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Description of problem: This is a fresh install of Fedora 28. When running dnf update today, I got failures related to the nss package. Here is the console output: [root@localhost-live log]# dnf clean all 0 files removed [root@localhost-live log]# dnf update -v Loaded plugins: builddep, config-manager, copr, debug, debuginfo-install, download, generate_completion_cache, needs-restarting, playground, repoclosure, repograph, repomanage, reposync DNF version: 2.7.5 cachedir: /var/cache/dnf Fedora 28 - x86_64 - Updates 1.4 MB/s | 6.0 MB 00:04 updates: using metadata from Wed 09 May 2018 02:11:35 PM PDT. Fedora 28 - x86_64 2.0 MB/s | 60 MB 00:30 not found deltainfo for: Fedora 28 - x86_64 not found updateinfo for: Fedora 28 - x86_64 fedora: using metadata from Thu 26 Apr 2018 04:12:28 AM PDT. google-chrome 20 kB/s | 3.8 kB 00:00 not found deltainfo for: google-chrome not found updateinfo for: google-chrome google-chrome: using metadata from Wed 09 May 2018 10:45:41 AM PDT. Last metadata expiration check: 0:00:00 ago on Thu 10 May 2018 12:28:54 PM PDT. Missing file *modules.yaml in metadata cache dir: /var/cache/dnf/updates-8bd9ef368505a5fd Missing file *modules.yaml in metadata cache dir: /var/cache/dnf/fedora-f21308f6293b3270 Missing file *modules.yaml in metadata cache dir: /var/cache/dnf/google-chrome-eb0d6f10ccbdafba Completion plugin: Generating completion cache... --> Starting dependency resolution ---> Package nss.i686 3.36.1-1.0.fc28 will be upgraded ---> Package nss.i686 3.36.1-1.1.fc28 will be an upgrade --> Finished dependency resolution Dependencies resolved. ================================================================================================= Package Arch Version Repository Size ================================================================================================= Upgrading: nss i686 3.36.1-1.1.fc28 updates 716 k Transaction Summary ================================================================================================= Upgrade 1 Package Total download size: 716 k Is this ok [y/N]: y Downloading Packages: nss-3.36.1-1.0.fc28_3.36.1-1.1.fc28.i686.drpm 156 kB/s | 87 kB 00:00 /usr/share/man/man5/cert8.db.5.gz: read error (tried to read 909 bytes from offset 0) cannot reconstruct rpm from disk files Some packages were not downloaded. Retrying. nss-3.36.1-1.1.fc28.i686.rpm 619 kB/s | 716 kB 00:01 ------------------------------------------------------------------------------------------------- Total 342 kB/s | 803 kB 00:02 Failed Delta RPMs increased 0.7 MB of updates to 0.8 MB (-12.1% wasted) Running transaction check Transaction check succeeded. Running transaction test The downloaded packages were saved in cache until the next successful transaction. You can remove cached packages by executing 'dnf clean packages'. Error: Transaction check error: file /usr/share/man/man5/cert8.db.5.gz from install of nss-3.36.1-1.1.fc28.i686 conflicts with file from package nss-3.36.1-1.0.fc28.x86_64 file /usr/share/man/man5/cert9.db.5.gz from install of nss-3.36.1-1.1.fc28.i686 conflicts with file from package nss-3.36.1-1.0.fc28.x86_64 file /usr/share/man/man5/key3.db.5.gz from install of nss-3.36.1-1.1.fc28.i686 conflicts with file from package nss-3.36.1-1.0.fc28.x86_64 file /usr/share/man/man5/key4.db.5.gz from install of nss-3.36.1-1.1.fc28.i686 conflicts with file from package nss-3.36.1-1.0.fc28.x86_64 file /usr/share/man/man5/pkcs11.txt.5.gz from install of nss-3.36.1-1.1.fc28.i686 conflicts with file from package nss-3.36.1-1.0.fc28.x86_64 file /usr/share/man/man5/secmod.db.5.gz from install of nss-3.36.1-1.1.fc28.i686 conflicts with file from package nss-3.36.1-1.0.fc28.x86_64 How reproducible: Not sure if this could be reproduced if done again today, but this is pretty much what I did: 1. Install Fedora 28 2. # dnf install wine (yesterday) 3. # dnf update (today) Actual results: Error message above. Expected results: nss gets updated. Additional Notes: Installing wine installs a bunch of i686 packages, apparently including nss.i686.
