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coreos / rpm-ostree

⚛📦 Hybrid image/package system with atomic upgrades and package layering
https://coreos.github.io/rpm-ostree
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Conflict between same packages #1799

Open Zlopez opened 5 years ago

Zlopez commented 5 years ago

Host system details

# rpm-ostree status                                                                                                                                                                                State: idle                                                                                                                                         
AutomaticUpdates: disabled                                                                                                                              
Deployments:                                                                                                                                                      
● ostree://fedora-workstation:fedora/30/x86_64/silverblue                                                                                              
                   Version: 30.20190321.n.0 (2019-03-21T08:56:43Z)                                                                                         
                BaseCommit: 115522cb141729c6803c7bb6143c207de8226332181140743e88fb9156815f3b                                                      
              GPGSignature: Valid signature by F1D8EC98F241AAF20DF69420EF3C111FCFC659B9                                                               
           LayeredPackages: ansible cherrytree fish gobby05 krb5-workstation powerline powerline-fonts tmux tmux-powerline traceroute vagrant vagrant-sshfs vim vim-powerline
             LocalPackages: redhat-internal-cert-install-0.1-7.el7.csb.noarch nautilus-dropbox-2015.10.28-1.fc10.x86_64                                  

  ostree://fedora-workstation:fedora/30/x86_64/silverblue                                                                                             
                   Version: 30.20190316.n.1 (2019-03-16T18:01:18Z)                                                                              
                BaseCommit: 70f07325c3f0f0ab3dab30ec0590bddee593a6151f0ffdcfa0e074ba7cf974e0                                                            
              GPGSignature: Valid signature by F1D8EC98F241AAF20DF69420EF3C111FCFC659B9                                                            
           LayeredPackages: ansible cherrytree fish gobby05 krb5-workstation powerline powerline-fonts tmux tmux-powerline traceroute vagrant vagrant-sshfs vim vim-powerline
             LocalPackages: redhat-internal-cert-install-0.1-7.el7.csb.noarch nautilus-dropbox-2015.10.28-1.fc10.x86_64

Expected vs actual behavior

# rpm-ostree upgrade                                                                                                                                                                                   
1 metadata, 0 content objects fetched; 569 B transferred in 1 seconds
Checking out tree 9550d7e... done
Enabled rpm-md repositories: updates fedora-cisco-openh264 fedora updates-testing
rpm-md repo 'updates' (cached); generated: 2018-02-20T19:18:14Z
rpm-md repo 'fedora-cisco-openh264' (cached); generated: 2018-09-12T14:36:30Z
rpm-md repo 'fedora' (cached); generated: 2019-03-24T09:38:11Z
rpm-md repo 'updates-testing' (cached); generated: 2019-03-24T03:09:21Z
Importing rpm-md... done
Resolving dependencies... done
Checking out packages... done
Running pre scripts... done
Running post scripts... done
Writing rpmdb... done
error: Error running transaction: file /usr/share/ruby/irb/cmd/chws.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/cmd/fork.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/cmd/help.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/cmd/load.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/cmd/nop.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/cmd/pushws.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/cmd/subirb.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/completion.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/context.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/ext/change-ws.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/ext/history.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/ext/loader.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/ext/multi-irb.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/ext/save-history.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/ext/tracer.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/ext/use-loader.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/ext/workspaces.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/extend-command.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/frame.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/help.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/init.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/input-method.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/inspector.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/lc/error.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/lc/help-message conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/lc/ja/encoding_aliases.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/lc/ja/error.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/lc/ja/help-message conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/locale.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/magic-file.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/notifier.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/output-method.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/ruby-lex.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/ruby-token.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/slex.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/src_encoding.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/version.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/workspace.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/ws-for-case-2.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch
file /usr/share/ruby/irb/xmp.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch

Expected:

# rpm-ostree upgrade
...
Success!

Steps to reproduce it

I'm currently running on F30 branch. My suspicion is that there is conflict between layered dependency for vagrant and packages provided by ostree image.

To reproduce this with my current rpm-ostree status all I need to do is execute rpm-ostree upgrade.

Would you like to work on the issue?

I can test this issue if needed.

jlebon commented 5 years ago 
file /usr/share/ruby/irb/cmd/chws.rb conflicts between attempted installs of rubygem-irb-1.0.0-118.fc30.noarch and rubygem-irb-1.0.0-118.fc30.noarch

Hmm, that's weird indeed. This might also be libdnf not reporting the error correctly and printing the same package twice, which... I think I've encountered something similar in the past. Would be cool to test this using the latest rpm-ostree master, which has an updated libdnf.

