Description of problem: I have followed the fedora upgrade instructions at https://docs.fedoraproject.org/en-US/quick-docs/dnf-system-upgrade/ and in the end they always end up breaking the consistency of some rpm packages When executing the symlinks -r -d /usr a fair number of rpms break. State immediately before the symlinks step ``` [root@minerva ~]# rpm -qa --verify S.5....T. c /etc/krb5.conf S.5....T. c /etc/samba/smb.conf .M....... g /var/lib/selinux/targeted/active/modules/200/smartmon .......T. c /etc/pcp/pmcd/pmcd.conf S.5....T. c /etc/chrony.conf S.5....T. /var/log/salt/minion SM5....T. c /etc/salt/minion .M....... n /etc/salt/pki/minion .M....... /var/lib/samba/sysvol .....UG.. g /var/lib/nfs/statd/state S.5....T. c /etc/ssh/sshd_config .M....... c /boot/grub2/grub.cfg S.5....T. c /root/.bashrc ``` Finding dangling symlinks... ``` [root@minerva ~]# symlinks -r /usr | grep dangling dangling: /usr/lib/.build-id/c1/7bd973c1e316bfee4f4aa5ac16830a5dc3bcd3 -> ../../../../usr/sbin/quota_nld dangling: /usr/lib/.build-id/e3/dab686192ee682c642dc1a1e3e894e88a5af63 -> ../../../../usr/sbin/warnquota dangling: /usr/lib/.build-id/55/486e343b14b6f6badd7275b014dd82f44680d3 -> ../../../../usr/lib64/libncurses++.so.6.3 dangling: /usr/lib/.build-id/6a/d960b89a4448d76ead4892524133af065748b2 -> ../../../../usr/sbin/rpc.rquotad dangling: /usr/lib/.build-id/7e/36f7119010825fb025ca944a61801662c7aa11 -> ../../../../usr/bin/coreutils.single dangling: /usr/lib/.build-id/a1/d1843eed661509d750d69baef2a61e1fbf19e7 -> ../../../../usr/sbin/tc dangling: /usr/lib/.build-id/18/186f3e1b1b577a19b2f1f296dbc2e41b6970f2 -> ../../../../usr/lib64/libncurses++w.so.6.3 dangling: /usr/lib/.build-id/67/0f5d8033ec23ca4777aeca9ff236608e5e11af -> ../../../../usr/sbin/grub2-sparc64-setup dangling: /usr/lib/.build-id/67/66146da07119be1e86dfcf4aa867f5e30bea43 -> ../../../../usr/sbin/xfs_scrub dangling: /usr/lib/.build-id/2f/767bee207dca37dc5105a599722d6f2f4106f3 -> ../../../../usr/sbin/grub2-ofpathname dangling: /usr/lib/firmware/qcom/LENOVO/21BX.xz -> ../sc8280xp/LENOVO/21BX.xz dangling: /usr/lib/modules/6.2.7-200.fc37.x86_64/build -> /usr/src/kernels/6.2.7-200.fc37.x86_64 dangling: /usr/lib/modules/6.2.7-200.fc37.x86_64/source -> build dangling: /usr/share/doc/hunspell/README -> README.md dangling: /usr/share/cockpit/branding/arch/apple-touch-icon.png -> ../../../pixmaps/archlinux-logo.png dangling: /usr/share/cockpit/branding/arch/favicon.ico -> ../../../pixmaps/archlinux-logo.png dangling: /usr/share/cockpit/branding/arch/logo.png -> ../../../pixmaps/archlinux-logo.png dangling: /usr/share/cockpit/branding/debian/favicon.ico -> ../../../pixmaps/debian-logo.png dangling: /usr/share/cockpit/branding/debian/logo.png -> ../../../pixmaps/debian-logo.png dangling: /usr/share/cockpit/branding/opensuse/default-1920x1200.jpg -> ../../../wallpapers/default-1920x1200.jpg dangling: /usr/share/cockpit/branding/opensuse/favicon.ico -> ../../../pixmaps/distribution-logos/favicon.ico dangling: /usr/share/cockpit/branding/opensuse/square-hicolor.svg -> ../../../pixmaps/distribution-logos/square-hicolor.svg dangling: /usr/share/cockpit/branding/ubuntu/logo.png -> ../../../plymouth/ubuntu-logo.png [root@minerva ~]# ls -l /usr/lib/.build-id/c1/7bd973c1e316bfee4f4aa5ac16830a5dc3bcd3 lrwxrwxrwx. 