (< 5.2.0+dfsg~)
Broken libharfbuzz0b:amd64 Conflicts on libharfbuzz0a [ amd64 ] < 0.9.19-1 > ( libs )
Broken cups-filters:amd64 Conflicts on foomatic-filters [ amd64 ] < 4.0.17-1ubuntu1 > ( universe/text )
Broken libboost1.54-dev:amd64 Conflicts on libboost1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libclutter-1.0-0:amd64 Breaks on libcogl12 [ amd64 ] < 1.14.0-2 > ( libs )
Broken unity-control-center:amd64 Conflicts on gnome-control-center-unity [ amd64 ] < 1.3+13.10.20131004-0ubuntu1 > ( gnome )
Broken libgoa-1.0-0b:amd64 Conflicts on libgoa-1.0-0 [ amd64 ] < 3.8.3-2 > ( libs )
Broken libtcl8.6:amd64 Conflicts on tcl8.6-lib [ amd64 ] < 8.6.0-1ubuntu1 > ( interpreters ) (< 8.6.0-2)
Broken unity-control-center-signon:amd64 Conflicts on gnome-control-center-signon [ amd64 ] < 0.1.7~+13.10.20130724.1-0ubuntu1 > ( gnome )
Broken libboost-serialization1.54-dev:amd64 Conflicts on libboost-serialization1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken evolution-data-server:amd64 Conflicts on evolution-data-server-goa [ amd64 ] < 3.8.5-1ubuntu3 > ( gnome ) (< 3.10.3-0ubuntu2~)
Broken libopenmpi1.6:amd64 Conflicts on libopenmpi1.3 [ amd64 ] < 1.4.5-1ubuntu2 > ( libs )
Broken libopenmpi1.6:amd64 Conflicts on openmpi-libs0 [ amd64 ] < none > ( none )
Broken libtk8.6:amd64 Conflicts on tk8.6-lib [ amd64 ] < 8.6.0-1ubuntu1 > ( libs ) (< 8.6.0-2)
Broken libboost-system1.54-dev:amd64 Conflicts on libboost-system1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken tk:amd64 Conflicts on tk-lib [ amd64 ] < 8.5.0-2ubuntu5 > ( libs )
Broken tk:amd64 Conflicts on tk8.5-lib [ amd64 ] < 8.5.11-2ubuntu4 > ( libs )
Broken tcl:amd64 Conflicts on tcl-lib [ amd64 ] < 8.5.0-2ubuntu5 > ( interpreters )
Broken tcl:amd64 Conflicts on tcl8.5-lib [ amd64 ] < 8.5.13-1ubuntu4 > ( interpreters )
Broken libboost-filesystem1.54-dev:amd64 Conflicts on libboost-filesystem1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-date-time1.54-dev:amd64 Conflicts on libboost-date-time1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-test1.54-dev:amd64 Conflicts on libboost-test1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-atomic1.54-dev:amd64 Conflicts on libboost-atomic1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-chrono1.54-dev:amd64 Conflicts on libboost-chrono1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-mpi1.54-dev:amd64 Conflicts on libboost-mpi1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libunity-core-6.0-9:amd64 Conflicts on libunity-core-6.0-8 [ amd64 ] < 7.1.2+13.10.20131014.1-0ubuntu1 > ( libs )
Broken libunity-core-6.0-9:amd64 Conflicts on unity-common [ amd64 ] < none > ( none )
Broken libboost-mpi1.53.0:amd64 Depends on libopenmpi1.3 [ amd64 ] < 1.4.5-1ubuntu2 > ( libs )
Broken libboost-regex1.54-dev:amd64 Conflicts on libboost-regex1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-program-options1.54-dev:amd64 Conflicts on libboost-program-options1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-thread1.54-dev:amd64 Conflicts on libboost-thread1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken icu-devtools:amd64 Breaks on icu-tools [ amd64 ] < 4.8.1.1-12ubuntu2 > ( libdevel ) (< 52.1-3~)
Broken icu-devtools:amd64 Breaks on icu-tools [ i386 ] < none > ( none ) (< 52.1-3~)
Broken libboost-context1.54-dev:amd64 Conflicts on libboost-context1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-mpi-python1.54-dev:amd64 Conflicts on libboost-mpi-python1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-exception1.54-dev:amd64 Conflicts on libboost-exception1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-graph1.54-dev:amd64 Conflicts on libboost-graph1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-locale1.54-dev:amd64 Conflicts on libboost-locale1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost1.54-tools-dev:amd64 Conflicts on libboost1.53-tools-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost1.54-tools-dev:amd64 Conflicts on libboost1.53-tools-dev [ i386 ] < none > ( none )
Broken libboost-python1.54-dev:amd64 Conflicts on libboost-python1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-graph-parallel1.54-dev:amd64 Conflicts on libboost-graph-parallel1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-wave1.54-dev:amd64 Conflicts on libboost-wave1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-iostreams1.54-dev:amd64 Conflicts on libboost-iostreams1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken xserver-xorg-video-intel:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-ati:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken libboost-timer1.54-dev:amd64 Conflicts on libboost-timer1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-math1.54-dev:amd64 Conflicts on libboost-math1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-signals1.54-dev:amd64 Conflicts on libboost-signals1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken libboost-random1.54-dev:amd64 Conflicts on libboost-random1.53-dev [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libdevel )
