Borked apt-get, maybe found bug, need help fixing system

[jamesisin]

And by that you mean the user must remember any and all software installed (including any dependencies) from a non-Ubuntu source and purge said software prior to running the version upgrade for the OS?

[ian-weisser]

Yes.
You -the system owner or admin- are ultimately responsible for the stuff you choose to install on your system, including if you choose to install unsupported stuff that breaks the package manager.

You can install unsupported stuff from PPAs all you want. Go ahead. I do it too. But you must keep track of it...because it occasionally causes problems like yours. Not every time. Not most times. But enough.

That's why we recommend using the Ubuntu Repositories when possible. If you fish around these forums, you will find no less than six active threads that I'm following where a PPA or other non-Ubuntu software has broken a user's system by breaking package management. None are the fault of the package manager. I know of zero active threads where Ubuntu Repository software has broken a user's system the same way.

[jamesisin]

If that's important and if the system allows the adding of additional repositories, why has no one created a simple method by which one might ask the system "which packages do I have installed from repository X?"?

This would seem obvious if one is expected to remove said packages prior to upgrading the OS.

I mean, the upgrading software (update-manager installs an additional piece of software to manage the version upgrade but I don't recall its name) does warn users to disable additional repositories; in fact if memory serves it disables them itself; but there is certainly no mention of rooting out any packages which may have been previously installed through said repos.

I should think if this were, as you seem to imply, a best practice there would be some mention of it. Here are the three top hits from Google for upgrading from 13.10 to 14.04:

http://www.tecmint.com/upgrade-ubuntu-to-14-04/

https://wiki.ubuntu.com/TrustyTahr/R...m_Ubuntu_13.10

https://help.ubuntu.com/community/TrustyUpgrades

None of them make any mention of removing non-Ubuntu repositories, software, or dependencies.

In my case there were other anomalies in the list of repositories. I am dubious of the idea that the mere presence of those packages is what broke the package manager. Apt was unable to overwrite a file; regardless of the source of said file, that's a different sort of issue.

Why wasn't apt able to overwrite the file? Why wasn't apt able to remove the file?

Finally I have upgraded other machines having those same repositories and not run into this same issue (nor the odd entries in the repo list).

Yes, I am going to remain dubious that your theory is exactly correct (though there are compelling elements to it). Perhaps though I have misunderstood your case and your forensic analysis is more enticing than my vision of it.

[Yellow Pasque]

If that's important and if the system allows the adding of additional repositories, why has no one created a simple method by which one might ask the system "which packages do I have installed from repository X?"?

You can see that in Synaptic by sorting with the 'Origin' button.

This would seem obvious if one is expected to remove said packages prior to upgrading the OS.

That's what ppa-purge is for.

Why wasn't apt able to overwrite the file? Why wasn't apt able to remove the file?

Because it's against Debian policy to overwrite files from other packages or just remove individual files. If apt did that, things would get very messy...

I do feel your pain, though. I'm not a big fan of the 6 month upgrade dance or its many anomalies (that's why I switched to Debian sid so I could just roll). I;m of the opinion that Ubuntu should only release LTS versions and just let the non-LTS users roll (especially since they cut down non-LTS support to 9 months). I'm getting off-topic though...

[bapoumba]

Why wasn't apt able to overwrite the file? Why wasn't apt able to remove the file?

Finally I have upgraded other machines having those same repositories and not run into this same issue (nor the odd entries in the repo list).

apt deals with dependencies. dpkg does what apt instructs it to do, ie install this or remove that. dpkg does not care about dependencies, that is left to the package manager to decide. Packages tell the package manager which versions of which file they depend upon, and the package manager's duty is to keep all dependencies and all versions coherent in a given distribution. If there is a conflict, then they tell the user and the user has to fix it.

Maybe the other machines did not have the same packages installed than the one giving you troubles ?