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Conflicts between attempted installs of gawk-5.3.1-1.x86_64 and gawk-5.3.1-1.x86_64 #2189

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arteze opened this issue Dec 22, 2024 · 3 comments

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@arteze
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arteze commented Dec 22, 2024

When trying to update using dnf update I get a conflict with gawk-5.3.1-1.x86_64 and gawk-5.3.1-1.x86_64, that is, it is the same package, it is actually a single package, but it is in conflict with itself.

And the same thing happens with some other packages.

With gawk as an example (in my case).

  file /usr/libexec/awk conflicts between attempted installs of gawk-5.3.1-1.x86_64 and gawk-5.3.1-1.x86_64

Errors:

  file /usr/lib64/qt5/bin/uic conflicts between attempted installs of lib64qt5gui-devel-5.15.15-1.x86_64 and lib64qt5gui-devel-5.15.15-1.x86_64
  installing package lib64qt5gui-devel-5.15.15-1.x86_64 needs 175MB more space on the / filesystem
  installing package lib64qt5qmlmodels-devel-5.15.15-1.x86_64 needs 166MB more space on the / filesystem
  file /usr/lib64/qt5/bin/qmlformat conflicts between attempted installs of lib64qt5qml-devel-5.15.15-1.x86_64 and lib64qt5qml-devel-5.15.15-1.x86_64
  file /usr/lib64/qt5/bin/qmltyperegistrar conflicts between attempted installs of lib64qt5qml-devel-5.15.15-1.x86_64 and lib64qt5qml-devel-5.15.15-1.x86_64
  installing package lib64qt5qml-devel-5.15.15-1.x86_64 needs 184MB more space on the / filesystem
  installing package lib64qt5quick-devel-5.15.15-1.x86_64 needs 167MB more space on the / filesystem
  installing package qemu-ui-opengl-1:9.2.0-0.rc3.1.x86_64 needs 165MB more space on the / filesystem
  installing package qemu-ui-spice-core-1:9.2.0-0.rc3.1.x86_64 needs 165MB more space on the / filesystem
  installing package qemu-user-1:9.2.0-0.rc3.1.x86_64 needs 433MB more space on the / filesystem
  file /usr/bin/qmlcachegen conflicts between attempted installs of pyside6-devel-6.8.0.2-2.x86_64 and qt5-qtdeclarative-5.15.15-1.x86_64
  file /usr/bin/qmlimportscanner conflicts between attempted installs of pyside6-devel-6.8.0.2-2.x86_64 and qt5-qtdeclarative-5.15.15-1.x86_64
  file /usr/bin/qmllint conflicts between attempted installs of pyside6-devel-6.8.0.2-2.x86_64 and qt5-qtdeclarative-5.15.15-1.x86_64
  file /usr/libexec/awk conflicts between attempted installs of gawk-5.3.1-1.x86_64 and gawk-5.3.1-1.x86_64
  file /usr/bin/gdb conflicts between attempted installs of gdb-15.2-1.x86_64 and gdb-headless-15.2-1.x86_64
  file /usr/libexec/postfix conflicts between attempted installs of postfix-3.9.1-1.x86_64 and postfix-3.9.1-1.x86_64
  file /usr/libexec/file-roller conflicts between attempted installs of file-roller-44.4-2.x86_64 and file-roller-44.4-2.x86_64
  file /usr/lib64/qt5/bin/qdbus conflicts between attempted installs of qt5-qttools-qtdbus-5.15.15-1.x86_64 and qt5-qttools-qtdbus-5.15.15-1.x86_64
  file /usr/lib64/qt5/bin/qdbusviewer conflicts between attempted installs of qt5-qttools-qtdbus-5.15.15-1.x86_64 and qt5-qttools-qtdbus-5.15.15-1.x86_64
  file /usr/libexec/gpg-wks-client conflicts between attempted installs of gnupg-2.5.0-1.x86_64 and gnupg-2.5.0-1.x86_64
  file /usr/lib64/Mcrt1.o conflicts between attempted installs of glibc-devel-6:2.40-1.x86_64 and glibc-devel-6:2.40-1.x86_64
  file /usr/lib64/Scrt1.o conflicts between attempted installs of glibc-devel-6:2.40-1.x86_64 and glibc-devel-6:2.40-1.x86_64
  file /usr/lib64/crt1.o conflicts between attempted installs of glibc-devel-6:2.40-1.x86_64 and glibc-devel-6:2.40-1.x86_64
  file /usr/lib64/crti.o conflicts between attempted installs of glibc-devel-6:2.40-1.x86_64 and glibc-devel-6:2.40-1.x86_64
  file /usr/lib64/crtn.o conflicts between attempted installs of glibc-devel-6:2.40-1.x86_64 and glibc-devel-6:2.40-1.x86_64
  file /usr/lib64/gcrt1.o conflicts between attempted installs of glibc-devel-6:2.40-1.x86_64 and glibc-devel-6:2.40-1.x86_64
  file /usr/lib64/grcrt1.o conflicts between attempted installs of glibc-devel-6:2.40-1.x86_64 and glibc-devel-6:2.40-1.x86_64
  file /usr/lib64/libc.so conflicts between attempted installs of glibc-devel-6:2.40-1.x86_64 and glibc-devel-6:2.40-1.x86_64
  file /usr/lib64/libc_nonshared.a conflicts between attempted installs of glibc-devel-6:2.40-1.x86_64 and glibc-devel-6:2.40-1.x86_64
  file /usr/lib64/libg.a conflicts between attempted installs of glibc-devel-6:2.40-1.x86_64 and glibc-devel-6:2.40-1.x86_64
  file /usr/lib64/libm.so conflicts between attempted installs of glibc-devel-6:2.40-1.x86_64 and glibc-devel-6:2.40-1.x86_64
  file /usr/lib64/libmcheck.a conflicts between attempted installs of glibc-devel-6:2.40-1.x86_64 and glibc-devel-6:2.40-1.x86_64
  file /usr/lib64/rcrt1.o conflicts between attempted installs of glibc-devel-6:2.40-1.x86_64 and glibc-devel-6:2.40-1.x86_64

