[SOLVED]Made mistake in Jessie upgrade - should I reinstall?

[chairs]

I have a Mbp 9,2 and I upgraded from Wheezy to Jessie. I thought that everything I did in the terminal was as the Jessie amd64 release notes say but I think that I may have accidentally hit

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apt-get upgrade

instead of

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apt-get dist-upgrade

right after the repositories had been switched to Jessie. The computer is pretty much totally screwed. I can't delete files, install any new packages or really do anything at all. (I previously started a thread about how the wi-fi would work but it is no longer relevant because I can't install firmware and the system configuration issue is different; I'd delete the thread if I could.) Should I just get rid of everything on my mbp now and reinstall Debian 8?

This is the code I receive when I do

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apt-get upgrade

:

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Setting up biomaj (1.2.3-4) ...
Option dbhost requires an argument
You need to configure the database access before executing the upgrade
Execute the script manually once configuration is done
 ***************************************************************************************
Before running the migration, please check that database configuration is correctly set 
and that the database schema and user are correctly created.
To upgrade the database, the script must be run with the following arguments:
  For a first install, all arguments are mandatory, for an upgrade, only some parameters are required.
  - First install: [ -dbuser DBUSER -dbpwd DBPASSWORD -dbhost DBHOST -db (mysql|hsql)]
  - From v1.1 : 	  [ -admin LOGIN -adminpwd PASSWORD -adminemail  ADMINEMAIL]

To get the current version, execute: biomaj --version
Died at /var/lib/biomaj/migration/update.pl line 32.
dpkg: error processing package biomaj (--configure):
 subprocess installed post-installation script returned error exit status 2
dpkg: dependency problems prevent configuration of biomaj-watcher:
 biomaj-watcher depends on biomaj (>= 1.2.1); however:
  Package biomaj is not configured yet.

dpkg: error processing package biomaj-watcher (--configure):
 dependency problems - leaving unconfigured
Errors were encountered while processing:
 biomaj
 biomaj-watcher
E: Sub-process /usr/bin/dpkg returned an error code (1)

When I did

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apt-get install firmware-linux-nonfree

I was given nearly the same message:

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Reading package lists... Done
Building dependency tree       
Reading state information... Done
firmware-linux-nonfree is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
2 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Do you want to continue? [Y/n] y
Setting up biomaj (1.2.3-4) ...
Option dbhost requires an argument
You need to configure the database access before executing the upgrade
Execute the script manually once configuration is done
 ***************************************************************************************
Before running the migration, please check that database configuration is correctly set 
and that the database schema and user are correctly created.
To upgrade the database, the script must be run with the following arguments:
  For a first install, all arguments are mandatory, for an upgrade, only some parameters are required.
  - First install: [ -dbuser DBUSER -dbpwd DBPASSWORD -dbhost DBHOST -db (mysql|hsql)]
  - From v1.1 : 	  [ -admin LOGIN -adminpwd PASSWORD -adminemail  ADMINEMAIL]

To get the current version, execute: biomaj --version
Died at /var/lib/biomaj/migration/update.pl line 32.
dpkg: error processing package biomaj (--configure):
 subprocess installed post-installation script returned error exit status 2
dpkg: dependency problems prevent configuration of biomaj-watcher:
 biomaj-watcher depends on biomaj (>= 1.2.1); however:
  Package biomaj is not configured yet.

dpkg: error processing package biomaj-watcher (--configure):
 dependency problems - leaving unconfigured
Errors were encountered while processing:
 biomaj
 biomaj-watcher
E: Sub-process /usr/bin/dpkg returned an error code (1)

I'm not sure what went wrong. I didn't have a ton of unnecessary packages; maybe I upgraded to the Jessie sources before doing

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dist-upgrade

. I looked on the Debian bug e-mailing list for an issue with biomaj, and similar issues involving errors processing and configuring it were posted by Debian users but they were apparently solved months before Jessie was released, so I am very sure than it isn't biomaj.

So, guys, should I just erase everything on the hard drive and reinstall? Thanks.[/quote]

[Head_on_a_Stick]

Have you tried:

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# apt-get dist-upgrade

You haven't read the release notes carefully enough:
https://www.debian.org/releases/stable/ ... al-upgrade

[Bulkley]

Can you post your /etc/apt/sources.list, /etc/apt/preferences and /etc/apt/trusted.gpg.d. What I'm looking for is anything that would give you a bum steer.

BTW, it is always safer to do major upgrades from a console.

