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Installing something with pending systemd update fails because rpm-ostree thinks it'll remove systemd #3175

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YaLTeR opened this issue Oct 14, 2021 · 8 comments
Open

Installing something with pending systemd update fails because rpm-ostree thinks it'll remove systemd #3175

YaLTeR opened this issue Oct 14, 2021 · 8 comments

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@YaLTeR
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YaLTeR commented Oct 14, 2021

Host system details

  fedora:fedora/35/x86_64/silverblue
                   Version: 35.20211011.n.0 (2021-10-11T08:10:46Z)
                BaseCommit: 85556706484e0aeeeca99137df9d5308dc2bcd960e40e767402ff98facfc7d10
              GPGSignature: Valid signature by 787EA6AE1147EEE56C40B30CDB4639719867C58F
                      Diff: 7 removed
       RemovedBasePackages: firefox 93.0-2.fc35
      ReplacedBasePackages: gnome-shell 41.0-1.fc35 -> 41.0-3.4.fc35
           LayeredPackages: akmod-nvidia xorg-x11-drv-nvidia-cuda xorg-x11-drv-nvidia-cuda-libs exa bcache-tools fish flatpak-builder
             LocalPackages: edid-asus-1-1.fc34.noarch kgx-development-0.5.0-0.20210319.gitbb57ffe3.fc34.x86_64 kgx-development-nautilus-0.5.0-0.20210319.gitbb57ffe3.fc34.x86_64 rpmfusion-free-release-35-0.2.noarch rpmfusion-nonfree-release-35-0.2.noarch
                 Initramfs: --include /etc/initramfs-overlay /

(uninstalled previously installed sysprof)

Expected vs actual behavior

$ rpm-ostree install sysprof
Checking out tree 8555670... done
Enabled rpm-md repositories: fedora-cisco-openh264 updates-testing updates fedora rpmfusion-free-updates-testing rpmfusion-free rpmfusion-nonfree-updates-testing rpmfusion-nonfree updates-archive
Importing rpm-md... done
rpm-md repo 'fedora-cisco-openh264' (cached); generated: 2021-02-23T00:47:28Z solvables: 4
rpm-md repo 'updates-testing' (cached); generated: 2021-10-13T18:48:01Z solvables: 12361
rpm-md repo 'updates' (cached); generated: 2018-02-20T19:18:14Z solvables: 0
rpm-md repo 'fedora' (cached); generated: 2021-10-13T10:46:05Z solvables: 65738
rpm-md repo 'rpmfusion-free-updates-testing' (cached); generated: 2021-10-11T10:31:27Z solvables: 21
rpm-md repo 'rpmfusion-free' (cached); generated: 2021-10-11T10:43:59Z solvables: 521
rpm-md repo 'rpmfusion-nonfree-updates-testing' (cached); generated: 2021-10-11T11:08:35Z solvables: 9
rpm-md repo 'rpmfusion-nonfree' (cached); generated: 2021-10-11T11:46:02Z solvables: 206
rpm-md repo 'updates-archive' (cached); generated: 2021-08-18T13:30:23Z solvables: 0
Resolving dependencies... done
error: Could not depsolve transaction; 2 problems detected:
 Problem 1: The operation would result in removing the following protected packages: systemd
 Problem 2: The operation would result in removing the following protected packages: systemd

Expected:

$ rpm-ostree install sysprof
...
Success!

