[SOLVED] Pamac confused about what is installed - Pacman isn't

I’ve been having an issue with copy+paste stopping working on my manjaro gnome install. Fixed by logging out and in again, but I decided to try a different clipboard manager.

That’s when I found things are a bit messed up with Pamac. Using the GUI to install Gpaste pamac wanted to install a tonne of packages - quite clearly base system packages that we already installed. It seems to have forgotten what I have installed at some point today.

Pacman however seems OK. Here’s what happened when I tried to remove my current clipboard manager on the cli, first search - shows its installed:

pamac search clipit
clipit                                                                                 [Installed] 1:1.4.3-2  community 
Lightweight GTK+ clipboard manager (fork of Parcellite)

Then try to remove:

pamac remove clipit
Error: Failed to prepare transaction: target not found: clipit
Error: Failed to prepare transaction: target not found: clipit

Try pacman instead:

sudo pacman -R clipit
checking dependencies...

Packages (1) clipit-1:1.4.3-2

Total Removed Size:  0.38 MiB

:: Do you want to remove these packages? [Y/n] 
:: Processing package changes...
(1/1) removing clipit    [########################################] 100%
:: Running post-transaction hooks...
(1/3) Arming ConditionNeedsUpdate...
(2/3) Updating icon theme caches...
(3/3) Updating the desktop file MIME type cache...

And its gone, as pamac also shows:

pamac search clipit
clipit                                   1.4.5-3    AUR
Lightweight GTK+ clipboard manager (fork of Parcellite)
clipit                                   1:1.4.3-2  community 
Lightweight GTK+ clipboard manager (fork of Parcellite)

So lets try to install again to show the insanity of Pamac:

pamac install clipit 
Synchronizing package databases...
Resolving dependencies...
Checking inter-conflicts...
Warning: dependency cycle detected:
Warning: bashrc-manjaro will be installed before its bash dependency
Warning: dependency cycle detected:
Warning: harfbuzz will be installed before its freetype2 dependency

