Problems updating AUR using yay (local newer, missing)

So an issue arose today where I am unable to update packages correctly using yay. Below is the output:

[bitwise@manjaro-desktop ~]$ yay
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
:: Starting full system upgrade...
 there is nothing to do
:: Searching databases for updates...
:: Searching AUR for updates...
 -> game-devices-udev: local (0.4-1) is newer than AUR (0.4-0)
 -> libwpe: local (1.3.91-1) is newer than AUR (1.2.1-0)
 -> matcha-gtk-theme: local (20190622-1) is newer than AUR (20190605-1)
 -> python-npyscreen: local (4.10.5-2) is newer than AUR (4.10.5-1)
 -> wpebackend-fdo: local (1.3.91-1) is newer than AUR (1.2.2-0)
 -> Missing AUR Packages:  kvantum-theme-matcha  lib32-gtk3-classic  lib32-nvidia-430xx-utils  manjaro-application-utility  manjaro-browser-settings  manjaro-xfce-gtk3-settings  microsoft-office-online-jak  papirus-maia-icon-theme  python-jade-application-kit  steam-manjaro  wallpapers-2018  xfce4-whiskermenu-plugin-gtk3
 -> Out Of Date AUR Packages:  matcha-gtk-theme  minecraft-launcher  nordvpn-bin  uvesafb-dkms
 there is nothing to do

I've tried running yay -Suu to allow downgrading of the packages that are newer than AUR, however, yay decides there is nothing to do. Additionally, the missing AUR packages appeared today, and many of the packages are either things I use or things I don't know whether or not to remove. Is there any way to fix these two errors?

From my understanding, Out-of-Date AUR packages are just AUR packages being flagged out-of-date. If the AUR maintainers don't modify the PKGBUILD, there is nothing the package manager can do.

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The packages it's listing that are newer and missing are all Manjaro community packages. Those should not be appearing unless you installed them from the AUR first then updated them with the Manjaro community packages. Some aren't in the AUR to begin with, so that possibility partially goes out the window.

I would clear yay's cache by running rm -rf ~/.cache/yay/* and try again.

As far as out of date AUR packages, see:

An Out Of Date AUR Packages message is displayed. Why doesn't Yay update them?

This message does not mean that updated AUR packages are available. It means the packages have been flagged out of date on the AUR, but their maintainers have not yet updated the PKGBUILD s (see outdated AUR packages).

Where did you get 1.3.91-1 from? Did you use your own PKGBUILD?

I tried clearing the cache with no avail:

[bitwise@manjaro-desktop ~]$ ls -la .cache/yay/
total 8
drwxr-xr-x  2 bitwise bitwise 4096 Sep 10 19:16 .
drwx------ 15 bitwise bitwise 4096 Sep 10 14:36 ..
[bitwise@manjaro-desktop ~]$ yay -Syua
:: Searching AUR for updates...
 -> game-devices-udev: local (0.4-1) is newer than AUR (0.4-0)
 -> libwpe: local (1.3.91-1) is newer than AUR (1.2.1-0)
 -> matcha-gtk-theme: local (20190622-1) is newer than AUR (20190605-1)
 -> python-npyscreen: local (4.10.5-2) is newer than AUR (4.10.5-1)
 -> wpebackend-fdo: local (1.3.91-1) is newer than AUR (1.2.2-0)
 -> Missing AUR Packages:  kvantum-theme-matcha  lib32-gtk3-classic  lib32-nvidia-430xx-utils  manjaro-application-utility  manjaro-browser-settings  manjaro-xfce-gtk3-settings  microsoft-office-online-jak  papirus-maia-icon-theme  python-jade-application-kit  steam-manjaro  wallpapers-2018  xfce4-whiskermenu-plugin-gtk3
 -> Out Of Date AUR Packages:  matcha-gtk-theme  minecraft-launcher  nordvpn-bin  uvesafb-dkms
 there is nothing to do

It's worth noting that in an attempt to fix the issue, one of the things I did was rebuild the mirrors list using pacman-mirrors. I also reinstalled all 1118 packages, which failed to resolve the issue.

As for the new libwpe version, I don't know. I never used any PKGBUILD on this machine apart from the initial installation for yay, so the only place I can reasonably infer that it came from was at some point in reinstalling all the packages, which even then doesn't make perfect sense because it used the same repositories as it has now.

I believe these are indicating that they aren't in the AUR.

These are MARKED out-of-date on AUR. A new version hasn't been uploaded yet.

Downgrading is a bad idea (unless you know what you're doing), because some programs uses the newer versions. Also, it's better to use the version in the Manjaro repo rather than from the AUR.

I don't see what the issue is. Yay seems to be preforming correctly to me.

Right, they're not. However, yay should be detecting those packages came from the community repo and not display them. I have some of them installed and they don't show for me. Here's my output as a comparison.

:: Searching AUR for updates...
:: Checking development packages...
 -> ddcutil: local (0.9.7-1) is newer than AUR (0.9.5-1)
 -> libmodule: local (5.0.0-1) is newer than AUR (4.2.0-1)
 -> Missing AUR Packages:  adwaita-maia  gst-plugin-jamesdsp-git  jdsp4linux-git  jdsp4linux-gui-git  mullpy  paper-maia-icon-theme-git
 -> Out Of Date AUR Packages:  ddcutil  gdm3setup-utils  libmodule
 there is nothing to do

The newer or missing packages are not in the AUR, they're my own PKGBUILDs.

I wonder if there's a way to edit yay in such a way so that the packages point back to coming from the community repository?

Doing manjaro for quite some time now.
It is not good habit to use yay for whole system update.
The conservative way (I prefer) is to use pacman first.
Then solve your AUR problems (reminder: AUR is not synct with manjaro, so problems will come up, especially when using outdated packages).
Use yay for AUR only.

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