PI B+ install error and Firmware update fail

[pcote_pi]

Performed script to install, upgrade, update distribution and update firmware

pi@pi-clear ~/my_scripts $ sudo ./update_pi.sh
Sun Feb 15 11:04:06 EST 2015
**********************************
UPDATING SYSTEM SOFTWARE – UPDATE
**********************************
Hit http://repository.wolfram.com stable Release.gpg
Hit http://repository.wolfram.com stable Release
Hit http://raspberrypi.collabora.com wheezy Release.gpg
Hit http://mirrordirector.raspbian.org wheezy Release.gpg
Hit http://archive.raspberrypi.org wheezy Release.gpg
Hit http://raspberrypi.collabora.com wheezy Release
Hit http://mirrordirector.raspbian.org wheezy Release
Hit http://repository.wolfram.com stable/non-free armhf Packages
Hit http://archive.raspberrypi.org wheezy Release
Hit http://raspberrypi.collabora.com wheezy/rpi armhf Packages
Hit http://mirrordirector.raspbian.org wheezy/main armhf Packages
Hit http://mirrordirector.raspbian.org wheezy/contrib armhf Packages
Hit http://archive.raspberrypi.org wheezy/main armhf Packages
Hit http://mirrordirector.raspbian.org wheezy/non-free armhf Packages
Ign http://repository.wolfram.com stable/non-free Translation-en_GB
Ign http://repository.wolfram.com stable/non-free Translation-en
Hit http://mirrordirector.raspbian.org wheezy/rpi armhf Packages
Ign http://raspberrypi.collabora.com wheezy/rpi Translation-en_GB
Ign http://raspberrypi.collabora.com wheezy/rpi Translation-en
Ign http://archive.raspberrypi.org wheezy/main Translation-en_GB
Ign http://archive.raspberrypi.org wheezy/main Translation-en
Ign http://mirrordirector.raspbian.org wheezy/contrib Translation-en_GB
Ign http://mirrordirector.raspbian.org wheezy/contrib Translation-en
Ign http://mirrordirector.raspbian.org wheezy/main Translation-en_GB
Ign http://mirrordirector.raspbian.org wheezy/main Translation-en
Ign http://mirrordirector.raspbian.org wheezy/non-free Translation-en_GB
Ign http://mirrordirector.raspbian.org wheezy/non-free Translation-en
Ign http://mirrordirector.raspbian.org wheezy/rpi Translation-en_GB
Ign http://mirrordirector.raspbian.org wheezy/rpi Translation-en
Reading package lists... Error!
E: Problem syncing the file - sync (5: Input/output error)
E: The package lists or status file could not be parsed or opened.
**********************************
UPDATING SYSTEM SOFTWARE – UPGRADE
**********************************
Reading package lists... Done
Building dependency tree
Reading state information... Done
You might want to run 'apt-get -f install' to correct these.
The following packages have unmet dependencies:
libraspberrypi-doc : Depends: libraspberrypi0 (= 1.20150130-1) but 1.20150212-1 is installed
libraspberrypi0 : Depends: raspberrypi-bootloader (= 1.20150212-1) but 1.20150130-1 is installed
E: Unmet dependencies. Try using -f.
***************************************
UPDATING SYSTEM SOFTWARE – DISTRIBUTION
***************************************
Reading package lists... Done
Building dependency tree
Reading state information... Done
You might want to run 'apt-get -f install' to correct these.
The following packages have unmet dependencies:
libraspberrypi-doc : Depends: libraspberrypi0 (= 1.20150130-1) but 1.20150212-1 is installed
libraspberrypi0 : Depends: raspberrypi-bootloader (= 1.20150212-1) but 1.20150130-1 is installed
E: Unmet dependencies. Try using -f.
*****************************
REMOVING APPLICATION ORPHANS
*****************************
Reading package lists... Done
Building dependency tree
Reading state information... Done
You might want to run 'apt-get -f install' to correct these.
The following packages have unmet dependencies:
libraspberrypi-doc : Depends: libraspberrypi0 (= 1.20150130-1) but 1.20150212-1 is installed
libraspberrypi0 : Depends: raspberrypi-bootloader (= 1.20150212-1) but 1.20150130-1 is installed
E: Unmet dependencies. Try using -f.
*****************
UPDATING FIRMWARE
*****************
*** Raspberry Pi firmware updater by Hexxeh, enhanced by AndrewS and Dom
*** Performing self-update
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 7938 100 7938 0 0 18848 0 --:--:-- --:--:-- --:--:-- 31375
*** Relaunching after update
*** Raspberry Pi firmware updater by Hexxeh, enhanced by AndrewS and Dom
*** Downloading specific firmware revision (this will take a few minutes)
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 168 0 168 0 0 458 0 --:--:-- --:--:-- --:--:-- 815
100 43.3M 100 43.3M 0 0 690k 0 0:01:04 0:01:04 --:--:-- 869k
*** Updating firmware
*** Updating kernel modules
cp: cannot overwrite non-directory `//lib/modules/3.18.7-v7+/kernel/drivers/net/bonding' with directory `//root/.rpi-firmware/modules/3.18.7-v7+/kernel/drivers/net/bonding'
cp: cannot overwrite non-directory `//lib/modules/3.18.7-v7+/kernel/drivers/net/irda' with directory `//root/.rpi-firmware/modules/3.18.7-v7+/kernel/drivers/net/irda'
Press [Enter] to exit