1 root root 30 Jul 23 2022 /usr/lib/.build-id/c1/7bd973c1e316bfee4f4aa5ac16830a5dc3bcd3 -> ../../../../usr/sbin/quota_nld ``` Yes, they appear to be dangling when inspected Follow instructions... ``` [root@minerva ~]# symlinks -r -d /usr absolute: /usr/bin/ex -> /usr/libexec/vi absolute: /usr/bin/rvi -> /usr/libexec/vi absolute: /usr/bin/rview -> /usr/libexec/vi absolute: /usr/bin/soelim -> /etc/alternatives/soelim messy: /usr/bin/pydoc -> ./pydoc3 absolute: /usr/bin/abrt-cli -> /usr/bin/abrt absolute: /usr/bin/whois -> /etc/alternatives/whois absolute: /usr/bin/apropos -> /etc/alternatives/apropos absolute: /usr/bin/whatis -> /etc/alternatives/whatis absolute: /usr/bin/nc -> /etc/alternatives/nc absolute: /usr/bin/man -> /etc/alternatives/man absolute: /usr/bin/yum-debug-restore -> /usr/libexec/dnf-utils absolute: /usr/bin/find-repos-of-install -> /usr/libexec/dnf-utils absolute: /usr/bin/repomanage -> /usr/libexec/dnf-utils absolute: /usr/bin/clevis-decrypt-tpm2plus -> /usr/bin/clevis-pin-tpm2 absolute: /usr/bin/yum-groups-manager -> /usr/libexec/dnf-utils absolute: /usr/bin/yumdownloader -> /usr/libexec/dnf-utils absolute: /usr/bin/package-cleanup -> /usr/libexec/dnf-utils absolute: /usr/bin/repotrack -> /usr/libexec/dnf-utils absolute: /usr/bin/yum-builddep -> /usr/libexec/dnf-utils absolute: /usr/bin/yum-config-manager -> /usr/libexec/dnf-utils absolute: /usr/bin/repoclosure -> /usr/libexec/dnf-utils absolute: /usr/bin/yum-debug-dump -> /usr/libexec/dnf-utils absolute: /usr/bin/debuginfo-install -> /usr/libexec/dnf-utils absolute: /usr/bin/repo-graph -> /usr/libexec/dnf-utils absolute: /usr/bin/repoquery -> /usr/libexec/dnf-utils absolute: /usr/bin/repodiff -> /usr/libexec/dnf-utils absolute: /usr/bin/needs-restarting -> /usr/libexec/dnf-utils absolute: /usr/bin/reposync -> /usr/libexec/dnf-utils messy: /usr/bin/python -> ./python3 absolute: /usr/bin/clevis-encrypt-tpm2plus -> /usr/bin/clevis-pin-tpm2 absolute: /usr/sbin/ipset-translate -> /usr/sbin/ipset absolute: /usr/sbin/pidof -> /usr/bin/pidof absolute: /usr/sbin/iptables-save -> /etc/alternatives/iptables-save absolute: /usr/sbin/arptables -> /etc/alternatives/arptables absolute: /usr/sbin/ip6tables-save -> /etc/alternatives/ip6tables-save absolute: /usr/sbin/arptables-save -> /etc/alternatives/arptables-save absolute: /usr/sbin/iptables-restore -> /etc/alternatives/iptables-restore absolute: /usr/sbin/ebtables-restore -> /etc/alternatives/ebtables-restore absolute: /usr/sbin/ebtables -> /etc/alternatives/ebtables absolute: /usr/sbin/ifup -> /etc/alternatives/ifup absolute: /usr/sbin/arptables-restore -> /etc/alternatives/arptables-restore absolute: /usr/sbin/iptables -> /etc/alternatives/iptables absolute: /usr/sbin/ip6tables -> /etc/alternatives/ip6tables absolute: /usr/sbin/ip6tables-restore -> /etc/alternatives/ip6tables-restore absolute: /usr/sbin/ebtables-save -> /etc/alternatives/ebtables-save absolute: /usr/sbin/mkfs.ntfs -> /usr/sbin/mkntfs absolute: /usr/sbin/ifdown -> /etc/alternatives/ifdown absolute: /usr/sbin/mount.lowntfs-3g -> /usr/bin/lowntfs-3g absolute: /usr/sbin/mount.ntfs-3g -> /usr/bin/ntfs-3g dangling: /usr/lib/.build-id/c1/7bd973c1e316bfee4f4aa5ac16830a5dc3bcd3 -> ../../../../usr/sbin/quota_nld deleted: /usr/lib/.build-id/c1/7bd973c1e316bfee4f4aa5ac16830a5dc3bcd3 -> ../../../../usr/sbin/quota_nld dangling: /usr/lib/.build-id/e3/dab686192ee682c642dc1a1e3e894e88a5af63 -> ../../../../usr/sbin/warnquota deleted: /usr/lib/.build-id/e3/dab686192ee682c642dc1a1e3e894e88a5af63 -> ../../../../usr/sbin/warnquota dangling: /usr/lib/.build-id/55/486e343b14b6f6badd7275b014dd82f44680d3 -> ../../../../usr/lib64/libncurses++.so.6.3 deleted: /usr/lib/.build-id/55/486e343b14b6f6badd7275b014dd82f44680d3 -> ../../../../usr/lib64/libncurses++.so.6.3 dangling: /usr/lib/.build-id/6a/d960b89a4448d76ead4892524133af065748b2 -> ../../../../usr/sbin/rpc.rquotad deleted: /usr/lib/.build-id/6a/d960b89a4448d76ead4892524133af065748b2 -> ../../../../usr/sbin/rpc.rquotad dangling: /usr/lib/.build-id/7e/36f7119010825fb025ca944a61801662c7aa11 -> ../../../../usr/bin/coreutils.single deleted: /usr/lib/.build-id/7e/36f7119010825fb025ca944a61801662c7aa11 -> ../../../../usr/bin/coreutils.single dangling: /usr/lib/.build-id/a1/d1843eed661509d750d69baef2a61e1fbf19e7 -> ../../../../usr/sbin/tc deleted: /usr/lib/.build-id/a1/d1843eed661509d750d69baef2a61e1fbf19e7 -> ../../../../usr/sbin/tc dangling: /usr/lib/.build-id/18/186f3e1b1b577a19b2f1f296dbc2e41b6970f2 -> ../../../../usr/lib64/libncurses++w.so.6.3 deleted: /usr/lib/.build-id/18/186f3e1b1b577a19b2f1f296dbc2e41b6970f2 -> ../../../../usr/lib64/libncurses++w.so.6.3 dangling: /usr/lib/.build-id/67/0f5d8033ec23ca4777aeca9ff236608e5e11af -> ../../../../usr/sbin/grub2-sparc64-setup deleted: /usr/lib/.build-id/67/0f5d8033ec23ca4777aeca9ff236608e5e11af -> ../../../../usr/sbin/grub2-sparc64-setup dangling: /usr/lib/.build-id/67/66146da07119be1e86dfcf4aa867f5e30bea43 -> ../../../../usr/sbin/xfs_scrub deleted: /usr/lib/.build-id/67/66146da07119be1e86dfcf4aa867f5e30bea43 -> ../../../../usr/sbin/xfs_scrub dangling: /usr/lib/.build-id/2f/767bee207dca37dc5105a599722d6f2f4106f3 -> ../../../../usr/sbin/grub2-ofpathname deleted: /usr/lib/.build-id/2f/767bee207dca37dc5105a599722d6f2f4106f3 -> ../../../../usr/sbin/grub2-ofpathname dangling: /usr/lib/firmware/qcom/LENOVO/21BX.xz -> ../sc8280xp/LENOVO/21BX.xz deleted: /usr/lib/firmware/qcom/LENOVO/21BX.xz -> ../sc8280xp/LENOVO/21BX.xz dangling: /usr/lib/modules/6.2.7-200.fc37.x86_64/build -> /usr/src/kernels/6.2.7-200.fc37.x86_64 deleted: /usr/lib/modules/6.2.7-200.fc37.x86_64/build -> /usr/src/kernels/6.2.7-200.fc37.x86_64 dangling: /usr/lib/modules/6.2.7-200.fc37.x86_64/source -> build deleted: /usr/lib/modules/6.2.7-200.fc37.x86_64/source -> build absolute: /usr/lib/python3.11/site-packages/urllib3/packages/__pycache__/six.cpython-311.opt-1.pyc -> /usr/lib/python3.11/site-packages/__pycache__/six.cpython-311.opt-1.pyc absolute: /usr/lib/python3.11/site-packages/urllib3/packages/__pycache__/six.cpython-311.pyc -> /usr/lib/python3.11/site-packages/__pycache__/six.cpython-311.pyc absolute: /usr/lib/python3.11/site-packages/urllib3/packages/six.py -> /usr/lib/python3.11/site-packages/six.py absolute: /usr/lib64/libnssckbi.so -> /etc/alternatives/libnssckbi.so.x86_64 absolute: /usr/lib64/libwbclient.so.0.15 -> /etc/alternatives/libwbclient.so.0.15-64 dangling: /usr/share/doc/hunspell/README -> README.md deleted: /usr/share/doc/hunspell/README -> README.md absolute: /usr/share/doc/python-systemd/html/_static/jquery.js -> /usr/share/javascript/jquery/latest/jquery.min.js absolute: /usr/share/doc/atmel-firmware/COPYING -> /lib/firmware/COPYING.atmel-firmware absolute: /usr/share/doc/atmel-firmware/COPYRIGHT-usb -> /lib/firmware/COPYRIGHT-usb.atmel-firmware absolute: /usr/share/doc/atmel-firmware/README -> /lib/firmware/README.atmel-firmware absolute: /usr/share/doc/atmel-firmware/README-usb -> /lib/firmware/README-usb.atmel-firmware absolute: /usr/share/man/man7/man.7.gz -> /etc/alternatives/man.7.gz absolute: /usr/share/man/man1/soelim.1.gz -> /etc/alternatives/soelim.1.gz absolute: /usr/share/man/man1/whatis.1.gz -> /etc/alternatives/whatis.1.gz absolute: /usr/share/man/man1/abrt-cli.1.gz -> /usr/share/man/man1/abrt.1.gz absolute: /usr/share/man/man1/man.1.gz -> /etc/alternatives/man.1.gz absolute: /usr/share/man/man1/apropos.1.gz -> /etc/alternatives/apropos.1.gz absolute: /usr/share/man/man1/nc.1.gz -> /etc/alternatives/nc-man absolute: /usr/share/man/man1/repoquery.1.gz -> /usr/share/man/man1/dnf-utils.1.gz absolute: /usr/share/man/man1/repotrack.1.gz -> /usr/share/man/man1/dnf-utils.1.gz absolute: /usr/share/man/man1/find-repos-of-install.1.gz -> /usr/share/man/man1/dnf-utils.1.gz messy: /usr/share/man/man1/python.1.gz -> ./python3.1.gz absolute: /usr/share/man/man1/whois.1.gz -> /etc/alternatives/whois-man absolute: /usr/share/man/man8/ebtables.8.gz -> /etc/alternatives/ebtables-man absolute: /usr/share/man/man8/arptables-restore.8.gz -> /etc/alternatives/arptables-restore-man absolute: /usr/share/man/man8/arptables.8.gz -> /etc/alternatives/arptables-man absolute: /usr/share/man/man8/arptables-save.8.gz -> /etc/alternatives/arptables-save-man absolute: /usr/share/man/man8/dnf-offline-distrosync.8.gz -> /usr/share/man/man8/dnf-system-upgrade.8.gz absolute: /usr/share/man/man8/dnf-offline-upgrade.8.gz -> /usr/share/man/man8/dnf-system-upgrade.8.gz absolute: /usr/share/gawk -> /usr/share/awk dangling: /usr/share/cockpit/branding/arch/apple-touch-icon.png -> ../../../pixmaps/archlinux-logo.png deleted: /usr/share/cockpit/branding/arch/apple-touch-icon.png -> ../../../pixmaps/archlinux-logo.png dangling: /usr/share/cockpit/branding/arch/favicon.ico -> ../../../pixmaps/archlinux-logo.png deleted: /usr/share/cockpit/branding/arch/favicon.ico -> ../../../pixmaps/archlinux-logo.png dangling: /usr/share/cockpit/branding/arch/logo.png -> ../../../pixmaps/archlinux-logo.png deleted: /usr/share/cockpit/branding/arch/logo.png -> ../../../pixmaps/archlinux-logo.png dangling: /usr/share/cockpit/branding/debian/favicon.ico -> ../../../pixmaps/debian-logo.png deleted: /usr/share/cockpit/branding/debian/favicon.ico -> ../../../pixmaps/debian-logo.png dangling: /usr/share/cockpit/branding/debian/logo.png -> ../../../pixmaps/debian-logo.png deleted: /usr/share/cockpit/branding/debian/logo.png -> ../../../pixmaps/debian-logo.png dangling: /usr/share/cockpit/branding/opensuse/default-1920x1200.jpg -> ../../../wallpapers/default-1920x1200.jpg deleted: /usr/share/cockpit/branding/opensuse/default-1920x1200.jpg -> ../../../wallpapers/default-1920x1200.jpg dangling: /usr/share/cockpit/branding/opensuse/favicon.ico -> ../../../pixmaps/distribution-logos/favicon.ico deleted: /usr/share/cockpit/branding/opensuse/favicon.ico -> ../../../pixmaps/distribution-logos/favicon.ico dangling: /usr/share/cockpit/branding/opensuse/square-hicolor.svg -> ../../../pixmaps/distribution-logos/square-hicolor.svg deleted: /usr/share/cockpit/branding/opensuse/square-hicolor.svg -> ../../../pixmaps/distribution-logos/square-hicolor.svg dangling: /usr/share/cockpit/branding/ubuntu/logo.png -> ../../../plymouth/ubuntu-logo.png deleted: /usr/share/cockpit/branding/ubuntu/logo.png -> ../../../plymouth/ubuntu-logo.png absolute: /usr/libexec/gawk -> /usr/libexec/awk absolute: /usr/libexec/arptables-helper -> /etc/alternatives/arptables-helper absolute: /usr/libexec/samba/cups_backend_smb -> /etc/alternatives/cups_backend_smb ``` Some rpms are now inconsistent ``` [root@minerva ~]# rpm -qa --verify missing /usr/lib/firmware/qcom/LENOVO/21BX.xz missing a /usr/lib/.build-id/18/186f3e1b1b577a19b2f1f296dbc2e41b6970f2 missing a /usr/lib/.build-id/55/486e343b14b6f6badd7275b014dd82f44680d3 missing d /usr/share/doc/hunspell/README missing a /usr/lib/.build-id/67/66146da07119be1e86dfcf4aa867f5e30bea43 missing a /usr/lib/.build-id/a1/d1843eed661509d750d69baef2a61e1fbf19e7 missing a /usr/lib/.build-id/7e/36f7119010825fb025ca944a61801662c7aa11 S.5....T. c /etc/krb5.conf missing a /usr/lib/.build-id/2f/767bee207dca37dc5105a599722d6f2f4106f3 missing a /usr/lib/.build-id/67/0f5d8033ec23ca4777aeca9ff236608e5e11af S.5....T. c /etc/samba/smb.conf missing /lib/modules/6.2.7-200.fc37.x86_64/build missing /lib/modules/6.2.7-200.fc37.x86_64/source .M....... g /var/lib/selinux/targeted/active/modules/200/smartmon .......T. c /etc/pcp/pmcd/pmcd.conf S.5....T. c /etc/chrony.conf missing a /usr/lib/.build-id/6a/d960b89a4448d76ead4892524133af065748b2 missing a /usr/lib/.build-id/c1/7bd973c1e316bfee4f4aa5ac16830a5dc3bcd3 missing a /usr/lib/.build-id/e3/dab686192ee682c642dc1a1e3e894e88a5af63 