Broken xserver-xorg-video-nouveau:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken libboost-mpi-python1.53.0:amd64 Depends on libboost-mpi1.53.0 [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libs )
Broken xserver-xorg-video-glamoregl:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-radeon:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken libboost-graph-parallel1.53.0:amd64 Depends on libboost-mpi1.53.0 [ amd64 ] < 1.53.0-6+exp3ubuntu8 > ( libs )
Broken libcogl-pango12:amd64 Depends on libcogl12 [ amd64 ] < 1.14.0-2 > ( libs ) (>= 1.13.4)
Broken libgd-gd2-perl:amd64 Conflicts on libgd-gd2-noxpm-perl [ amd64 ] < none -> 1:2.46-2.1build1 > ( universe/perl )
Broken gnome-control-center-datetime:amd64 Depends on indicator-datetime [ amd64 ] < 13.10.0+13.10.20131023.2-0ubuntu1.1 -> 13.10.0+14.04.20140415.3-0ubuntu1 > ( misc ) (= 13.10.0+13.10.20131023.2-0ubuntu1.1)
Broken libvlccore5:amd64 Depends on vlc-data [ amd64 ] < 2.0.8-1 -> 2.1.2-2build2 > ( universe/graphics ) (= 2.0.8-1)
Broken libperl5.14:amd64 Depends on perl-base [ amd64 ] < 5.14.2-21build1 -> 5.18.2-2ubuntu1 > ( perl ) (= 5.14.2-21build1)
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-ati [ amd64 ] < 1:7.3.99+git20140420.48d3dbc8-0ubuntu0ricotz~saucy > ( x11 )
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-intel [ amd64 ] < 2:2.99.911+git20140429.2fd1a05a-0ubuntu0ricotz~saucy > ( x11 )
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-nouveau [ amd64 ] < 1:1.0.10+git20140220.480f0998-0ubuntu0sarvatt~saucy > ( x11 )
Broken xserver-xorg-video-intel:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-ati:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-nouveau:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-ati [ amd64 ] < 1:7.3.99+git20140420.48d3dbc8-0ubuntu0ricotz~saucy > ( x11 )
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-intel [ amd64 ] < 2:2.99.911+git20140429.2fd1a05a-0ubuntu0ricotz~saucy > ( x11 )
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-nouveau [ amd64 ] < 1:1.0.10+git20140220.480f0998-0ubuntu0sarvatt~saucy > ( x11 )
Broken xserver-xorg-video-intel:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-ati:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-nouveau:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-ati [ amd64 ] < 1:7.3.99+git20140420.48d3dbc8-0ubuntu0ricotz~saucy > ( x11 )
Broken xserver-xorg-video-intel:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-ati:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-nouveau:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-ati [ amd64 ] < 1:7.3.99+git20140420.48d3dbc8-0ubuntu0ricotz~saucy > ( x11 )
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-intel [ amd64 ] < 2:2.99.911+git20140429.2fd1a05a-0ubuntu0ricotz~saucy > ( x11 )
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-nouveau [ amd64 ] < 1:1.0.10+git20140220.480f0998-0ubuntu0sarvatt~saucy > ( x11 )
Broken xserver-xorg-video-intel:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-ati:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-nouveau:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-ati [ amd64 ] < 1:7.3.99+git20140420.48d3dbc8-0ubuntu0ricotz~saucy > ( x11 )
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-intel [ amd64 ] < 2:2.99.911+git20140429.2fd1a05a-0ubuntu0ricotz~saucy > ( x11 )
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-nouveau [ amd64 ] < 1:1.0.10+git20140220.480f0998-0ubuntu0sarvatt~saucy > ( x11 )
Broken xserver-xorg-video-intel:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-ati:amd64 Depends on xserver-xorg-video-glamoregl [ amd64 ] < 0.6.0+git20140313.a4fbc773-0ubuntu0sarvatt~saucy > ( x11 )
Broken xserver-xorg-video-ati:amd64 Depends on xserver-xorg-video-radeon [ amd64 ] < 1:7.3.99+git20140420.48d3dbc8-0ubuntu0ricotz~saucy > ( x11 )
Broken xserver-xorg-video-mach64:amd64 Depends on xorg-video-abi-15 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-r128:amd64 Depends on xorg-video-abi-15 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-glamoregl:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-intel:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-ati:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-radeon:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-nouveau:amd64 Depends on xorg-video-abi-14 [ amd64 ] < none > ( none )
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-ati [ amd64 ] < 1:7.3.99+git20140420.48d3dbc8-0ubuntu0ricotz~saucy > ( x11 )
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-intel [ amd64 ] < 2:2.99.911+git20140429.2fd1a05a-0ubuntu0ricotz~saucy > ( x11 )
Broken xserver-xorg-video-all:amd64 Depends on xserver-xorg-video-nouveau [ amd64 ] < 1:1.0.10+git20140220.480f0998-0ubuntu0sarvatt~saucy > ( x11 )