Try to repair:

pi@pi-clear ~ $ sudo apt-get -f install
Reading package lists... Done
Building dependency tree
Reading state information... Done
Correcting dependencies... Done
The following extra packages will be installed:
libraspberrypi-doc raspberrypi-bootloader
The following packages will be upgraded:
libraspberrypi-doc raspberrypi-bootloader
2 upgraded, 0 newly installed, 0 to remove and 7 not upgraded.
6 not fully installed or removed.
Need to get 0 B/72.2 MB of archives.
After this operation, 437 kB of additional disk space will be used.
Do you want to continue [Y/n]? y
dpkg: warning: parsing file '/var/lib/dpkg/available' near line 5926 package 'libobt0':
missing description
dpkg: error: parsing file '/var/lib/dpkg/available' near line 5926 package 'libobt0':
missing version
E: Sub-process /usr/bin/dpkg returned an error code (2)

[rpdom]

It looks like the script failed during the update phase. There is no point carrying on with the other steps after that because the index files are damaged and need to be rebuilt.

First try manually running "sudo apt-get update" and see what that shows. It may give additional messages.

[pcote_pi]

Allo,
To correct I did the following:

sudo apt-get -y -f update
sudo apt-get -y -f upgrade
rebooted

Result:
Unable to boot, raspbian no longer works. OpenElec does work OK.

I am forced to re-install everything.

[rpdom]

That sounds like it may have been some corruption on the SD card

[pcote_pi]

Maybe but since sept 2014 to pi2 release ... never add problems?

I restored twice the model B+. Now I am getting:

pi@pi-clear ~/my_scripts $ sudo apt-get upgrade -f
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be upgraded:
wolfram-engine
1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/229 MB of archives.
After this operation, 3,674 kB disk space will be freed.
Do you want to continue [Y/n]? y
Preconfiguring packages ...
(Reading database ... 96656 files and directories currently installed.)
Preparing to replace wolfram-engine 10.0.0+2014080602 (using .../wolfram-engine_10.0.2+2015020304_armhf.deb) ...
wolfram-eula license has already been accepted
Unpacking replacement wolfram-engine ...
dpkg-deb (subprocess): decompressing archive member: internal gzip read error: '<fd:4>: incorrect data check'
dpkg-deb: error: subprocess <decompress> returned error exit status 2
dpkg: error processing /var/cache/apt/archives/wolfram-engine_10.0.2+2015020304_armhf.deb (--unpack):
subprocess dpkg-deb --fsys-tarfile returned error exit status 2
Processing triggers for desktop-file-utils ...
Processing triggers for hicolor-icon-theme ...
Processing triggers for man-db ...
Processing triggers for shared-mime-info ...
Errors were encountered while processing:
/var/cache/apt/archives/wolfram-engine_10.0.2+2015020304_armhf.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)
pi@pi-clear ~/my_scripts $


Since the pi2 release, unable to get flawless B+ apt-get.