Anyway, re. the underlying conflict itself: can you sanity check that upgrading without vagrant works? E.g. rpm-ostree upgrade --uninstall vagrant --uninstall vagrant-sshfs.

Zlopez commented 5 years ago

I did rpm-ostree uninstall vagrant vagrant-sshfs and tried rpm-ostree upgrade again. This time the upgrade ended with success.

When layering the vagrant and vagrant-sshfs again I noticed that the rubygem-irb is really one of the layered packages.

rpm-ostree install vagrant vagrant-sshfs                                                                                                                                                                     Checking out tree 9550d7e... done                 
Enabled rpm-md repositories: updates fedora-cisco-openh264 fedora updates-testing
rpm-md repo 'updates' (cached); generated: 2018-02-20T19:18:14Z
rpm-md repo 'fedora-cisco-openh264' (cached); generated: 2018-09-12T14:36:30Z
rpm-md repo 'fedora' (cached); generated: 2019-03-24T09:38:11Z
rpm-md repo 'updates-testing' (cached); generated: 2019-03-24T03:09:21Z
Importing rpm-md... done                                           
Resolving dependencies... done                
Will download: 12 packages (9.6 MB)   
Downloading from 'updates-testing'... done         
Importing packages... done               
Checking out packages... done         
Running pre scripts... done           
Running post scripts... done               
Writing rpmdb... done                  
Writing OSTree commit... done            
Staging deployment... done             
Freed: 88.5 MB (pkgcache branches: 12)
Added:                                   
  SDL2-2.0.9-3.fc30.x86_64            
  augeas-libs-1.11.0-4.fc30.x86_64       
  brlapi-0.6.7-32.fc30.x86_64             
  brltty-5.6-32.fc30.x86_64           
  bsdtar-3.3.3-3.fc30.x86_64          
  capstone-4.0.1-3.fc30.x86_64         
  corosynclib-3.0.1-2.fc30.x86_64
  cyrus-sasl-2.1.27-0.6rc7.fc30.x86_64
  deltarpm-3.6-29.fc30.x86_64                      
  dmidecode-1:3.2-2.fc30.x86_64                      
  dnf-4.2.1-1.fc30.noarch                          
  dnf-data-4.2.1-1.fc30.noarch                     
  dnf-plugins-core-4.0.6-1.fc30.noarch              
  edk2-ovmf-20190308stable-1.fc30.noarch        
  genisoimage-1.1.11-41.fc30.x86_64               
  glusterfs-6.0-1.fc30.x86_64                      
  glusterfs-api-6.0-1.fc30.x86_64                       
  glusterfs-cli-6.0-1.fc30.x86_64                       
  glusterfs-client-xlators-6.0-1.fc30.x86_64               
  glusterfs-fuse-6.0-1.fc30.x86_64                       
  glusterfs-libs-6.0-1.fc30.x86_64                              
  hexedit-1.2.13-15.fc30.x86_64                            
  hivex-1.3.18-4.fc30.x86_64                             
  ima-evm-utils-1.1-5.fc30.x86_64                      
  ipxe-roms-qemu-20190125-1.git36a4c85f.fc30.noarch     
  iscsi-initiator-utils-6.2.0.876-8.gitf3c8e90.fc30.x86_64  
  iscsi-initiator-utils-iscsiuio-6.2.0.876-8.gitf3c8e90.fc30.x86_64
  isns-utils-libs-0.97-8.fc30.x86_64    
  libcacard-3:2.6.1-2.fc30.x86_64                       
  libcomps-0.1.11-1.fc30.x86_64       
  libconfig-1.7.2-3.fc30.x86_64       
  libfdt-1.4.7-3.fc30.x86_64             
  libguestfs-1:1.40.2-2.fc30.x86_64
  libguestfs-tools-c-1:1.40.2-2.fc30.x86_64                                                                                                                                                                                                   
  libguestfs-xfs-1:1.40.2-2.fc30.x86_64           
  libibumad-20.1-3.fc30.x86_64                                                   
  libibverbs-20.1-3.fc30.x86_64                                
  libiscsi-1.18.0-7.fc30.x86_64                                              
  libldm-0.2.4-4.fc30.x86_64                                  
  libnfs-1.11.0-3.fc30.x86_64                                          
  libpmem-1.5.1-1.fc30.x86_64                                      
