[BUG] Cannot update packages

[emptyVoid]

Describe the bug

MSYS2 base package no longer updates:

MSYS ~
$ pacman -Syu --noconfirm
:: Synchronizing package databases...
 mingw32                  467.1 KiB   439K/s 00:01 [#####################] 100%
 mingw32.sig              119.0   B  0.00B/s 00:00 [#####################] 100%
 mingw64                  469.7 KiB  2.40M/s 00:00 [#####################] 100%
 mingw64.sig              119.0   B  0.00B/s 00:00 [#####################] 100%
 msys                     187.6 KiB  11.5M/s 00:00 [#####################] 100%
 msys.sig                 119.0   B  0.00B/s 00:00 [#####################] 100%
:: Starting core system upgrade...
warning: terminate other MSYS2 programs before proceeding
resolving dependencies...
looking for conflicting packages...
error: failed to prepare transaction (could not satisfy dependencies)
:: installing filesystem (2020.02-3) breaks dependency 'msys2-base' required by dash

Steps to Reproduce the Problem

1. Run msys2.exe
2. Execute pacman -Syu --noconfirm
3. Catch the error

Expected behavior: the core system upgrade should complete without errors.

Additional Context: Operating System, Screenshots

• OS: Windows 10 Pro version 2004 64-bit
• MSYS2: msys2-base-x86_64-20190524.tar.xz and msys2-base-x86_64-20200602.tar.xz

[Biswa96]

Warning: Try this if you don't care about your MSYS2 installation to be nuked :)

1. Download the .tar.xz file from here https://packages.msys2.org/package/filesystem.
2. Assume that file is downloaded in C:\MyFiles folder. Run this command pacman -Udd /c/MyFiles/filesystem-2020.02-3-x86_64.pkg.tar.xz.
3. Kill every msys2 shell/program.
4. Run pacman -Syu again.

[lissyx]

Warning: Try this if you don't care about your MSYS2 installation to be nuked :)

1. Download the .tar.xz file from here https://packages.msys2.org/package/filesystem.

2. Assume that file is downloaded in `C:\MyFiles` folder. Run this command `pacman -Udd /c/MyFiles/filesystem-2020.02-3-x86_64.pkg.tar.xz`.

3. Kill every msys2 shell/program.

4. Run `pacman -Syu` again.

Same repro here, and we start a msys2 from scratch on new VMs (so no pacman -Udd):

    - >-
      "C:\Program Files\7-zip\7z.exe" x -txz -so msys2-base-x86_64.tar.xz |
      "C:\Program Files\7-zip\7z.exe" x -o%USERPROFILE% -ttar -aoa -si
    - >-
      .\msys64\usr\bin\bash.exe --login -cx "export THIS_BASH_PID=$$; ps -ef |
      grep '[?]' | awk '{print $2}' | grep -v $THIS_BASH_PID | xargs -r kill;
      exit 0"
    - .\msys64\usr\bin\bash.exe --login -cx "pacman -Syu --noconfirm"

[lissyx]

Warning: Try this if you don't care about your MSYS2 installation to be nuked :)

1. Download the .tar.xz file from here https://packages.msys2.org/package/filesystem.

2. Assume that file is downloaded in `C:\MyFiles` folder. Run this command `pacman -Udd /c/MyFiles/filesystem-2020.02-3-x86_64.pkg.tar.xz`.

3. Kill every msys2 shell/program.

4. Run `pacman -Syu` again.

Same repro here, and we start a msys2 from scratch on new VMs (so no pacman -Udd):

    - >-
      "C:\Program Files\7-zip\7z.exe" x -txz -so msys2-base-x86_64.tar.xz |
      "C:\Program Files\7-zip\7z.exe" x -o%USERPROFILE% -ttar -aoa -si
    - >-
      .\msys64\usr\bin\bash.exe --login -cx "export THIS_BASH_PID=$$; ps -ef |
      grep '[?]' | awk '{print $2}' | grep -v $THIS_BASH_PID | xargs -r kill;
      exit 0"
    - .\msys64\usr\bin\bash.exe --login -cx "pacman -Syu --noconfirm"

Correcting myself, placing the filesystem-2020.02-3 file and running pacman -Udd prior seems to do the trick.

[lazka]

See #2022

[GitHubAdi]

Same problem on my side with a clean install after downloading msys2-base-x86_64-20200602.tar.xz from http://repo.msys2.org/distrib/x86_64/

Pacman -Syuu gives the same filesystem breaks dependency error.

I add previously installed another clean install in the morning, limited to just a couple of "Pacman -Syuu", without downloading any other packages, note even msys2 base-devel, and this one could redo "Pacman -Syuu" and install the filesystem package after the repo update.