Error Summary
-------------
Disk Requirements:
   At least 433MB more space needed on the / filesystem.

I don't have any free space right now, but I plan to upgrade when I do.

How can this be fixed, if possible?

@ppisar
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ppisar commented Jan 3, 2025

In what phase od dnf execution do you see those errors?

Is it after you confirm the transaction ("Is this ok?" query) and after DNF starts the the RPM transaction ("Running transaction" line)? If it is so, those are messages from RPM library.

I've never seen a conflict between two same packages. It's quite possible that RPM library mishandles insufficient disk space.

Could you please try to simplify the problem by first making enough disk space and retrying the update?

Another reason could be that you actually have multiple same-named but different packages in your repositories and they indeed conflict.

@arteze
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arteze commented Feb 8, 2025

I accidentally touched something in the BIOS settings, it said Raid Wipe MBR and I had to format the system.

Again I decided to install everything again, and a similar error occurred again, I solved it by doing --allowerasing on the command line, or this in /etc/yum.conf.

/etc/yum.conf

[main]
cachedir=/var/cache/yum/$basearch/$releasever
debuglevel=2
exactarch=1
gpgcheck=0
installonly_limit=3
allowerasing=1
keepcache=1

Now I have this problem.

[RPM] unpacking of archive failed on file /bin;67a75d54: cpio: File from package already exists as a directory in system
Unpack error: filesystem-0:3.18-36.fc42.x86_64

Full error:

dnf install filesystem
Updating and loading repositories:
Repositories loaded.
Package                                  Arch        Version                                   Repository                 Size
Installing:
 filesystem                              x86_64      3.18-36.fc42                              rawhide               112.0   B
Installing dependencies:
 setup                                   noarch      2.15.0-10.fc42                            rawhide               720.7 KiB