To install (98):
  linux-api-headers      5.8-1                    (Required By: clipit)  core       
  tzdata                 2020f-1                  (Required By: clipit)  core       
  iana-etc               20201229-1               (Required By: clipit)  core       
  filesystem             2020.09-2                (Required By: clipit)  core       
  glibc                  2.32-5                   (Required By: clipit)  core       
  gcc-libs               10.2.0-4                 (Required By: clipit)  core       
  ncurses                6.2-1                                           core       
  readline               8.1.0-2                  (Required By: clipit)  core       
  zlib                   1:1.2.11-4               (Required By: clipit)  core       
  bashrc-manjaro         5.1.0-2                                         core       
  bash                   5.1.0-2                  (Required By: clipit)  core       
  bzip2                  1.0.8-4                  (Required By: clipit)  core       
  pcre                   8.44-1                   (Required By: clipit)  core       992.3 kB
  libffi                 3.3-4                    (Required By: clipit)  core       
  util-linux-libs        2.36.1-4                 (Required By: clipit)  core       
  glib2                  2.66.4-2                 (Required By: clipit)  core       
  atk                    2.36.0-1                 (Required By: clipit)  extra      398.7 kB
  libdatrie              0.2.12-2                 (Required By: clipit)  extra      28.8 kB
  libthai                0.1.28-2                 (Required By: clipit)  extra      181.7 kB
  lzo                    2.10-3                   (Required By: clipit)  core       84.5 kB
  libpng                 1.6.37-3                 (Required By: clipit)  extra      
  expat                  2.2.10-2                 (Required By: clipit)  core       
  graphite               1:1.3.14-1               (Required By: clipit)  extra      229.9 kB
  harfbuzz               2.7.4-1                  (Required By: clipit)  extra      
  freetype2              2.10.4-1                 (Required By: clipit)  extra      
  fontconfig             2:2.13.91+48+gfcb0420-2  (Required By: clipit)  extra      
  xcb-proto              1.14.1-3                 (Required By: clipit)  extra      
  libxdmcp               1.1.3-3                  (Required By: clipit)  extra      28.1 kB
  libxau                 1.0.9-3                  (Required By: clipit)  extra      11.1 kB
  libxcb                 1.14-1                   (Required By: clipit)  extra      1.0 MB
  xorgproto              2020.1-1                 (Required By: clipit)  extra      243.6 kB
  libx11                 1.7.0-3                  (Required By: clipit)  extra      
  libxext                1.3.4-3                  (Required By: clipit)  extra      109.9 kB
  libxrender             0.9.10-4                 (Required By: clipit)  extra      26.6 kB
  pixman                 0.40.0-1                 (Required By: clipit)  extra      268.1 kB
  cairo                  1.17.4-3                 (Required By: clipit)  extra      
  libxft                 2.3.3-2                  (Required By: clipit)  extra      50.7 kB
  fribidi                1.0.10-1                 (Required By: clipit)  extra      
  pango                  1:1.48.0-1               (Required By: clipit)  extra      
  libxfixes              5.0.3-4                  (Required By: clipit)  extra      13.8 kB
  libxcursor             1.2.0-2                  (Required By: clipit)  extra      29.1 kB
  libxinerama            1.1.4-3                  (Required By: clipit)  extra      10.4 kB
  libxrandr              1.5.2-3                  (Required By: clipit)  extra      27.8 kB
  libxi                  1.7.10-3                 (Required By: clipit)  extra      151.9 kB
  libxcomposite          0.4.5-3                  (Required By: clipit)  extra      11.7 kB
  libxdamage             1.1.5-3                  (Required By: clipit)  extra      7.3 kB
  xz                     5.2.5-1                  (Required By: clipit)  core       
  icu                    68.2-1                   (Required By: clipit)  core       
  libxml2                2.9.10-8                 (Required By: clipit)  extra      
  shared-mime-info       2.0+57+gc1d1c70-1        (Required By: clipit)  extra      
  libtasn1               4.16.0-1                 (Required By: clipit)  core       124.2 kB
  gmp                    6.2.1-1                  (Required By: clipit)  core       
  nettle                 3.7-1                    (Required By: clipit)  core       
  libp11-kit             0.23.22-1                (Required By: clipit)  core       
  attr                   2.4.48-3                 (Required By: clipit)  core       70.6 kB
  acl                    2.2.53-3                 (Required By: clipit)  core       139.9 kB
  e2fsprogs              1.45.6-3                 (Required By: clipit)  core       
  openssl                1.1.1.i-2                (Required By: clipit)  core       
  libsasl                2.1.27-3                 (Required By: clipit)  core       149.6 kB
  libldap                2.4.56-1                 (Required By: clipit)  core       
  keyutils               1.6.3-1                  (Required By: clipit)  core       
  krb5                   1.18.2-1                 (Required By: clipit)  core       
  libtirpc               1.3.1-1                  (Required By: clipit)  core       
  pambase                20200721.1-2             (Required By: clipit)  core       
  libcap-ng              0.8.2-1                  (Required By: clipit)  core       
  audit                  2.8.5-9                  (Required By: clipit)  core       
  libxcrypt              4.4.17-1                 (Required By: clipit)  core       
  pam                    1.5.0-2                  (Required By: clipit)  core       
  libcap                 2.46-1                   (Required By: clipit)  core       
  coreutils              8.32-1                   (Required By: clipit)  core       2.8 MB
  libgpg-error           1.41-1                   (Required By: clipit)  core       
  libgcrypt              1.8.7-1                  (Required By: clipit)  core       
  lz4                    1:1.9.3-1                (Required By: clipit)  core       
  zstd                   1.4.5-1                  (Required By: clipit)  core       
  systemd-libs           247.2-1                  (Required By: clipit)  core       
  p11-kit                0.23.22-1                (Required By: clipit)  core       
  libunistring           0.9.10-3                 (Required By: clipit)  core       
  libidn2                2.3.0-1                  (Required By: clipit)  core       118.7 kB
  gnutls                 3.7.0-1                  (Required By: clipit)  core       
  libjpeg-turbo          2.0.6-1                  (Required By: clipit)  extra      
  libtiff                4.1.0-2                  (Required By: clipit)  extra      
  libdaemon              0.14-5                   (Required By: clipit)  extra      19.6 kB
  gdbm                   1.19-1                   (Required By: clipit)  core       
  dbus                   1.12.20-1                (Required By: clipit)  core       
  avahi                  0.8+15+ge8a3dd0-3        (Required By: clipit)  extra      
  libusb                 1.0.24-2                 (Required By: clipit)  core       
  libcups                1:2.3.3op1-1             (Required By: clipit)  extra      
  gdk-pixbuf2            2.42.2-1                 (Required By: clipit)  extra      
  librsvg                2:2.50.2-1               (Required By: clipit)  extra      
  hicolor-icon-theme     0.17-2                   (Required By: clipit)  extra      10.5 kB
  gtk-update-icon-cache  1:4.0.1-2                (Required By: clipit)  extra      
  desktop-file-utils     0.26-1                   (Required By: clipit)  extra      
  gtk2                   2.24.33-1                (Required By: clipit)  extra      
  libdbusmenu-glib       16.04.0-4                (Required By: clipit)  community  72.1 kB
  libdbusmenu-gtk2       16.04.0-4                (Required By: clipit)  community  
  libindicator-gtk2      12.10.1-9                (Required By: clipit)  community  
  libappindicator-gtk2   12.10.0.r296-1           (Required By: clipit)  community  
  clipit                 1:1.4.3-2                                       community  

Total download size: 7.4 MB
Total installed size: 471.7 MB

Apply transaction ? [y/N] n
Transaction cancelled.

Whereas pacman:

sudo pacman -S clipit 
resolving dependencies...
looking for conflicting packages...

Packages (1) clipit-1:1.4.3-2

Total Installed Size:  0.38 MiB

:: Proceed with installation? [Y/n]

Sitting here writing this I remembered I installed Timeshift. So I’m about to revert to an earlier system snapshot.

But if that fails, any suggestions? Would a force reinstall of all installed packages with pacman trigger pamac to remember what is installed? Even though it seems to know what is installed but not when you try to uninstall…

Weird one :frowning:

Well, reverting to lunchtime with timeshift seems to have fixed things. At least on the CLI.

Actually I see that very same list of 98 packages to be installed here as well (Whereas pacman only shows me 4). As if I did not have a single package installed anymore.

I noticed that it if fixed with “Refresh databases”.
After doing that, I see only 4 packages to be installed in pamac as well.


There is also a “Refresh” button on the Updates tab, but that did NOT fix it.

Something odd is going on with the package databases in pamac.

Pinging @guinux

I must say that I use pacman in 90% of the cases (100% in case of updates) and only use pamac (gui) occasionally for installing some new packages.

The refresh button on the updates tab will be to check mirrors for updates, so quite different from the ‘Refresh databases’.

But ‘Refresh databases’ would probably have done the job for me too.
I use Pamac GUI for most day to day updates. I logout and switch to console for big updates (such as the recent stable updates batch), but tend to still use ‘pamac upgrade’.

Mostly only revert to pacman when something goes wrong :slight_smile:

Speaking in pacman terms, I would expect “Refresh” doing something similar as pacman -Sy while “Refresh databases” would be pacman -Syy

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