But, turns out there was a pending update including systemd:

$ rpm-ostree update
2 metadata, 0 content objects fetched; 788 B transferred in 1 seconds; 0 bytes content written
Checking out tree ba1844d... done
Enabled rpm-md repositories: fedora-cisco-openh264 updates-testing updates fedora rpmfusion-free-updates-testing rpmfusion-free rpmfusion-nonfree-updates-testing rpmfusion-nonfree updates-archive
Importing rpm-md... done
rpm-md repo 'fedora-cisco-openh264' (cached); generated: 2021-02-23T00:47:28Z solvables: 4
rpm-md repo 'updates-testing' (cached); generated: 2021-10-13T18:48:01Z solvables: 12361
rpm-md repo 'updates' (cached); generated: 2018-02-20T19:18:14Z solvables: 0
rpm-md repo 'fedora' (cached); generated: 2021-10-13T10:46:05Z solvables: 65738
rpm-md repo 'rpmfusion-free-updates-testing' (cached); generated: 2021-10-11T10:31:27Z solvables: 21
rpm-md repo 'rpmfusion-free' (cached); generated: 2021-10-11T10:43:59Z solvables: 521
rpm-md repo 'rpmfusion-nonfree-updates-testing' (cached); generated: 2021-10-11T11:08:35Z solvables: 9
rpm-md repo 'rpmfusion-nonfree' (cached); generated: 2021-10-11T11:46:02Z solvables: 206
rpm-md repo 'updates-archive' (cached); generated: 2021-08-18T13:30:23Z solvables: 0
Resolving dependencies... done
Will download: 1 package (28,7 kB)
Downloading from 'updates-testing'... done
Importing packages... done
Applying 2 overrides and 77 overlays
Processing packages... done
Running pre scripts... done
Running post scripts... done
Running posttrans scripts... done
Writing rpmdb... done
Generating initramfs... done
Writing OSTree commit... done
Staging deployment... done
Freed: 162,9 MB (pkgcache branches: 0)
Upgraded:
  fedora-gpg-keys 35-0.6 -> 35-1
  fedora-release-common 35-0.32 -> 35-33
  fedora-release-identity-silverblue 35-0.32 -> 35-33
  fedora-release-ostree-desktop 35-0.32 -> 35-33
  fedora-release-silverblue 35-0.32 -> 35-33
  fedora-repos 35-0.6 -> 35-1
  fedora-repos-archive 35-0.6 -> 35-1
  fedora-repos-modular 35-0.6 -> 35-1
  fedora-repos-ostree 35-0.6 -> 35-1
  flatpak 1.11.3-1.fc35 -> 1.12.1-1.fc35
  flatpak-libs 1.11.3-1.fc35 -> 1.12.1-1.fc35
  flatpak-selinux 1.11.3-1.fc35 -> 1.12.1-1.fc35
  flatpak-session-helper 1.11.3-1.fc35 -> 1.12.1-1.fc35
  gnome-software 41.0-3.fc35 -> 41.0-5.fc35
  gnome-software-rpm-ostree 41.0-3.fc35 -> 41.0-5.fc35
  kbd 2.4.0-6.fc35 -> 2.4.0-7.fc35
  kbd-misc 2.4.0-6.fc35 -> 2.4.0-7.fc35
  systemd 249.4-1.fc35 -> 249.4-2.fc35
  systemd-libs 249.4-1.fc35 -> 249.4-2.fc35
  systemd-networkd 249.4-1.fc35 -> 249.4-2.fc35
  systemd-oomd-defaults 249.4-1.fc35 -> 249.4-2.fc35
  systemd-pam 249.4-1.fc35 -> 249.4-2.fc35
  systemd-resolved 249.4-1.fc35 -> 249.4-2.fc35
  systemd-rpm-macros 249.4-1.fc35 -> 249.4-2.fc35
  systemd-udev 249.4-1.fc35 -> 249.4-2.fc35
Removed:
  kernel-tools-5.14.9-300.fc35.x86_64
  kernel-tools-libs-5.14.9-300.fc35.x86_64
  libdazzle-3.42.0-1.fc35.x86_64
  libsysprof-3.42.0-1.1.fc35.x86_64
  libsysprof-ui-3.42.0-1.1.fc35.x86_64
  sysprof-3.42.0-1.1.fc35.x86_64
  sysprof-cli-3.42.0-1.1.fc35.x86_64

After that the installation went fine.
@cgwalters
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Yes, this is tricky to solve. It's related to ye olde #415

I guess one thing we can do is at least check for new base image updates when an install is requested (or at least, any time we're fetching rpm-md, also check for a base image update) and emit a notice when it's out of date?