UPDATE Here is additional info:

[lucas@lucas-ThinkPad-W520]~$ less /etc/apt/sources.list.d/
bumblebee-stable-saucy.list
bumblebee-stable-saucy.list.distUpgrade
bumblebee-stable-saucy.list.save
cassou-emacs-saucy.list
cassou-emacs-saucy.list.distUpgrade
cassou-emacs-saucy.list.save
dropbox.list
dropbox.list.distUpgrade
dropbox.list.save
google-chrome.list
google-chrome.list.distUpgrade
google-chrome.list.save
google-talkplugin.list
google-talkplugin.list.distUpgrade
google-talkplugin.list.save
insync.list
insync.list.distUpgrade
insync.list.save
kilian-f_lux-saucy.list
kilian-f_lux-saucy.list.distUpgrade
kilian-f_lux-saucy.list.save
mongodb.list
mongodb.list.distUpgrade
mongodb.list.save
nemh-gambas3-saucy.list
nemh-gambas3-saucy.list.distUpgrade
nemh-gambas3-saucy.list.save
n-muench-calibre-saucy.list
n-muench-calibre-saucy.list.distUpgrade
n-muench-calibre-saucy.list.save
thefanclub-grive-tools-saucy.list
thefanclub-grive-tools-saucy.list.distUpgrade
thefanclub-grive-tools-saucy.list.save
webupd8team-java-saucy.list
webupd8team-java-saucy.list.distUpgrade
webupd8team-java-saucy.list.save
xorg-edgers-ppa-saucy.list
xorg-edgers-ppa-saucy.list.distUpgrade
xorg-edgers-ppa-saucy.list.save

and also my /etc/apt/sources.list below:

# deb cdrom:[Ubuntu 13.10 _Saucy Salamander_ - Release amd64 (20131016.1)]/ saucy main restricted

# See http://help.ubuntu.com/community/UpgradeNotes for how to upgrade to
# newer versions of the distribution.
deb http://us.archive.ubuntu.com/ubuntu/ saucy main restricted
deb-src http://us.archive.ubuntu.com/ubuntu/ saucy main restricted