(In reply to Tim Elliott from comment #0) I have tried to reproduce this problem various ways and could't. > Description of problem: > > This is a fresh install of Fedora 28. When running dnf update today, I got > failures related to the nss package. > > Here is the console output: > ..... > > ==================== > Upgrading: > nss i686 3.36.1-1.1.fc28 updates > 716 k ... > > Transaction Summary > ============================================================================= > ==================== > Upgrade 1 Package > Total download size: 716 k > Is this ok [y/N]: y > Downloading Packages: > nss-3.36.1-1.0.fc28_3.36.1-1.1.fc28.i686.drpm 156 kB/s | > 87 kB 00:00 > /usr/share/man/man5/cert8.db.5.gz: read error > (tried to read 909 bytes from offset 0) > cannot reconstruct rpm from disk files > Some packages were not downloaded. Retrying. > nss-3.36.1-1.1.fc28.i686.rpm 619 kB/s | > 716 kB 00:01 > ----------------------------------------------------------------------------- > -------------------- > Total 342 kB/s | > 803 kB 00:02 > Failed Delta RPMs increased 0.7 MB of updates to 0.8 MB (-12.1% wasted) > Running transaction check > Transaction check succeeded. > Running transaction test > The downloaded packages were saved in cache until the next successful > transaction. > You can remove cached packages by executing 'dnf clean packages'. > Error: Transaction check error: > file /usr/share/man/man5/cert8.db.5.gz from install of > nss-3.36.1-1.1.fc28.i686 conflicts with file from package > nss-3.36.1-1.0.fc28.x86_64 I notice that you have nss-3.36.1-1.0 but only the i686 is getting updated and that causes the problem. I have seen this problem before but I haven't seen it in a very long time. > > > How reproducible: > > Not sure if this could be reproduced if done again today, but this is pretty > much what I did: > > 1. Install Fedora 28 > 2. # dnf install wine (yesterday) > 3. # dnf update (today) You could you try # dnf --refresh update That way the cache get's clean up first and hopefully both the i686 and x86_64 will get included in the update. Sometimes I do # dnf --refresh --best --allowerasing update but I bet is not needed. > > Installing wine installs a bunch of i686 packages, apparently including > nss.i686. Yes, wine needs to support both as in Window there a still a lot 32-bit only applications.
# dnf --refresh --best --allowerasing update -y Last metadata expiration check: 0:00:00 ago on Mon 14 May 2018 09:03:16 AM PDT. Dependencies resolved. ================================================================================================================================================ Package Arch Version Repository Size ================================================================================================================================================ Upgrading: nss i686 3.36.1-1.1.fc28 updates 716 k Transaction Summary ================================================================================================================================================ Upgrade 1 Package Total size: 716 k Downloading Packages: [SKIPPED] nss-3.36.1-1.1.fc28.i686.rpm: Already downloaded Running transaction check Transaction check succeeded. Running transaction test The downloaded packages were saved in cache until the next successful transaction. You can remove cached packages by executing 'dnf clean packages'. Error: Transaction check error: file /usr/share/man/man5/cert8.db.5.gz from install of nss-3.36.1-1.1.fc28.i686 conflicts with file from package nss-3.36.1-1.0.fc28.x86_64 file /usr/share/man/man5/cert9.db.5.gz from install of nss-3.36.1-1.1.fc28.i686 conflicts with file from package nss-3.36.1-1.0.fc28.x86_64 file /usr/share/man/man5/key3.db.5.gz from install of nss-3.36.1-1.1.fc28.i686 conflicts with file from package nss-3.36.1-1.0.fc28.x86_64 file /usr/share/man/man5/key4.db.5.gz from install of nss-3.36.1-1.1.fc28.i686 conflicts with file from package nss-3.36.1-1.0.fc28.x86_64 file /usr/share/man/man5/pkcs11.txt.5.gz from install of nss-3.36.1-1.1.fc28.i686 conflicts with file from package nss-3.36.1-1.0.fc28.x86_64 file /usr/share/man/man5/secmod.db.5.gz from install of nss-3.36.1-1.1.fc28.i686 