@jlebon
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jlebon commented Oct 29, 2021

Can you provide the full diff of all your layered packages? You can take the BaseCommit field from rpm-ostree status and feed it to rpm-ostree db diff.

@jlebon
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jlebon commented Oct 29, 2021

In general, version mismatch issues should've been solved by the archive repo, but it was turned on for f35 only recently. I could imagine this error happening if one of your layered packages pulls in an additional subpackage of systemd, but it couldn't find the one that matched the base version so it tried to update all of systemd.

@YaLTeR
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YaLTeR commented Oct 29, 2021

Can you provide the full diff of all your layered packages? You can take the BaseCommit field from rpm-ostree status and feed it to rpm-ostree db diff.

I'm afraid I changed my layered packages a bit since then.

@lumingzh
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same issue here, can't upgrade.

@lumingzh
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same issue here, can't upgrade.

I run rpm-ostree reset uninstalled nvidia driver and upgraded, but now I can't install nvidia driver again because of this issue.

@lumingzh
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same issue here, can't upgrade.

I run rpm-ostree reset uninstalled nvidia driver and upgraded, but now I can't install nvidia driver again because of this issue.

Well, it seems like has been fixed because of rpm repository update or something.

@YaLTeR
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YaLTeR commented Jan 22, 2022

Currently cannot rebase to rawhide, not sure if related.

$ rpm-ostree rebase fedora:fedora/rawhide/x86_64/silverblue --uninstall rpmfusion-free-release-35-1.noarch --uninstall rpmfusion-nonfree-release-35-1.noarch --install https://mirrors.rpmfusion.org/free/fedora/rpmfusion-free-release-rawhide.noarch.rpm --install https://mirrors.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-rawhide.noarch.rpm
Downloading https://mirrors.rpmfusion.org/free/fedora/rpmfusion-free-release-rawhide.noarch.rpm...done
Downloading https://mirrors.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-rawhide.noarch.rpm...done
2 metadata, 0 content objects fetched; 788 B transferred in 2 seconds; 0 bytes content written
Checking out tree 0e1eebd... done
Enabled rpm-md repositories: fedora-cisco-openh264 updates fedora rpmfusion-free-updates rpmfusion-free rpmfusion-nonfree-updates rpmfusion-nonfree updates-archive
Importing rpm-md... done
rpm-md repo 'fedora-cisco-openh264' (cached); generated: 2021-09-22T15:57:13Z solvables: 4
rpm-md repo 'updates' (cached); generated: 2022-01-20T23:17:56Z solvables: 67306
rpm-md repo 'fedora' (cached); generated: 2022-01-20T23:17:56Z solvables: 67306
rpm-md repo 'rpmfusion-free-updates' (cached); generated: 2022-01-09T22:58:49Z solvables: 522
rpm-md repo 'rpmfusion-free' (cached); generated: 2022-01-09T22:58:49Z solvables: 522
rpm-md repo 'rpmfusion-nonfree-updates' (cached); generated: 2022-01-09T23:24:38Z solvables: 217
rpm-md repo 'rpmfusion-nonfree' (cached); generated: 2022-01-09T23:24:38Z solvables: 217
rpm-md repo 'updates-archive' (cached); generated: 2021-05-18T15:54:43Z solvables: 0
Resolving dependencies... done
error: Could not depsolve transaction; 3 problems detected:
 Problem 1: The operation would result in removing the following protected packages: systemd
 Problem 2: The operation would result in removing the following protected packages: systemd
 Problem 3: The operation would result in removing the following protected packages: systemd

Here's my pending and current deployment (I got rid of all overrides before trying to rebase as you can see):