[Ardouos]

Its generally recommended in a terminal environment to run upgrade before dist-upgrade

[fireExit]

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Execute the script manually once configuration is done
 ***************************************************************************************
Before running the migration, please check that database configuration is correctly set 
and that the database schema and user are correctly created.
To upgrade the database, the script must be run with the following arguments:
  For a first install, all arguments are mandatory, for an upgrade, only some parameters are required.
  - First install: [ -dbuser DBUSER -dbpwd DBPASSWORD -dbhost DBHOST -db (mysql|hsql)]
  - From v1.1 :      [ -admin LOGIN -adminpwd PASSWORD -adminemail  ADMINEMAIL]

To get the current version, execute: biomaj --version
Died at /var/lib/biomaj/migration/update.pl line 32.
dpkg: error processing package biomaj (--configure):

biomaj was not configured neither at install time nor now during the upgrade;
If you care for that app. see how to configure it properly (man biomaj; /usr/share/biomaj/bin$ /.biomaj.sh)
If not

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dpkg -r biomaj

it's a dirty workaround but clears the apt errors.

[chairs]

Thank you all for responses, guys! Still figuring it out. I also should've included that during boot I get an error involving the LSB dependency network. And, before I log in, I'm shown a black screen for a few seconds that shows "myname: login" with "Debian GNU/Linux" above it and then I'm given the "regular" login interface that every Debian user logs in with.

And there are only ten applications in the desktop environment (Iceweasel, VLC, Chromium, LibreOfficeWriter, Transmission, Terminal, Settings, Image Viewer, Tweak Tool and Files) and I can't delete any files (when looking through Files I don't have the option to delete a file, and a few other less than I had in the OS before.)
The terminal also responds that the non-free firmware is installed but the Network only displays the Wired connection and the Network Proxy.

Can you post your /etc/apt/sources.list, /etc/apt/preferences and /etc/apt/trusted.gpg.d. What I'm looking for is anything that would give you a bum steer.

BTW, it is always safer to do major upgrades from a console.

Yup! The /etc/apt/sources.list is:

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deb http://ftp.us.debian.org/debian/ jessie main contrib non-free
deb-src http://ftp.us.debian.org/debian/ jessie main contrib non-free

deb http://security.debian.org/ jessie/updates main contrib non-free
deb-src http://security.debian.org/ jessie/updates main contrib non-free

deb http://http.debian.net/debian jessie-updates main contrib non-free
deb-src http://http.debian.net/debian jessie-updates main contrib non-free

There is nothing written for "/etc/apt/preferences". Could the same thing be under a different name and if so what would that name be? And nothing for /etc/apt/trusted.gpg.d, either.
What next?

[Bulkley]

You have duplicate updates in your sources list. Do yourself a favour to start. Cut your sources back to deb http://ftp.ca.debian.org/debian/ jessie main. Block everything else. Then apt-get update && apt-get upgrade. After that apt-get update && apt-get dist.upgrade.
do this all in a console without X running. When your machine is running properly you can add contrib and do it again. If all is well, you can add the security and updates lines.

[fireExit]

You have duplicate updates in your sources list. Do yourself a favour to start. Cut your sources back to deb http://ftp.ca.debian.org/debian/ testing main contrib. Block everything else. Then apt-get update && apt-get upgrade. After that apt-get update && apt-get dist.upgrade.
do this all in a console without X running. When your machine is running properly you can add the security and updates lines.

Nonsense!
Advise the OP to swap repos to Testing and dist-upgrade, specially when apt is still broken!

[Bulkley]

Nonsense!
Advise the OP to swap repos to Testing and dist-upgrade, specially when apt is still broken!

Oops! You are absolutely right. It slipped my mind for a moment that Jessie isn't Testing anymore. Sorry. [I edited the above post to fix this.] So substitute Jessie for Testing and I would still do as I said. With the sources cut back to minimum, apt-get update && apt-get upgrade may clean it up. I've seen it before and that's where I would start.

When I do a big upgrade, such as Wheezy to Testing, I revert to basics, work as simply as possible with CLI in a console and test the machine at appropriate intervals. It may seem silly to some but it eliminates a lot of hassle.

fireExit, thanks for pointing out my error.

[chairs]

Nonsense!
Advise the OP to swap repos to Testing and dist-upgrade, specially when apt is still broken!

Oops! You are absolutely right. It slipped my mind for a moment that Jessie isn't Testing anymore. Sorry. [I edited the above post to fix this.] So substitute Jessie for Testing and I would still do as I said. With the sources cut back to minimum, apt-get update && apt-get upgrade may clean it up. I've seen it before and that's where I would start.

When I do a big upgrade, such as Wheezy to Testing, I revert to basics, work as simply as possible with CLI in a console and test the machine at appropriate intervals. It may seem silly to some but it eliminates a lot of hassle.

fireExit, thanks for pointing out my error.

This is what I did and everything is working well now. Gonna put 'solved' in the title. Thanks a lot guys!!!