  libqb-1.0.3-6.fc30.x86_64                   
  librados2-2:14.2.0-1.fc30.x86_64    
  librbd1-2:14.2.0-1.fc30.x86_64                   
  librdmacm-20.1-3.fc30.x86_64           
  libusal-1.1.11-41.fc30.x86_64       
  libvirt-daemon-5.1.0-3.fc30.x86_64  
  libvirt-daemon-config-network-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-interface-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-network-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-nodedev-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-nwfilter-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-qemu-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-secret-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-storage-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-storage-core-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-storage-disk-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-storage-gluster-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-storage-iscsi-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-storage-iscsi-direct-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-storage-logical-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-storage-mpath-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-storage-rbd-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-storage-scsi-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-storage-sheepdog-5.1.0-3.fc30.x86_64
  libvirt-daemon-driver-storage-zfs-5.1.0-3.fc30.x86_64
  libvirt-daemon-kvm-5.1.0-3.fc30.x86_64        
  libvirt-libs-5.1.0-3.fc30.x86_64                
  libwsman1-2.6.8-5.fc30.x86_64                    
  lsscsi-0.30-2.fc30.x86_64                             
  lttng-ust-2.10.2-2.fc30.x86_64                        
  lzop-1.03-22.fc30.x86_64                                 
  mtools-4.0.18-16.fc30.x86_64                           
  netcf-libs-0.2.8-13.fc30.x86_64                               
  nmap-ncat-2:7.70-6.fc30.x86_64                           
  numactl-libs-2.0.12-2.fc30.x86_64                      
  numad-0.5-28.20150602git.fc30.x86_64                 
  python3-dateutil-1:2.8.0-1.fc30.noarch                
  python3-distro-1.4.0-1.fc30.noarch                        
  python3-dnf-4.2.1-1.fc30.noarch                                  
  python3-dnf-plugins-core-4.0.6-1.fc30.noarch
  python3-gpg-1.12.0-1.fc30.x86_64                      
  python3-hawkey-0.28.0-1.fc30.x86_64 
  python3-libcomps-0.1.11-1.fc30.x86_64
  python3-libdnf-0.28.0-1.fc30.x86_64    
  python3-rpm-4.14.2.1-4.fc30.1.x86_64
  python3-unbound-1.8.3-4.fc30.x86_64                                                                                                                                                                                                         
  qemu-audio-alsa-2:3.1.0-5.fc30.x86_64           
  qemu-audio-oss-2:3.1.0-5.fc30.x86_64                                           
  qemu-audio-pa-2:3.1.0-5.fc30.x86_64                          
  qemu-audio-sdl-2:3.1.0-5.fc30.x86_64                                       
  qemu-block-curl-2:3.1.0-5.fc30.x86_64                       
  qemu-block-dmg-2:3.1.0-5.fc30.x86_64                                 
  qemu-block-iscsi-2:3.1.0-5.fc30.x86_64                           
  qemu-block-nfs-2:3.1.0-5.fc30.x86_64        
  qemu-block-rbd-2:3.1.0-5.fc30.x86_64
  qemu-block-ssh-2:3.1.0-5.fc30.x86_64             
  qemu-common-2:3.1.0-5.fc30.x86_64      
  qemu-img-2:3.1.0-5.fc30.x86_64      
  qemu-kvm-2:3.1.0-5.fc30.x86_64      
  qemu-system-x86-2:3.1.0-5.fc30.x86_64            
  qemu-system-x86-core-2:3.1.0-5.fc30.x86_64         
  qemu-ui-curses-2:3.1.0-5.fc30.x86_64             
  qemu-ui-gtk-2:3.1.0-5.fc30.x86_64                
  qemu-ui-sdl-2:3.1.0-5.fc30.x86_64                 
  radvd-2.17-19.fc30.x86_64                     
  rdma-core-20.1-3.fc30.x86_64                    
  rpm-build-libs-4.14.2.1-4.fc30.1.x86_64          
  rpm-plugin-systemd-inhibit-4.14.2.1-4.fc30.1.x86_64   
