[SOLVED] mdadm conflicts with mkinitcpio but it is not even installed

lucasyata · 2024-08-13 01:34:50

Hi

§ Conclusion

What I got wrong
When I was trying to install nautilus, I thought was pacman was saying "mdadm is installed and is conflicting with mkinitcpio" when I knew for a fact mdadm was not installed.
→This is why I thought it was some messed up configuration and not something caused by the age of my system.

But turns out what pacman was saying was "In order to install the package(nautilus) you need mdadm, but installing it would create a conflict with mkinitcpio".

It makes sense because my system was really old; 1 year+ since I installed it, and installing the last version of a program usually requires the last version of the packages it depends on, which depend on more last version packages, creating a chain of dependencies that at some point will create a conflict with some old package/s.

If I knew what pacman really meant, then I wouldn't have made this post. As I would have know that my options were to update the whole system or simply install an old version of the package that wouldn't create conflicts.

What I did
I updated the system. Even though it is something very inconvenient, I went ahead and did it. After that there was no conflict with any old package and nautilus installed just fine.

Thanks to both seth and Scimmia for taking the time to help me, for reading my lengthy replies and for being so patient with me ♥️

§ Original post: What the problem was

I just wanted to install some gui file explorer to use in my twm setup. But when trying to install it I was prompted this:

resolving dependencies...
looking for conflicting packages...
:: mdadm and mkinitcpio are in conflict. Remove mkinitcpio? [y/N] n
error: unresolvable package conflicts detected
error: failed to prepare transcription (conflicting dependencies)
:: mdadm and mkinitcpio are in conflict (mkinitcpio<38)

Note: I manually typed the console message here as I have found no way to copy and paste it directly out of xterm. Every output will be like that unless otherwise mentioned. If you find any typo, I apologize in advance and feel free to point it out to me if you want. I will happily correct it

Before I elaborate further, I want to point out an important detail: I have not updated my system since a lot of time.
I have internet access through a (very limited) mobile data plan and I cannot afford updating my system. And frankly, I would rather avoid it as I am happy with the use I give to my pc as it is right now. And updating comes with the risk of breaking stuff, which, because of my last point, I am not interested in running.
I mention this because I know that one of the rules is to update the system before posting and I don't want to waste your time guys. Updating my system is not completely off the table as I can pull some strings here and there and do it, but I would really like to not

Ok. So, getting deeper into the topic...

What I have tried: deleting mdadm

I first searched what mdadm is, and turns out is some kind of framework for raid volumes. As I don't use raid volumes and I don't ever see plausible for me to work with them anytime soon I decided to uninstall it. But turns out it seems to not be installed...
I executed `pacman -R mdadm` but it said that the target was not found.
`pacman -Ss mdadm` outputs:

core/mdadm 4.3-2
     A tool for managing/monitoring Linux md device arrays, also known as Software RAID

No tag about it being installed to be seen.
I have no idea why this happens...

What I have tried: updating mkinitcpio

at the end of the error message when updating nautilus it says `:: mdadm and mkinitcpio are in conflict (mkinitcpio<38)`, which I interpret as "mkinitcpio conflicts with mdadm because it is a version inferior to 38" so updating it would surely get it to a version above 38 and thus solve the problem. Thus, I tried that... `doas pacman -S mkinitcpio` outputs:

resolving dependencies...
looking for conflicting package...

Packages (1) mkinitcpio-39.2-2

Total Download Size:    0.06 MiB
Total Installed Size:       0.20 MiB
Net Upgrade Size:         0.04 MiB