$ rpm-ostree status
State: idle
Deployments:
  fedora:fedora/35/x86_64/silverblue
                   Version: 35.20220122.0 (2022-01-22T00:46:45Z)
                BaseCommit: 0dd1fb6f8e8aa9a79c166723aaaec320cd4766f1b451f52bd62a3e36d23bc831
              GPGSignature: Valid signature by 787EA6AE1147EEE56C40B30CDB4639719867C58F
                      Diff: 5 downgraded
       RemovedBasePackages: firefox 96.0-1.fc35
           LayeredPackages: akmod-nvidia bcache-tools exa fish flatpak-builder gnome-boxes libvirt-daemon-config-network nautilus-gsconnect sysprof wine-systemd xorg-x11-drv-nvidia-cuda xorg-x11-drv-nvidia-cuda-libs
             LocalPackages: edid-asus-1-1.fc34.noarch kgx-development-0.5.0-0.20211120.gitc327aa35.fc35.x86_64 kgx-development-nautilus-0.5.0-0.20211120.gitc327aa35.fc35.x86_64 rpmfusion-free-release-35-1.noarch rpmfusion-nonfree-release-35-1.noarch
                 Initramfs: --include /etc/initramfs-overlay / 

● fedora:fedora/35/x86_64/silverblue
                   Version: 35.20220122.0 (2022-01-22T00:46:45Z)
                BaseCommit: 0dd1fb6f8e8aa9a79c166723aaaec320cd4766f1b451f52bd62a3e36d23bc831
              GPGSignature: Valid signature by 787EA6AE1147EEE56C40B30CDB4639719867C58F
       RemovedBasePackages: firefox 96.0-1.fc35
      ReplacedBasePackages: gnome-control-center gnome-control-center-filesystem 41.2-1.fc35 -> 41.2-1.2.fc35 gnome-settings-daemon 41.0-1.fc35 -> 41.0-1.2.fc35 gnome-shell 41.3-1.fc35 -> 41.3-1.1.fc35 libhandy 1.4.0-1.fc35 -> 1.5.0-1.fc35
           LayeredPackages: akmod-nvidia bcache-tools exa fish flatpak-builder gnome-boxes libvirt-daemon-config-network nautilus-gsconnect sysprof wine-systemd xorg-x11-drv-nvidia-cuda xorg-x11-drv-nvidia-cuda-libs
             LocalPackages: edid-asus-1-1.fc34.noarch kgx-development-0.5.0-0.20211120.gitc327aa35.fc35.x86_64 kgx-development-nautilus-0.5.0-0.20211120.gitc327aa35.fc35.x86_64 rpmfusion-free-release-35-1.noarch rpmfusion-nonfree-release-35-1.noarch
                 Initramfs: --include /etc/initramfs-overlay / 
                    Pinned: yes

And here's the db diff from base to pending:

$ rpm-ostree db diff 0dd1fb6f8e8aa9a79c166723aaaec320cd4766f1b451f52bd62a3e36d23bc831 b568efa8f89af994b7c2d510bda088b92dd7ad3167018e64d15e178c93883188
ostree diff commit from: 0dd1fb6f8e8aa9a79c166723aaaec320cd4766f1b451f52bd62a3e36d23bc831
ostree diff commit to:   b568efa8f89af994b7c2d510bda088b92dd7ad3167018e64d15e178c93883188
Removed:
  firefox-96.0-1.fc35.x86_64
Added:
  SDL2-2.0.20-1.fc35.x86_64
  SDL2_image-2.0.5-7.fc35.x86_64
  akmod-nvidia-3:495.46-1.fc35.x86_64
  akmods-0.5.6-28.fc35.noarch
  annobin-docs-9.87-3.fc35.noarch
  annobin-plugin-gcc-9.87-3.fc35.x86_64
  bcache-tools-1.1-1.fc35.x86_64
  boost-iostreams-1.76.0-4.fc35.x86_64
  capstone-4.0.2-7.fc35.x86_64
  ccache-4.2.1-2.fc35.x86_64
  corosynclib-3.1.6-1.fc35.x86_64
  cyrus-sasl-2.1.27-13.fc35.x86_64
  daxctl-libs-72.1-1.fc35.x86_64
  debugedit-5.0-2.fc35.x86_64
  dwz-0.14-2.fc35.x86_64
  ed-1.14.2-11.fc35.x86_64
  edid-asus-1-1.fc34.noarch
  edk2-ovmf-20211126gitbb1bba3d7767-1.fc35.noarch
  efi-srpm-macros-5-4.fc35.noarch
  egl-wayland-1.1.9-3.fc35.x86_64
  elfutils-0.186-1.fc35.x86_64
  exa-0.10.1-2.fc35.x86_64
  fakeroot-1.26-4.fc35.x86_64
  fakeroot-libs-1.26-4.fc35.x86_64
  fish-3.3.1-2.fc35.x86_64
  flatpak-builder-1.2.0-1.fc35.x86_64
  fmt-8.1.1-1.fc35.x86_64
  fonts-srpm-macros-1:2.0.5-6.fc35.noarch
  fpc-srpm-macros-1.3-4.fc35.noarch
  gdb-minimal-11.1-5.fc35.x86_64
  genisoimage-1.1.11-48.fc35.x86_64
  ghc-srpm-macros-1.5.0-5.fc35.noarch
  glusterfs-9.4-1.fc35.x86_64
  glusterfs-cli-9.4-1.fc35.x86_64
  glusterfs-client-xlators-9.4-1.fc35.x86_64
  glusterfs-fuse-9.4-1.fc35.x86_64
  gnat-srpm-macros-4-14.fc35.noarch
  gnome-boxes-41.1-1.fc35.x86_64
  gnome-shell-extension-gsconnect-48-1.fc35.x86_64
  gnutls-dane-3.7.2-2.fc35.x86_64
  gnutls-utils-3.7.2-2.fc35.x86_64
  go-srpm-macros-3.0.11-2.fc35.noarch
  gtk-vnc2-1.3.0-1.fc35.x86_64
  gtksourceview4-4.8.2-1.fc35.x86_64
  gvnc-1.3.0-1.fc35.x86_64
  gvncpulse-1.3.0-1.fc35.x86_64
  http-parser-2.9.4-5.fc35.x86_64
  info-6.8-2.fc35.x86_64
  ipxe-roms-qemu-20200823-7.git4bd064de.fc35.noarch
  iscsi-initiator-utils-6.2.1.4-0.git095f59c.fc35.2.x86_64
  iscsi-initiator-utils-iscsiuio-6.2.1.4-0.git095f59c.fc35.2.x86_64
  isns-utils-libs-0.101-2.fc35.x86_64
  kernel-srpm-macros-1.0-6.fc35.noarch
  kernel-tools-5.15.4-200.fc35.x86_64
  kernel-tools-libs-5.15.4-200.fc35.x86_64
  kgx-development-0.5.0-0.20211120.gitc327aa35.fc35.x86_64
  kgx-development-nautilus-0.5.0-0.20211120.gitc327aa35.fc35.x86_64
  kmodtool-1-43.fc35.noarch
  koji-1.27.1-1.fc35.noarch
  libcacard-3:2.8.0-5.20210801gitcf6121deb4.fc35.x86_64
  libcomps-0.1.18-1.fc35.x86_64
  libdazzle-3.42.0-1.fc35.x86_64
  libdecor-0.1.0-1.fc35.x86_64
  libfdt-1.6.1-2.fc35.x86_64
  libgfapi0-9.4-1.fc35.x86_64
  libgfrpc0-9.4-1.fc35.x86_64
  libgfxdr0-9.4-1.fc35.x86_64
  libgit2-1.1.0-5.fc35.x86_64
  libglusterd0-9.4-1.fc35.x86_64
  libglusterfs0-9.4-1.fc35.x86_64
  libiscsi-1.19.0-4.fc35.x86_64
  libnfs-4.0.0-5.fc35.x86_64
  libphodav-2.5-5.fc35.x86_64
  libpmem-1.11.0-3.fc35.x86_64
  libqb-2.0.4-1.fc35.x86_64
  librados2-2:16.2.7-2.fc35.x86_64
  librbd1-2:16.2.7-2.fc35.x86_64
  librdmacm-38.1-2.fc35.x86_64