missing /usr/share/cockpit/branding/arch/apple-touch-icon.png missing /usr/share/cockpit/branding/arch/favicon.ico missing /usr/share/cockpit/branding/arch/logo.png missing /usr/share/cockpit/branding/debian/favicon.ico missing /usr/share/cockpit/branding/debian/logo.png missing /usr/share/cockpit/branding/opensuse/default-1920x1200.jpg missing /usr/share/cockpit/branding/opensuse/favicon.ico missing /usr/share/cockpit/branding/opensuse/square-hicolor.svg missing /usr/share/cockpit/branding/ubuntu/logo.png S.5....T. /var/log/salt/minion SM5....T. c /etc/salt/minion .M....... n /etc/salt/pki/minion .M....... /var/lib/samba/sysvol missing a /usr/lib/.build-id/2f/767bee207dca37dc5105a599722d6f2f4106f3 missing a /usr/lib/.build-id/67/0f5d8033ec23ca4777aeca9ff236608e5e11af .....UG.. g /var/lib/nfs/statd/state S.5....T. c /etc/ssh/sshd_config .M....... c /boot/grub2/grub.cfg S.5....T. c /root/.bashrc ``` Version-Release number of selected component (if applicable): Fedora upgrade to 35, 36 and 37 (at least) How reproducible: Very, very, very often Steps to Reproduce: 1. Use fedora on a VM for a while 2. Follow instructions at https://docs.fedoraproject.org/en-US/quick-docs/dnf-system-upgrade/ 3. rpm -qa --verify now show broken contents Actual results: rpm -qa --verify shows broken packages Expected results: Successful upgrade with consistent rpms Additional info:
This message is a reminder that Fedora Linux 37 is nearing its end of life. Fedora will stop maintaining and issuing updates for Fedora Linux 37 on 2023-12-05. It is Fedora's policy to close all bug reports from releases that are no longer maintained. At that time this bug will be closed as EOL if it remains open with a 'version' of '37'. Package Maintainer: If you wish for this bug to remain open because you plan to fix it in a currently maintained version, change the 'version' to a later Fedora Linux version. Note that the version field may be hidden. Click the "Show advanced fields" button if you do not see it. Thank you for reporting this issue and we are sorry that we were not able to fix it before Fedora Linux 37 is end of life. If you would still like to see this bug fixed and are able to reproduce it against a later version of Fedora Linux, you are encouraged to change the 'version' to a later version prior to this bug being closed.
Fedora Linux 37 entered end-of-life (EOL) status on 2023-12-05. Fedora Linux 37 is no longer maintained, which means that it will not receive any further security or bug fix updates. As a result we are closing this bug. If you can reproduce this bug against a currently maintained version of Fedora Linux please feel free to reopen this bug against that version. Note that the version field may be hidden. Click the "Show advanced fields" button if you do not see the version field. If you are unable to reopen this bug, please file a new report against an active release. Thank you for reporting this bug and we are sorry it could not be fixed.