:: Proceed with installation? [Y/n] Y
:: Retrieving packages...
mkinitcpio-39.2...    64.1 KiB  45.7 KiB/s 00:01 [######################] 100%
(1/1) checking keys in keyring                             [######################] 100%
(1/1) checking package integrity                         [######################] 100%
(1/1) loading package files                                   [######################] 100%
(1/1) checking for file conflicts                             [######################] 100%
error: failed to commit transaction (conflicting files)
mkinitcpio: /usr/lib/initcpio/hooks/encrypt exists in filesystem (owned by cryptsetup)
mkinitcpio: /usr/lib/initcpio/hooks/udev exists in filesystem (owned by systemd)
mkinitcpio: /usr/lib/initcpio/install/encrypt exists in filesystem (owned by cryptsetup)
mkinitcpio: /usr/lib/initcpio/install/sd-encrypt exists in filesystem (owned by cryptsetup)
mkinitcpio: /usr/lib/initcpio/install/systemd exists in filesystem (owned by systemd)
mkinitcpio: /usr/lib/initcpio/install/udev exists in filesystem (owned by systemd)
Errors occured, no packages were updated.

Ok. Clearly I cannot. One thing to point out is that I have never done anything with pacman hooks myself. I have read about them and I think I have an idea of what they do and how they work. But I had left the system take care of them as I have not desired to do anything especial with them. I say this because some of the conflicting files seem to be hooks.

One thing that gets my attention is that pacman checks for conflicting packages right away, but the error comes out after I proceed with the installation. Weird.

What I have tried: Removing cryptsetup

A google search later I find out this package is for handling encripted partitions(luks and stuff). Well, not like I care so if I removed the package, part of the conflict, at least, would be solved. But it would break a dependency with systemd. and of course I wouldn't uninstall systemd because of this-- it would be far too much of an overkill. Although I have heard of many people that are unsettled by the amount of things systemd handles. For me tho it works fine and that's what I care right now--

What I have read

Pacman's troubleshooting section
Regarding 3.1: I didn't wanna file a bug report just yet because I feel it's something on my side. I don't want to send out red hearings and waste someone else's time without having some reasons to think it's an error of the packages.
Regarding 3.2: doesn't seem to be fault of the keyring or some partial packages as those I have tried to install seem fine; they don't seem to be corrupted, or invalid or anything.
This post related to files already existing
I didn't install any packages manually.

Thanks for reading and have a good day

Last edited by lucasyata (2024-08-19 23:29:11)

Scimmia · 2024-08-13 02:00:51

Full system update. Always.Stop doing partial updates, you WILL destroy your system.

If you can't update, you can't really use Arch.

ETA: If you're that limited, you really need to be using an LTS distro that only gets infrequent security-only updates.

Last edited by Scimmia (2024-08-13 03:44:06)

lucasyata · 2024-08-13 17:08:24

Scimmia wrote:

Full system update. Always.Stop doing partial updates, you WILL destroy your system.

I understand the rolling release/cutting edge dilema. But I don't randomly update parts of my system. I don't remember to ever have updated a package. I really don't care about most functionality nor about the security updates can provide.

If you can't update, you can't really use Arch.

I've had this arch installation for over a year, almost two years now and never run into any problem of the type "system breaking". This seems to be a trivial pacman issue. But with "trivial" I don't mean I know how to solve it, but rather that it is a small scope problem; it affects only three packages. Based on (the little) I know of pacman, this doesn't seem to be a problem derived from not updating the system; not updating shouldn't create conflicts between the packages' files right? Also it seems weird to me that the the files in conflict create problems... Like ".../initcpio/install/systemd is owned by systemd" why wouldn't it? Why does that create conflict? The same with cryptsetup.

To be frank, I don't even know since when this is occuring since I very occasionally install anything in the system.

ETA: If you're that limited, you really need to be using an LTS distro that only gets infrequent security-only updates.

As system reasons go, I like the minimalism arch provides; it allows me to have as much as I need, using little bandwidth every absurdly long periods of time and using little disk space. Also I like pacman.
There's also community reasons, I like the people I have met in the community, I like the philosophy arch is founded on and I like the wiki(really good stuff)

Anyway... I will keep trying stuff up. In any case if I succeed maybe someone who finds this post with a similar problem can find a solution or something to work with. After all, Life is a two-way street isn't it?