Transaction Summary:
 Installing:         2 packages

Total size of inbound packages is 1 MiB. Need to download 0 B.
After this operation, 721 KiB extra will be used (install 721 KiB, remove 0 B).
Is this ok [y/N]: y
[1/2] filesystem-0:3.18-36.fc42.x86_64                                                100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                                                                        
[2/2] setup-0:2.15.0-10.fc42.noarch                                                   100% |   0.0   B/s |   0.0   B |  00m00s
>>> Already downloaded                                                                                                        
------------------------------------------------------------------------------------------------------------------------------
[2/2] Total                                                                           100% |   0.0   B/s |   0.0   B |  00m00s
Running transaction
[1/4] Verify package files                                                            100% |  35.0   B/s |   2.0   B |  00m00s
>>> Running pre-transaction scriptlet: filesystem-0:3.18-36.fc42.x86_64                                                       
>>> Finished pre-transaction scriptlet: filesystem-0:3.18-36.fc42.x86_64                                                      
>>> [RPM] /var/cache/libdnf5/rawhide-056724bf31e61e5e/packages/filesystem-3.18-36.fc42.x86_64.rpm: Header V4 RSA/SHA256 Signat
[2/4] Prepare transaction                                                             100% |  11.0   B/s |   2.0   B |  00m00s
>>> Running unknown scriptlet: setup-0:2.15.0-10.fc42.noarch                                                                  
>>> Error in unknown scriptlet: setup-0:2.15.0-10.fc42.noarch                                                                 
>>> Scriptlet output:                                                                                                         
>>> Creating group 'adm' with GID 4.                                                                                          
>>> Creating group 'games' with GID 20.                                                                                       
>>> Creating group 'kvm' with GID 36.                                                                                         
>>> Creating group 'lock' with GID 54.                                                                                        
>>> Creating group 'man' with GID 15.                                                                                         
>>> Creating group 'mem' with GID 8.                                                                                          
>>> Suggested group ID 105 for render already used.                                                                           
>>> Creating group 'render' with GID 999.                                                                                     
>>> Suggested group ID 106 for sgx already used.                                                                              
>>> Creating group 'sgx' with GID 998.                                                                                        
>>> Creating group 'sys' with GID 3.                                                                                          
>>> Creating group 'utmp' with GID 22.                                                                                        
>>> Suggested group ID 10 for wheel already used.                                                                             
>>> Creating group 'wheel' with GID 997.                                                                                      
>>> Creating group 'polkitd' with GID 996.                                                                                    
>>> Creating user 'polkitd' (User for polkitd) with UID 996 and GID 996.                                                      
>>> /etc/gshadow: Group "sys" already exists.                                                                                 
>>>                                                                                                                           
>>> [RPM] %sysusers(setup-2.15.0-10.fc42.noarch) scriptlet failed, exit status 1                                              
[3/4] Installing filesystem-0:3.18-36.fc42.x86_64                                     100% | 343.1 KiB/s | 212.4 KiB |  00m01s
>>> [RPM] setup-2.15.0-10.fc42.noarch: install failed                                                                         
>>> [RPM] unpacking of archive failed on file /bin;67a75e10: cpio: File from package already exists as a directory in system  
>>> Unpack error: filesystem-0:3.18-36.fc42.x86_64                                                                            
Transaction failed: Rpm transaction failed.
Warning: skipped OpenPGP checks for 2 packages from repository: rawhide

sha256sum

sha256sum /var/cache/libdnf5/rawhide-056724bf31e61e5e/packages/filesystem-3.18-36.fc42.x86_64.rpm
7e8237e818800630a783dce3ec9f4b211f0cc89fe7abba9965a2e0cdea6adb76  /var/cache/libdnf5/rawhide-056724bf31e61e5e/packages/filesystem-3.18-36.fc42.x86_64.rpm

cpio version

cpio --version
cpio (GNU cpio) 2.15
Copyright (C) 2024 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by Phil Nelson, David MacKenzie, John Oleynick,
and Sergey Poznyakoff.

rpm version

rpm --version
RPM version 4.20.0

@arteze
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arteze commented Feb 9, 2025

I symlinked /usr/bin to /bin, same with lib, lib64, and sbin, and it's fixed now.

@arteze arteze closed this as completed Feb 9, 2025
@github-project-automation github-project-automation bot moved this from Backlog to Done in DNF team Feb 9, 2025
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