  libretls-3.4.2-1.fc35.x86_64
  libssh2-1.10.0-1.fc35.x86_64
  libsysprof-3.42.1-1.fc35.x86_64
  libsysprof-ui-3.42.1-1.fc35.x86_64
  libtpms-0.9.2-0.20220106gite81d634c27.fc35.0.x86_64
  libusal-1.1.11-48.fc35.x86_64
  libvdpau-1.4-6.fc35.x86_64
  libvirt-daemon-7.6.0-5.fc35.x86_64
  libvirt-daemon-config-network-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-interface-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-network-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-nodedev-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-nwfilter-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-qemu-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-secret-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-storage-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-storage-core-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-storage-disk-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-storage-gluster-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-storage-iscsi-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-storage-iscsi-direct-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-storage-logical-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-storage-mpath-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-storage-rbd-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-storage-scsi-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-storage-sheepdog-7.6.0-5.fc35.x86_64
  libvirt-daemon-driver-storage-zfs-7.6.0-5.fc35.x86_64
  libvirt-daemon-kvm-7.6.0-5.fc35.x86_64
  libvirt-gconfig-4.0.0-3.fc35.x86_64
  libvirt-glib-4.0.0-3.fc35.x86_64
  libvirt-gobject-4.0.0-3.fc35.x86_64
  libvirt-libs-7.6.0-5.fc35.x86_64
  libwsman1-2.7.0-5.fc35.x86_64
  lttng-ust-2.12.2-5.fc35.x86_64
  lua-srpm-macros-1-5.fc35.noarch
  lzop-1.04-7.fc35.x86_64
  mdevctl-1.1.0-2.fc35.x86_64
  mtools-4.0.37-1.fc35.x86_64
  nautilus-gsconnect-48-1.fc35.noarch
  nautilus-python-1.2.3-9.fc35.x86_64
  ndctl-libs-72.1-1.fc35.x86_64
  netcat-1.218-2.fc35.x86_64
  nim-srpm-macros-3-5.fc35.noarch
  numactl-libs-2.0.14-4.fc35.x86_64
  numad-0.5-35.20150602git.fc35.x86_64
  nvidia-persistenced-3:495.46-1.fc35.x86_64
  nvidia-settings-3:495.46-1.fc35.x86_64
  ocaml-srpm-macros-6-5.fc35.noarch
  ocl-icd-2.3.0-2.fc35.x86_64
  openblas-srpm-macros-2-10.fc35.noarch
  opencl-filesystem-1.0-14.fc35.noarch
  openssl-1:1.1.1l-2.fc35.x86_64
  patch-2.7.6-15.fc35.x86_64
  perl-srpm-macros-1-42.fc35.noarch
  python-srpm-macros-3.10-10.fc35.noarch
  python3-argcomplete-1.12.3-3.fc35.noarch
  python3-cffi-1.14.6-2.fc35.x86_64
  python3-dateutil-1:2.8.1-7.fc35.noarch
  python3-decorator-5.0.9-3.fc35.noarch
  python3-gssapi-1.6.14-2.fc35.x86_64
  python3-koji-1.27.1-1.fc35.noarch
  python3-libcomps-0.1.18-1.fc35.x86_64
  python3-ply-3.11-13.fc35.noarch
  python3-progressbar2-3.53.2-2.fc35.noarch
  python3-pycparser-2.20-5.fc35.noarch
  python3-pygit2-1.6.1-1.fc35.x86_64
  python3-requests-gssapi-1.2.3-3.fc35.noarch
  python3-rpmautospec-0.2.5-1.fc35.noarch
  python3-utils-2.5.6-3.fc35.noarch
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