Last edited by lucasyata (2024-08-13 17:11:17)

Scimmia · 2024-08-13 17:15:26

You're trying to install newer software than is on the rest of your system, that's a partial update. This isn't a trivial pacman issue, it's an issue with how Arch is designed and packaged. Doing what you're doing is specifically not supported by Arch, by choice, at the most basic level.

And for the record, yes, this problem is ENTIRELY because you're not updating the system.

Last edited by Scimmia (2024-08-13 17:21:05)

xerxes_ · 2024-08-13 17:39:46

@lucasyata

So you are saying that command 'sudo pacman -Syu' don't work for you or you just don't want to use it?

Scimmia · 2024-08-13 17:46:30

xerxes_ wrote:

@lucasyata
So you are saying that command 'sudo pacman -Syu' don't work for you or you just don't want to use it?

From the original post:

lucasyata wrote:

Before I elaborate further, I want to point out an important detail: I have not updated my system since a lot of time.
I have internet access through a (very limited) mobile data plan and I cannot afford updating my system. And frankly, I would rather avoid it as I am happy with the use I give to my pc as it is right now. And updating comes with the risk of breaking stuff, which, because of my last point, I am not interested in running.
I mention this because I know that one of the rules is to update the system before posting and I don't want to waste your time guys. Updating my system is not completely off the table as I can pull some strings here and there and do it, but I would really like to not

seth · 2024-08-13 23:29:02

Note: I manually typed the console message here as I have found no way to copy and paste it directly out of xterm.

https://wiki.archlinux.org/title/Clipboard#Selections - PRIMARY

I executed `pacman -R mdadm` but it said that the target was not found.

Your desired filebrowser will depend on udisks2, udisks2 on libblockdev-mdraid and that on mdadm which (next to all the other issues w/ partial updates) conflicts with older versions of mkinitcpio.
You could install older versions of filebrowser, udisks and mdadm from the ALA, https://wiki.archlinux.org/title/Arch_L … cific_date but that's completely insane.

I have internet access through a (very limited) mobile data plan

I'm not telling you to violate any TOS but a cursory google suggests that uruguay is a free-wifi heaven?
nb. that you can can separate download(s) into the local cache and actual update, "pacman -Sw"

lucasyata · 2024-08-18 05:58:04

Sorry for the delay, I have been pretty busy this week

seth wrote:

https://wiki.archlinux.org/title/Clipboard#Selections - PRIMARY

Oh sweet! I didn't know and I always forget my laptop's mouse pad has a middle mouse click so never tried that. Thanks!

You could install older versions of filebrowser, udisks and mdadm from the ALA, https://wiki.archlinux.org/title/Arch_L … cific_date but that's completely insane.

Yeah, not doing that lol
Seems too much of an overkill bc to downgrade udisks I should probably downgrade a lot of stuff and bc of the partial updates deal, I should probably downgrade the whole system. Plus it's likely I break a lot of things and possibly lose configurations and stuff. And rather than spending a lot of bandwidth downgrading the system, and risking to break stuff I would rather spend a lot of bandwidth updating the system risking to break stuff that way.

Your desired filebrowser will depend on udisks2, udisks2 on libblockdev-mdraid and that on mdadm which (next to all the other issues w/ partial updates) conflicts with older versions of mkinitcpio.

Oh! So you imply that what pacman was saying is that mdadm is a dependecy(indirect in this case) of the file explorer I was trying to install, and that it couldn't be installed because of the conflict with mkinitcpio. Not that the package was installed and there was a conflict, but that if the package were to be installed, there would be a conflict, so pacman wouldn't install it. Now it makes sense...
I just tested it installing the last version of nano, which didn't had any dependency to be installed and consumed next to no bandwidth. And it let me do it...

That never crossed my mind, I would imagine it would say something that lets you know explicitly that it is not installed...
As I couldn't find much explanation for what was going on navigating the documentation I could find, I have been reading pacman's source code. And I managed to trace what was going on in my screen, from the main function(start of the program) down to a function of the alpm library called "_alpm_sync_prepare". I wanted to know what pacman was doing to think mdadm was installed when it wasn't. But now I know I interpreted it wrong. Although his week I have been busy and I couldn't take a further look into it. May I ask...