  rpm-sign-libs-4.14.2.1-4.fc30.1.x86_64                
  ruby-2.6.2-118.fc30.x86_64                               
  ruby-libs-2.6.2-118.fc30.x86_64                        
  rubygem-bigdecimal-1.4.1-118.fc30.x86_64                      
  rubygem-builder-3.2.3-6.fc30.noarch                      
  rubygem-childprocess-0.5.9-5.fc29.noarch               
  rubygem-concurrent-ruby-1.0.5-5.fc30.noarch          
  rubygem-did_you_mean-1.3.0-118.fc30.noarch            
  rubygem-domain_name-0.5.20180417-3.fc30.noarch            
  rubygem-erubis-2.7.0-17.fc29.noarch                  
  rubygem-excon-0.62.0-2.fc30.noarch            
  rubygem-ffi-1.10.0-2.fc30.x86_64                
  rubygem-fog-core-2.1.2-2.fc30.noarch             
  rubygem-fog-json-1.2.0-2.fc30.noarch                  
  rubygem-fog-libvirt-0.5.0-3.fc30.noarch               
  rubygem-fog-xml-0.1.3-2.fc30.noarch                      
  rubygem-formatador-0.2.5-7.fc30.noarch                 
  rubygem-hashicorp-checkpoint-0.1.5-3.fc30.noarch              
  rubygem-http-cookie-1.0.3-6.fc30.noarch                  
  rubygem-i18n-1.1.1-3.fc30.noarch                       
  rubygem-io-console-0.4.7-118.fc30.x86_64             
  rubygem-irb-1.0.0-118.fc30.noarch                     
  rubygem-json-2.2.0-200.fc30.x86_64                        
  rubygem-listen-3.1.5-7.fc30.noarch                               
  rubygem-log4r-1.1.10-10.fc30.noarch         
  rubygem-mime-types-3.1-6.fc30.noarch                  
  rubygem-mime-types-data-3.2016.0521-6.fc30.noarch
  rubygem-multi_json-1.13.1-3.fc30.noarch
  rubygem-net-scp-1.2.1-10.fc30.noarch   
  rubygem-net-sftp-2.1.2-9.fc30.noarch                                                                                                                                                                                                       
  rubygem-net-ssh-5.1.0-1.fc30.noarch              
  rubygem-netrc-0.11.0-5.fc30.noarch                 
  rubygem-nokogiri-1.10.1-1.fc30.1.x86_64          
  rubygem-openssl-2.1.2-118.fc30.x86_64            
  rubygem-psych-3.1.0-118.fc30.x86_64               
  rubygem-rb-inotify-0.10.0-1.fc30.noarch       
  rubygem-rdoc-6.1.0-118.fc30.noarch              
  rubygem-rest-client-2.0.0-6.fc30.noarch          
  rubygem-ruby-libvirt-0.7.1-5.fc30.x86_64              
  rubygem-rubyzip-1.1.7-8.fc30.noarch                   
  rubygem-unf-0.1.4-13.fc30.noarch                         
  rubygem-unf_ext-0.0.7.5-4.fc30.x86_64                  
  rubygems-3.0.3-118.fc30.noarch                                
  rubypick-1.1.1-10.fc30.noarch                            
  scrub-2.5.2-14.fc30.x86_64                             
  seabios-bin-1.12.0-2.fc30.noarch                     
  seavgabios-bin-1.12.0-2.fc30.noarch                   
  sgabios-bin-1:0.20180715git-2.fc30.noarch                 
  sheepdog-1.0.1-9.fc30.x86_64                         
  snappy-1.1.7-8.fc30.x86_64                    
  spice-server-0.14.1-3.fc30.x86_64               
  sqlite-3.26.0-3.fc30.x86_64                      
  squashfs-tools-4.3-16.fc28.x86_64                     
  supermin-5.1.20-3.fc30.x86_64                         
  syslinux-6.04-0.8.fc28.x86_64                            
  syslinux-extlinux-6.04-0.8.fc28.x86_64                 
  syslinux-extlinux-nonlinux-6.04-0.8.fc28.noarch               
  syslinux-nonlinux-6.04-0.8.fc28.noarch                   
  systemd-container-241-2.gita09c170.fc30.x86_64         
  unbound-libs-1.8.3-4.fc30.x86_64                     
  usbredir-0.8.0-2.fc30.x86_64                          
  vagrant-2.2.3-1.fc30.noarch                               
  vagrant-libvirt-0.0.45-1.fc30.noarch                             
  vagrant-sshfs-1.3.1-3.fc30.noarch           
  virglrenderer-0.7.0-2.20180919git402c22886.fc30.x86_64
  zerofree-1.1.1-3.fc30.x86_64                     
  zfs-fuse-0.7.2.2-11.fc30.x86_64        
Run "systemctl reboot" to start a reboot

So I tried rpm-ostree upgrade again and everything went OK.