## Major bug fix updates produced after the final release of the
## distribution.
deb http://us.archive.ubuntu.com/ubuntu/ saucy-updates main restricted
deb-src http://us.archive.ubuntu.com/ubuntu/ saucy-updates main restricted

## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team. Also, please note that software in universe WILL NOT receive any
## review or updates from the Ubuntu security team.
deb http://us.archive.ubuntu.com/ubuntu/ saucy universe
deb-src http://us.archive.ubuntu.com/ubuntu/ saucy universe
deb http://us.archive.ubuntu.com/ubuntu/ saucy-updates universe
deb-src http://us.archive.ubuntu.com/ubuntu/ saucy-updates universe

## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu 
## team, and may not be under a free licence. Please satisfy yourself as to 
## your rights to use the software. Also, please note that software in 
## multiverse WILL NOT receive any review or updates from the Ubuntu
## security team.
deb http://us.archive.ubuntu.com/ubuntu/ saucy multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ saucy multiverse
deb http://us.archive.ubuntu.com/ubuntu/ saucy-updates multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ saucy-updates multiverse

## N.B. software from this repository may not have been tested as
## extensively as that contained in the main release, although it includes
## newer versions of some applications which may provide useful features.
## Also, please note that software in backports WILL NOT receive any review
## or updates from the Ubuntu security team.
deb http://us.archive.ubuntu.com/ubuntu/ saucy-backports main restricted universe multiverse
deb-src http://us.archive.ubuntu.com/ubuntu/ saucy-backports main restricted universe multiverse

deb http://security.ubuntu.com/ubuntu saucy-security main restricted
deb-src http://security.ubuntu.com/ubuntu saucy-security main restricted
deb http://security.ubuntu.com/ubuntu saucy-security universe
deb-src http://security.ubuntu.com/ubuntu saucy-security universe
deb http://security.ubuntu.com/ubuntu saucy-security multiverse
deb-src http://security.ubuntu.com/ubuntu saucy-security multiverse

## Uncomment the following two lines to add software from Canonical's
## 'partner' repository.
## This software is not part of Ubuntu, but is offered by Canonical and the
## respective vendors as a service to Ubuntu users.
# deb http://archive.canonical.com/ubuntu saucy partner
# deb-src http://archive.canonical.com/ubuntu saucy partner

## This software is not part of Ubuntu, but is offered by third-party
## developers who want to ship their latest software.
# deb http://extras.ubuntu.com/ubuntu saucy main
# deb-src http://extras.ubuntu.com/ubuntu saucy main
deb http://repository.spotify.com stable non-free
# deb-src http://repository.spotify.com stable non-free

To upgrade the core system packages to Trusty, simply run the following:

sudo sed 's/saucy/trusty/g' -i /etc/apt/sources.list
sudo mv /etc/apt/sources.list.d /etc/apt/sources.list.d.bak
sudo apt-get update
sudo apt-get dist-upgrade -y

To upgrade your PPAs, you can either manually select the ones to enable, or do the following:

sudo mv /etc/apt/sources.list.d.bak /etc/apt/sources.list.d
sudo sed 's/saucy/trusty/g' -i /etc/apt/sources.list.d/*
sudo apt-get update
sudo apt-get dist-upgrade -y

I've been upgrading my machines like this for years now without any problems. Sometimes you need to run dist-upgrade a few times, or some new package may overwrite a file that APT refuses to do, so in those cases you can manually dpkg --force-overwrite those packages if you come across them.

Well, I too had a lot of broken packages. I just downloaded the 14.04 ISO and installed with the preserver data option. It preserves all your data, but it will delete all non-supported packages.

But when you reinstall them, their data is not lost.

The above applies, of course, if your /home and / are on different partitions. If they are on the same partition, you'll either want to back up /home, reinstall and restore or fix your packages.

Also try:

$ sudo apt-get install --fix-broken

That will clean up as much as it can.

Happy to help.