[DaveThornton]

Fixed it for me also!! Thanks

[tomyri]

pacman -Sydd filesystem; pacman -Su works also.

[marler8997]

This broke ziglang's azure pipelines that use MSYS2. Tried @Biswa96 suggestion of downloading the filesystem package archive and installing from that, but it failed because it conflicted with the pre-existing filesystem package. @tomyri suggestion of force upgrading the filesystem pacakge with dependency checking disabled seemed to work.

see ziglang/zig#5688

[Jimmy-Z]

I'd like to re-post here that pacman -S dash before pacman -Syu is a simpler (and safer) workaround instead of force upgrade filesystem, as #2022 (comment).

[RobertBColton]

@Jimmy-Z that did not seem to work for me.

[Jimmy-Z]

@RobertBColton works on my desktop and my laptop. No idea why it doesn't work for you though. And, you should probably share some details, like which exact step doesn't work, and the output could help too.

[RobertBColton]

@Jimmy-Z Azure build below, we're checking it out fresh. It may look different because I keep committing different variations of what you guys propose here, nothing's cutting it though.
https://github.com/enigma-dev/RadialGM/pull/134/files#diff-3364e2ba7fdae37fba56fa0d6d765896R63

[jbruchon]

Manually installing the filesystem tar.xz worked for me.

[RobertBColton]

Is it necessary to download that tar for the fixes @Jimmy-Z and stuff mentioned?

[emptyVoid]

@RobertBColton, you could possibly use the same workaround implemented in vcpkg -- remove it before making the core system upgrade (if you don't need dash of course), e.g.:

%CD:~0,2%\msys64\usr\bin\pacman --noconfirm -Rc dash
%CD:~0,2%\msys64\usr\bin\pacman --noconfirm -Syu
...

[RobertBColton]

Hey, that did do the trick! Thanks!

[Jimmy-Z]

@RobertBColton it could be that your system is too far behind that dash needs a newer filesystem, that again brought up the problem, you should be able to install dash afterwards I assume.

[DDoSolitary]

I followed @Jimmy-Z's suggestion and the upgrade completed successfully. However, after that I can no longer run any msys executables (including bash, pacman, etc), getting the following error:

      0 [main] pacman (16444) shared_info::initialize: size of shared memory region changed from 51128 to 40888

pacman log:

[2020-06-25T20:08:57+0800] [PACMAN] Running 'pacman -S dash'
[2020-06-25T20:08:59+0800] [ALPM] transaction started
[2020-06-25T20:08:59+0800] [ALPM] upgraded dash (0.5.10.2-1 -> 0.5.11-1)
[2020-06-25T20:08:59+0800] [ALPM] transaction completed
[2020-06-25T20:09:03+0800] [PACMAN] Running 'pacman -Syu'
[2020-06-25T20:09:03+0800] [PACMAN] synchronizing package lists
[2020-06-25T20:09:07+0800] [PACMAN] starting core system upgrade
[2020-06-25T20:09:33+0800] [ALPM] transaction started
[2020-06-25T20:09:33+0800] [ALPM] upgraded filesystem (2020.02-2 -> 2020.02-3)
[2020-06-25T20:09:34+0800] [ALPM] upgraded msys2-runtime (3.0.7-6 -> 3.1.5-3)
[2020-06-25T20:09:34+0800] [ALPM] upgraded mintty (1~3.1.4-1 -> 1~3.2.0-1)
[2020-06-25T20:09:35+0800] [ALPM] upgraded msys2-runtime-devel (3.0.7-6 -> 3.1.5-3)
[2020-06-25T20:09:36+0800] [ALPM] upgraded pacman (5.2.1-6 -> 5.2.1-12)
[2020-06-25T20:09:36+0800] [ALPM] transaction completed

UPDATE

Strangely, after rebooting my computer it works without problems. I guess there's some background processes that I forgot to kill after the upgrade.

[trini]

It looks like the underlying problem has been resolved and you can go back to installing+updating as before. At least, my Azure CI jobs are once again completing and I re-ran the failed ones and they work now.

[emptyVoid]

@DDoSolitary, have you tried killing gpg-agent and dirmngr with Task Manager, or restarting your PC?
This kind of messages usually appear when some of the MSYS2-spawned processes keeps running preventing the core system upgrade from completing.

[DDoSolitary]

@emptyVoid Yeah I think that is the problem. I got it working by restarting the computer.

[goyalyashpal]

is this fixed, can this be closed?

[Jimmy-Z]

I believe this was fixed by pr #2022