conflicts with file from package nss-3.36.1-1.0.fc28.x86_64 Error Summary -------------
After manually removing nss-3.36.1-1.0.fc28.x86_64, dnf update works again: # sudo dnf remove nss-3.36.1-1.0.fc28.x86_64 Dependencies resolved. ================================================================================================================================================ Package Arch Version Repository Size ================================================================================================================================================ Removing: nss x86_64 3.36.1-1.0.fc28 @updates 1.9 M Removing dependent packages: nss-tools x86_64 3.36.1-1.0.fc28 @updates 2.1 M Transaction Summary ================================================================================================================================================ Remove 2 Packages Freed space: 3.9 M Is this ok [y/N]: y Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Erasing : nss-tools-3.36.1-1.0.fc28.x86_64 1/2 Erasing : nss-3.36.1-1.0.fc28.x86_64 2/2 Running scriptlet: nss-3.36.1-1.0.fc28.x86_64 2/2 Verifying : nss-tools-3.36.1-1.0.fc28.x86_64 1/2 Verifying : nss-3.36.1-1.0.fc28.x86_64 2/2 Removed: nss.x86_64 3.36.1-1.0.fc28 nss-tools.x86_64 3.36.1-1.0.fc28 Complete! # sudo dnf update Last metadata expiration check: 0:12:09 ago on Mon 14 May 2018 09:03:16 AM PDT. Dependencies resolved. ================================================================================================================================================ Package Arch Version Repository Size ================================================================================================================================================ Upgrading: nss i686 3.36.1-1.1.fc28 updates 716 k Removing dependent packages: nss-sysinit x86_64 3.36.1-1.0.fc28 @updates 14 k Transaction Summary ================================================================================================================================================ Upgrade 1 Package Remove 1 Package Total size: 716 k Is this ok [y/N]: y Downloading Packages: [SKIPPED] nss-3.36.1-1.1.fc28.i686.rpm: Already downloaded Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Upgrading : nss-3.36.1-1.1.fc28.i686 1/3 Running scriptlet: nss-3.36.1-1.1.fc28.i686 1/3 Cleanup : nss-3.36.1-1.0.fc28.i686 2/3 Running scriptlet: nss-3.36.1-1.0.fc28.i686 2/3 Erasing : nss-sysinit-3.36.1-1.0.fc28.x86_64 3/3 Running scriptlet: nss-sysinit-3.36.1-1.0.fc28.x86_64 3/3 Verifying : nss-3.36.1-1.1.fc28.i686 1/3 Verifying : nss-3.36.1-1.0.fc28.i686 2/3 Verifying : nss-sysinit-3.36.1-1.0.fc28.x86_64 3/3 Removed: nss-sysinit.x86_64 3.36.1-1.0.fc28 Upgraded: nss.i686 3.36.1-1.1.fc28 Complete! [root@localhost-live ~]#
Tim, If you execute "rpm -q nss nss-softokn nss-util", what does it show?
(In reply to Elio Maldonado Batiz from comment #4) Never mind, just did in a system similiar to yours and got nss-3.36.1-1.1.fc28.x86_64 nss-3.36.1-1.1.fc28.i686 nss-softokn-3.36.1-1.1.fc28.x86_64 nss-softokn-3.36.1-1.1.fc28.i686 nss-util-3.36.1-1.0.fc28.x86_64 nss-util-3.36.1-1.0.fc28.i686 all at 3.36.1 which we wanted. When doing a fresh install or a release upgrade I tend to do to an update before installing additional packages as it may help avoid such problems as having out synch packages for multi-arch stuff. Thank you Tim for reporting and trying things out.
To summarize: - you had both nss*.i686 and nss*.x86_64 installed - newer updates for both were available - dnf update attempted to update nss*.i686, only, but that doesn't work, because the conflicts with duplicate files only are avoided if both architectures get updated at the same time. - we don't know why dnf attempted to update i686, only Is this correct? Instead of removing nss.x86_64, explicitly telling dnf to upgrade all in parallel might have worked, too. IIUC your immediate problem is solved, but there might be a general underlying bug. The bug might be either in dnf, or in incorrect dependencies in the nss* packages. We'd have to attempt to reproduce this to solve it.
This is turning out to be a dnf issue. Closing as a duplicate. *** This bug has been marked as a duplicate of bug 1653683 ***