Do you know why does pacman check the dependencies twice? Or rather, what is pacman doing the first and second time it checks for dependencies?
I just thought that before even prompting you to continue the sync it would check for conflicts between packages already installed, and before the prompt it would check for conflicts between the packages already installed and the ones to be installed. But in my case it prompted the conflict before even asking me if I would like to continue. So may it be that it does those two checks but in the inverse order or something?

I'm not telling you to violate any TOS but a cursory google suggests that uruguay is a free-wifi heaven?

I would guess you have found an old new about the government installing free wifi in every house of the country. It was something the president of the year 2012 wanted to do. For obvious reasons it never came to be turn into a reality (costs and stuff). Anyway, here where I live there are some places with a free wifi connection but they're very inconvenient; some are provided by business and you can only access those networks at the entrance. Some are very far from home. And some are pretty noise(I am pretty sensitive to loud noises). Wouldn't call it free-wiki heaven lol
But I can do it and now that I understand the whole thing with the partial updates; I will make an effort and update the system.

nb. that you can can separate download(s) into the local cache and actual update, "pacman -Sw"

I don't get what you mean... `pacman -Sw` would download the packages and store them into the cache. But I don't get what you mean with "actual update".

So, I will update my system the next monday and let you guys know. Thanks for your help and patience so far

Last edited by lucasyata (2024-08-18 06:01:07)

seth · 2024-08-18 08:19:58

I don't get what you mean...

pacman -Syuw
# be informed that you finished your coffee like 10 minutes ago and have to buy another one or leave
# go home
pacman -Su # you didn't spend the entire offline part of the installation annoying the starbucks staff

Or rather, what is pacman doing the first and second time it checks for dependencies?

You mean

pacman wrote:

looking for conflicting package...
…
(1/1) checking for file conflicts

ie. database and filesystem related conflicts?
What do I need?
Are there any issues with this constellation?
I guess running two passes is simpler than pre-tracing the

lucasyata · 2024-08-19 03:40:43

seth wrote:

pacman -Syuw
# be informed that you finished your coffee like 10 minutes ago and have to buy another one or leave
# go home
pacman -Su # you didn't spend the entire offline part of the installation annoying the starbucks staff

Oh, ok. Neat! Very considered of your part, thanks!

Are there any issues with this constellation?

No there are not. It's just that it's something itchy to read it does the same thing twice and not know why. And it's something I never read about anywhere. So I just asked 'cuz you might have knew. It was merely out of curiosity really. That's it

Last edited by lucasyata (2024-08-19 03:41:01)

seth · 2024-08-19 08:12:09

No, I meant "Are there any issues with this constellation" as the second question pacman has to answer in an admittedly somewhat incoherent rambling of a post that ends with the residual fragment of a sentence that I abandoned after noticing that that would not adequately explain the problem

lucasyata · 2024-08-19 22:50:07

seth wrote:

No, I meant "Are there any issues with this constellation" as the second question pacman has to answer in an admittedly somewhat incoherent rambling of a post that ends with the residual fragment of a sentence that I abandoned after noticing that that would not adequately explain the problem

Oh I see
Sometimes I also leave fragments of text around my replies hahahha

Well...

lucasyata wrote:

So, I will update my system the next monday and let you guys know.

Ok. So I updated my system today. The only thing that got messed around was my grub configuration and the intiramfs image for the linux zen kernel. But I manually booted with the lts kernel for now and rigged grub to boot that way. In the future I will fix both the linux zen thing and the grub configurations whenever the system or the kernels get updated. But that's another story...

I got pretty lucky considering that I basically updated(installed) the system the last blue moon lol

After the system update I could install nautilus as I intended without any problems.

So...
I will update the post to add the conclusion, and then mark it as solved

Arch Linux

#1 2024-08-13 01:34:50