Re: [Bug 1956094] Re: deborphan guess-work removes too many files
Hi Tony, Am Sat, Jan 01, 2022 at 01:18:40PM + schrieb Tony Travis: > > The Debian/Ubuntu "upgrade-system" package automates updating the APT > package list, installing updated packages and removing 'orphaned' packages. > It is very convenient for unattended upgrades of multiple computers because > it can either be run interactively, or without a controlling terminal. Ahhh, I was not aware of this package. ;-) > It appears that a recent upgrade unconditionally overwrote my edited > "upgrade-system.conf", Hmmm, that should not happen by definition of "config file" since these should not be overridden, > which resulted in most of the packages installed by > "med-bio-dev" being removed from five of my bioinformatics servers. That should also not happen even if you do not configure anything. As far as I understood `deborphan` it reports only those packages that are installed via dependencies while the package that needed those dependencies was removed. So if your system is featuring med-bio-dev none of its dependencies should be reported by deborphan. To track down the issue you should probably report apt policy med-bio-dev and also report what packages were reported by deborphan. Kind regards Andreas. -- http://fam-tille.de
Re: [Bug 1956094] Re: deborphan guess-work removes too many files
On 31/12/2021 21:53, Andreas Tille wrote: [...] Sorry, but I do not understand the problem. What config files are you talking about? What is "upgrade-system"? I'm using the command `deborphan` itself just to learn what package might be a potential candidate for removal. From time to time I'm using apt purge `deborphan` but well, that's users responsibility. To learn what is really a "bug" we need more information that this quoted mail. Hi, Andreas. The Debian/Ubuntu "upgrade-system" package automates updating the APT package list, installing updated packages and removing 'orphaned' packages. It is very convenient for unattended upgrades of multiple computers because it can either be run interactively, or without a controlling terminal. The "upgrade-system" config file is: /etc/upgrade-system.conf By default, "upgrade-system" allows "deborphan to 'guess' which packages to remove: ORPHANOPTS="--guess-all --libdevel" This removes too many packages that are installed by "med-bio-dev' in particular, so I edited the config file to stop "deborphan" guessing: ORPHANOPTS="--no-guess-all --libdevel" It appears that a recent upgrade unconditionally overwrote my edited "upgrade-system.conf", which resulted in most of the packages installed by "med-bio-dev" being removed from five of my bioinformatics servers. Yes, it is a user's responsibility to check but I was caught out by it recently so I posted a bug report because I thought other people might also have the same problem when using "upgrade-system" with defaults. The "upgrade-system" package is very convenient, but the default settings allow "deborphan" to guess what to remove. In my experience, that often results in "deborphan" removing packages that are needed. Happy New Year :-) Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548http://minke-informatics.co.uk mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk
Re: [Bug 1956094] Re: deborphan guess-work removes too many files
Hi Tony, Am Fri, Dec 31, 2021 at 12:42:38PM + schrieb Tony Travis: > > I *have* edited the configuration file, but the "deborphan" default has just > caused a lot of damage on multiple systems where I use "upgrade-system" it > appears to have overwritten my edited config files during a recent upgrade > and, as I reported, "deborphan" removed a large number of packages from five > of my servers where I have installed "med-bio" and "med-bio-dev" from the > Debian-Med project. I edited the config file after initially running > "upgrade-system" precisely because of this. > > I'm surprised that nobody else has been bitten by this bug! Sorry, but I do not understand the problem. What config files are you talking about? What is "upgrade-system"? I'm using the command `deborphan` itself just to learn what package might be a potential candidate for removal. From time to time I'm using apt purge `deborphan` but well, that's users responsibility. To learn what is really a "bug" we need more information that this quoted mail. Kind regards Andreas. -- http://fam-tille.de
Re: [Bug 1956094] Re: deborphan guess-work removes too many files
On 31/12/2021 12:23, Martin-Éric Racine wrote: Those defaults work for the majority of people. Settings can be changed as desired by editing the configuration file. ** Changed in: upgrade-system (Ubuntu) Status: New => Won't Fix Hi, Marin. I *have* edited the configuration file, but the "deborphan" default has just caused a lot of damage on multiple systems where I use "upgrade-system" it appears to have overwritten my edited config files during a recent upgrade and, as I reported, "deborphan" removed a large number of packages from five of my servers where I have installed "med-bio" and "med-bio-dev" from the Debian-Med project. I edited the config file after initially running "upgrade-system" precisely because of this. I'm surprised that nobody else has been bitten by this bug! Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548http://minke-informatics.co.uk mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk
