Description of problem: I use "dnf distro-sync" often, because I use updates-testing. A few weeks back, it started occurring that distro-sync wants to remove some of my packages without any good reason. The affected packages always seem to be orphans - in my case skype, atom and hamster-applet - they are not available in any repositories, but their dependencies are fine and there's no reason to remove them. Dnf seems to be doing something similar to remove-or-distro-sync, even though only distro-sync is run. This also happens only in certain cases, most probably when kernel update is involved. Today's example: $ dnf distro-sync Last metadata expiration check performed 0:20:11 ago on Fri Jul 17 13:09:21 2015. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: kernel x86_64 4.0.8-300.fc22 updates-testing 67 k kernel-core x86_64 4.0.8-300.fc22 updates-testing 19 M kernel-modules x86_64 4.0.8-300.fc22 updates-testing 18 M kernel-modules-extra x86_64 4.0.8-300.fc22 updates-testing 2.2 M Upgrading: NetworkManager x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 2.0 M NetworkManager-adsl x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 111 k NetworkManager-bluetooth x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 134 k NetworkManager-config-connectivity-fedora x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 101 k NetworkManager-glib x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 366 k NetworkManager-libnm x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 476 k NetworkManager-wifi x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 141 k NetworkManager-wwan x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 134 k abrt x86_64 2.6.1-1.fc22 updates-testing 517 k abrt-addon-ccpp x86_64 2.6.1-1.fc22 updates-testing 187 k abrt-addon-coredump-helper x86_64 2.6.1-1.fc22 updates-testing 105 k abrt-addon-kerneloops x86_64 2.6.1-1.fc22 updates-testing 122 k abrt-addon-pstoreoops x86_64 2.6.1-1.fc22 updates-testing 100 k abrt-addon-python x86_64 2.6.1-1.fc22 updates-testing 101 k abrt-addon-python3 x86_64 2.6.1-1.fc22 updates-testing 99 k abrt-addon-vmcore x86_64 2.6.1-1.fc22 updates-testing 110 k abrt-addon-xorg x86_64 2.6.1-1.fc22 updates-testing 101 k abrt-cli x86_64 2.6.1-1.fc22 updates-testing 91 k abrt-dbus x86_64 2.6.1-1.fc22 updates-testing 126 k abrt-desktop x86_64 2.6.1-1.fc22 updates-testing 91 k abrt-gui x86_64 2.6.1-1.fc22 updates-testing 188 k abrt-gui-libs x86_64 2.6.1-1.fc22 updates-testing 101 k abrt-libs x86_64 2.6.1-1.fc22 updates-testing 118 k abrt-plugin-bodhi x86_64 2.6.1-1.fc22 updates-testing 100 k abrt-python x86_64 2.6.1-1.fc22 updates-testing 114 k abrt-python3 x86_64 2.6.1-1.fc22 updates-testing 115 k abrt-retrace-client x86_64 2.6.1-1.fc22 updates-testing 127 k abrt-tui x86_64 2.6.1-1.fc22 updates-testing 103 k autocorr-cs noarch 1:4.4.4.3-4.fc22 updates 161 k autocorr-en noarch 1:4.4.4.3-4.fc22 updates 175 k bind-libs x86_64 32:9.10.2-3.P2.fc22 updates-testing 149 k bind-libs-lite x86_64 32:9.10.2-3.P2.fc22 updates-testing 1.0 M bind-license noarch 32:9.10.2-3.P2.fc22 updates-testing 87 k bind-utils x86_64 32:9.10.2-3.P2.fc22 updates-testing 400 k devscripts-minimal x86_64 2.15.5-6.fc22 updates-testing 38 k environment-modules x86_64 3.2.10-16.fc22 updates-testing 113 k evolution x86_64 3.16.4-1.fc22 updates-testing 8.6 M evolution-data-server x86_64 3.16.4-1.fc22 updates-testing 3.0 M firefox x86_64 39.0-8.fc22 updates 70 M glibc i686 2.21-7.fc22 updates-testing 4.2 M glibc x86_64 2.21-7.fc22 updates-testing 3.5 M glibc-common x86_64 2.21-7.fc22 updates-testing 11 M glibc-devel x86_64 2.21-7.fc22 updates-testing 903 k glibc-headers x86_64 2.21-7.fc22 updates-testing 494 k glusterfs x86_64 3.6.4-1.fc22 updates-testing 1.3 M glusterfs-api x86_64 3.6.4-1.fc22 updates-testing 73 k glusterfs-fuse x86_64 3.6.4-1.fc22 updates-testing 102 k glusterfs-libs x86_64 3.6.4-1.fc22 updates-testing 295 k gnome-abrt x86_64 1.2.0-3.fc22 updates-testing 235 k gnutls i686 3.3.16-1.fc22 updates-testing 616 k gnutls x86_64 3.3.16-1.fc22 updates-testing 627 k gnutls-dane x86_64 3.3.16-1.fc22 updates-testing 36 k gnutls-utils x86_64 3.3.16-1.fc22 updates-testing 238 k gzip x86_64 1.6-8.fc22 updates 155 k jwhois x86_64 4.0-41.fc22 updates-testing 119 k kernel-headers x86_64 4.0.8-300.fc22 updates-testing 996 k libgusb x86_64 0.2.6-1.fc22 updates-testing 43 k libidn i686 1.31-1.fc22 updates-testing 229 k libidn x86_64 1.31-1.fc22 updates-testing 228 k libinput x86_64 0.19.0-3.fc22 updates-testing 80 k libipa_hbac x86_64 1.13.0-1.fc22 updates-testing 71 k libreoffice-calc x86_64 1:4.4.4.3-4.fc22 updates 8.5 M libreoffice-core x86_64 1:4.4.4.3-4.fc22 updates 77 M libreoffice-draw x86_64 1:4.4.4.3-4.fc22 updates 677 k libreoffice-emailmerge x86_64 1:4.4.4.3-4.fc22 updates 80 k libreoffice-filters x86_64 1:4.4.4.3-4.fc22 updates 66 k libreoffice-graphicfilter x86_64 1:4.4.4.3-4.fc22 updates 445 k libreoffice-impress x86_64 1:4.4.4.3-4.fc22 updates 1.3 M libreoffice-langpack-cs x86_64 1:4.4.4.3-4.fc22 updates 6.7 M libreoffice-math x86_64 1:4.4.4.3-4.fc22 updates 1.0 M libreoffice-opensymbol-fonts noarch 1:4.4.4.3-4.fc22 updates 241 k libreoffice-pdfimport x86_64 1:4.4.4.3-4.fc22 updates 306 k libreoffice-pyuno x86_64 1:4.4.4.3-4.fc22 updates 516 k libreoffice-ure x86_64 1:4.4.4.3-4.fc22 updates 2.6 M libreoffice-writer x86_64 1:4.4.4.3-4.fc22 updates 4.2 M libreoffice-xsltfilter x86_64 1:4.4.4.3-4.fc22 updates 408 k libreport x86_64 2.6.1-1.fc22 updates-testing 459 k libreport-cli x86_64 2.6.1-1.fc22 updates-testing 56 k libreport-fedora x86_64 2.6.1-1.fc22 updates-testing 50 k libreport-filesystem x86_64 2.6.1-1.fc22 updates-testing 43 k libreport-gtk x86_64 2.6.1-1.fc22 updates-testing 108 k libreport-plugin-bugzilla x86_64 2.6.1-1.fc22 updates-testing 87 k libreport-plugin-kerneloops x86_64 2.6.1-1.fc22 updates-testing 54 k libreport-plugin-logger x86_64 2.6.1-1.fc22 updates-testing 59 k libreport-plugin-reportuploader x86_64 2.6.1-1.fc22 updates-testing 65 k libreport-plugin-ureport x86_64 2.6.1-1.fc22 updates-testing 62 k libreport-python x86_64 2.6.1-1.fc22 updates-testing 77 k libreport-python3 x86_64 2.6.1-1.fc22 updates-testing 78 k libreport-web x86_64 2.6.1-1.fc22 updates-testing 60 k libseccomp x86_64 2.2.3-0.fc22 updates-testing 55 k libsss_idmap x86_64 1.13.0-1.fc22 updates-testing 76 k libsss_nss_idmap x86_64 1.13.0-1.fc22 updates-testing 75 k libtirpc x86_64 0.3.2-2.0.fc22 updates-testing 100 k libunwind x86_64 1.1-10.fc22 updates-testing 64 k meld noarch 3.13.3-1.fc22 updates-testing 717 k openssl x86_64 1:1.0.1k-11.fc22 updates 496 k openssl-libs i686 1:1.0.1k-11.fc22 updates 944 k openssl-libs x86_64 1:1.0.1k-11.fc22 updates 941 k pam_pkcs11 x86_64 0.6.8-6.fc22 updates-testing 213 k pango i686 1.36.8-6.fc22 updates-testing 296 k pango x86_64 1.36.8-6.fc22 updates-testing 294 k pango-devel x86_64 1.36.8-6.fc22 updates-testing 327 k perl-HTTP-Message noarch 6.08-1.fc22 updates-testing 87 k php-cli x86_64 5.6.11-1.fc22 updates-testing 4.0 M php-common x86_64 5.6.11-1.fc22 updates-testing 1.1 M php-gd x86_64 5.6.11-1.fc22 updates-testing 96 k php-pdo x86_64 5.6.11-1.fc22 updates-testing 150 k php-process x86_64 5.6.11-1.fc22 updates-testing 86 k php-xml x86_64 5.6.11-1.fc22 updates-testing 257 k polkit x86_64 0.113-2.fc22 updates-testing 127 k polkit-libs x86_64 0.113-2.fc22 updates-testing 70 k python x86_64 2.7.10-4.fc22 updates-testing 93 k python-ipython-console noarch 2.4.1-6.fc22 updates-testing 1.5 M python-ipython-notebook noarch 2.4.1-6.fc22 updates-testing 874 k python-libs x86_64 2.7.10-4.fc22 updates-testing 5.8 M python-sssdconfig noarch 1.13.0-1.fc22 updates-testing 98 k python-tornado x86_64 3.2.2-2.fc22 updates-testing 628 k python3 x86_64 3.4.2-6.fc22 updates-testing 53 k python3-libs x86_64 3.4.2-6.fc22 updates-testing 6.6 M rpmlint noarch 1.7-1.fc22 updates 250 k satyr x86_64 0.19-1.fc22 updates-testing 105 k sg3_utils-libs x86_64 1.41-1.fc22 updates-testing 68 k tkinter x86_64 2.7.10-4.fc22 updates-testing 381 k unoconv noarch 0.7-1.fc22 updates-testing 58 k webkitgtk4 x86_64 2.8.4-2.fc22 updates-testing 20 M xorg-x11-drv-libinput x86_64 0.11.0-3.fc22 updates-testing 28 k Removing: atom x86_64 1.0.0-0.1.fc21 @System 198 M hamster-applet x86_64 2.32.1-3.fc17 @System 2.2 M kernel x86_64 4.0.5-300.fc22 @System 0 kernel-core x86_64 4.0.5-300.fc22 @System 41 M kernel-modules x86_64 4.0.5-300.fc22 @System 17 M kernel-modules-extra x86_64 4.0.5-300.fc22 @System 2.1 M skype i586 4.3.0.37-fc16 @System 42 M Transaction Summary ================================================================================ Install 4 Packages Upgrade 126 Packages Remove 7 Packages Total download size: 307 M Note that atom, hamster-applet and skype are marked for removal. However, look what happens when I exclude kernel: $ dnf distro-sync --exclude kernel* Last metadata expiration check performed 0:20:21 ago on Fri Jul 17 13:09:21 2015. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Upgrading: NetworkManager x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 2.0 M NetworkManager-adsl x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 111 k NetworkManager-bluetooth x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 134 k NetworkManager-config-connectivity-fedora x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 101 k NetworkManager-glib x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 366 k NetworkManager-libnm x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 476 k NetworkManager-wifi x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 141 k NetworkManager-wwan x86_64 1:1.0.4-0.4.git20150713.38bf2cb0.fc22 updates-testing 134 k abrt x86_64 2.6.1-1.fc22 updates-testing 517 k abrt-addon-ccpp x86_64 2.6.1-1.fc22 updates-testing 187 k abrt-addon-coredump-helper x86_64 2.6.1-1.fc22 updates-testing 105 k abrt-addon-kerneloops x86_64 2.6.1-1.fc22 updates-testing 122 k abrt-addon-pstoreoops x86_64 2.6.1-1.fc22 updates-testing 100 k abrt-addon-python x86_64 2.6.1-1.fc22 updates-testing 101 k abrt-addon-python3 x86_64 2.6.1-1.fc22 updates-testing 99 k abrt-addon-vmcore x86_64 2.6.1-1.fc22 updates-testing 110 k abrt-addon-xorg x86_64 2.6.1-1.fc22 updates-testing 101 k abrt-cli x86_64 2.6.1-1.fc22 updates-testing 91 k abrt-dbus x86_64 2.6.1-1.fc22 updates-testing 126 k abrt-desktop x86_64 2.6.1-1.fc22 updates-testing 91 k abrt-gui x86_64 2.6.1-1.fc22 updates-testing 188 k abrt-gui-libs x86_64 2.6.1-1.fc22 updates-testing 101 k abrt-libs x86_64 2.6.1-1.fc22 updates-testing 118 k abrt-plugin-bodhi x86_64 2.6.1-1.fc22 updates-testing 100 k abrt-python x86_64 2.6.1-1.fc22 updates-testing 114 k abrt-python3 x86_64 2.6.1-1.fc22 updates-testing 115 k abrt-retrace-client x86_64 2.6.1-1.fc22 updates-testing 127 k abrt-tui x86_64 2.6.1-1.fc22 updates-testing 103 k autocorr-cs noarch 1:4.4.4.3-4.fc22 updates 161 k autocorr-en noarch 1:4.4.4.3-4.fc22 updates 175 k bind-libs x86_64 32:9.10.2-3.P2.fc22 updates-testing 149 k bind-libs-lite x86_64 32:9.10.2-3.P2.fc22 updates-testing 1.0 M bind-license noarch 32:9.10.2-3.P2.fc22 updates-testing 87 k bind-utils x86_64 32:9.10.2-3.P2.fc22 updates-testing 400 k devscripts-minimal x86_64 2.15.5-6.fc22 updates-testing 38 k environment-modules x86_64 3.2.10-16.fc22 updates-testing 113 k evolution x86_64 3.16.4-1.fc22 updates-testing 8.6 M evolution-data-server x86_64 3.16.4-1.fc22 updates-testing 3.0 M firefox x86_64 39.0-8.fc22 updates 70 M glibc i686 2.21-7.fc22 updates-testing 4.2 M glibc x86_64 2.21-7.fc22 updates-testing 3.5 M glibc-common x86_64 2.21-7.fc22 updates-testing 11 M glibc-devel x86_64 2.21-7.fc22 updates-testing 903 k glibc-headers x86_64 2.21-7.fc22 updates-testing 494 k glusterfs x86_64 3.6.4-1.fc22 updates-testing 1.3 M glusterfs-api x86_64 3.6.4-1.fc22 updates-testing 73 k glusterfs-fuse x86_64 3.6.4-1.fc22 updates-testing 102 k glusterfs-libs x86_64 3.6.4-1.fc22 updates-testing 295 k gnome-abrt x86_64 1.2.0-3.fc22 updates-testing 235 k gnutls i686 3.3.16-1.fc22 updates-testing 616 k gnutls x86_64 3.3.16-1.fc22 updates-testing 627 k gnutls-dane x86_64 3.3.16-1.fc22 updates-testing 36 k gnutls-utils x86_64 3.3.16-1.fc22 updates-testing 238 k gzip x86_64 1.6-8.fc22 updates 155 k jwhois x86_64 4.0-41.fc22 updates-testing 119 k libgusb x86_64 0.2.6-1.fc22 updates-testing 43 k libidn i686 1.31-1.fc22 updates-testing 229 k libidn x86_64 1.31-1.fc22 updates-testing 228 k libinput x86_64 0.19.0-3.fc22 updates-testing 80 k libipa_hbac x86_64 1.13.0-1.fc22 updates-testing 71 k libreoffice-calc x86_64 1:4.4.4.3-4.fc22 updates 8.5 M libreoffice-core x86_64 1:4.4.4.3-4.fc22 updates 77 M libreoffice-draw x86_64 1:4.4.4.3-4.fc22 updates 677 k libreoffice-emailmerge x86_64 1:4.4.4.3-4.fc22 updates 80 k libreoffice-filters x86_64 1:4.4.4.3-4.fc22 updates 66 k libreoffice-graphicfilter x86_64 1:4.4.4.3-4.fc22 updates 445 k libreoffice-impress x86_64 1:4.4.4.3-4.fc22 updates 1.3 M libreoffice-langpack-cs x86_64 1:4.4.4.3-4.fc22 updates 6.7 M libreoffice-math x86_64 1:4.4.4.3-4.fc22 updates 1.0 M libreoffice-opensymbol-fonts noarch 1:4.4.4.3-4.fc22 updates 241 k libreoffice-pdfimport x86_64 1:4.4.4.3-4.fc22 updates 306 k libreoffice-pyuno x86_64 1:4.4.4.3-4.fc22 updates 516 k libreoffice-ure x86_64 1:4.4.4.3-4.fc22 updates 2.6 M libreoffice-writer x86_64 1:4.4.4.3-4.fc22 updates 4.2 M libreoffice-xsltfilter x86_64 1:4.4.4.3-4.fc22 updates 408 k libreport x86_64 2.6.1-1.fc22 updates-testing 459 k libreport-cli x86_64 2.6.1-1.fc22 updates-testing 56 k libreport-fedora x86_64 2.6.1-1.fc22 updates-testing 50 k libreport-filesystem x86_64 2.6.1-1.fc22 updates-testing 43 k libreport-gtk x86_64 2.6.1-1.fc22 updates-testing 108 k libreport-plugin-bugzilla x86_64 2.6.1-1.fc22 updates-testing 87 k libreport-plugin-kerneloops x86_64 2.6.1-1.fc22 updates-testing 54 k libreport-plugin-logger x86_64 2.6.1-1.fc22 updates-testing 59 k libreport-plugin-reportuploader x86_64 2.6.1-1.fc22 updates-testing 65 k libreport-plugin-ureport x86_64 2.6.1-1.fc22 updates-testing 62 k libreport-python x86_64 2.6.1-1.fc22 updates-testing 77 k libreport-python3 x86_64 2.6.1-1.fc22 updates-testing 78 k libreport-web x86_64 2.6.1-1.fc22 updates-testing 60 k libseccomp x86_64 2.2.3-0.fc22 updates-testing 55 k libsss_idmap x86_64 1.13.0-1.fc22 updates-testing 76 k libsss_nss_idmap x86_64 1.13.0-1.fc22 updates-testing 75 k libtirpc x86_64 0.3.2-2.0.fc22 updates-testing 100 k libunwind x86_64 1.1-10.fc22 updates-testing 64 k meld noarch 3.13.3-1.fc22 updates-testing 717 k openssl x86_64 1:1.0.1k-11.fc22 updates 496 k openssl-libs i686 1:1.0.1k-11.fc22 updates 944 k openssl-libs x86_64 1:1.0.1k-11.fc22 updates 941 k pam_pkcs11 x86_64 0.6.8-6.fc22 updates-testing 213 k pango i686 1.36.8-6.fc22 updates-testing 296 k pango x86_64 1.36.8-6.fc22 updates-testing 294 k pango-devel x86_64 1.36.8-6.fc22 updates-testing 327 k perl-HTTP-Message noarch 6.08-1.fc22 updates-testing 87 k php-cli x86_64 5.6.11-1.fc22 updates-testing 4.0 M php-common x86_64 5.6.11-1.fc22 updates-testing 1.1 M php-gd x86_64 5.6.11-1.fc22 updates-testing 96 k php-pdo x86_64 5.6.11-1.fc22 updates-testing 150 k php-process x86_64 5.6.11-1.fc22 updates-testing 86 k php-xml x86_64 5.6.11-1.fc22 updates-testing 257 k polkit x86_64 0.113-2.fc22 updates-testing 127 k polkit-libs x86_64 0.113-2.fc22 updates-testing 70 k python x86_64 2.7.10-4.fc22 updates-testing 93 k python-ipython-console noarch 2.4.1-6.fc22 updates-testing 1.5 M python-ipython-notebook noarch 2.4.1-6.fc22 updates-testing 874 k python-libs x86_64 2.7.10-4.fc22 updates-testing 5.8 M python-sssdconfig noarch 1.13.0-1.fc22 updates-testing 98 k python-tornado x86_64 3.2.2-2.fc22 updates-testing 628 k python3 x86_64 3.4.2-6.fc22 updates-testing 53 k python3-libs x86_64 3.4.2-6.fc22 updates-testing 6.6 M rpmlint noarch 1.7-1.fc22 updates 250 k satyr x86_64 0.19-1.fc22 updates-testing 105 k sg3_utils-libs x86_64 1.41-1.fc22 updates-testing 68 k tkinter x86_64 2.7.10-4.fc22 updates-testing 381 k unoconv noarch 0.7-1.fc22 updates-testing 58 k webkitgtk4 x86_64 2.8.4-2.fc22 updates-testing 20 M xorg-x11-drv-libinput x86_64 0.11.0-3.fc22 updates-testing 28 k Transaction Summary ================================================================================ Upgrade 125 Packages Total download size: 266 M Dnf no longer wants to remove them. Something is wrong in there. Version-Release number of selected component (if applicable): rpm-4.12.0.1-12.fc22.x86_64 libsolv-0.6.11-1.fc22.x86_64 librepo-1.7.16-1.fc22.x86_64 hawkey-0.5.7-1.fc22.x86_64 dnf-1.0.1-2.fc22.noarch How reproducible: sometimes, but once it happens, it is 100% reproducible (until I perform the operation, I guess update the kernel) Steps to Reproduce (not tested): 1. install some packages outside of system repos 2. run distro-sync when there is a kernel update, so that one of the existing kernel is to be removed
Created attachment 1053045 [details] verbose output of distro-sync
Created attachment 1053046 [details] debugdata from dnf
$ dnf list kernel* Last metadata expiration check performed 0:55:06 ago on Fri Jul 17 13:09:21 2015. Installed Packages kernel.x86_64 4.0.5-300.fc22 @System kernel.x86_64 4.0.6-300.fc22 @System kernel.x86_64 4.0.7-300.fc22 @System kernel-core.x86_64 4.0.5-300.fc22 @System kernel-core.x86_64 4.0.6-300.fc22 @System kernel-core.x86_64 4.0.7-300.fc22 @System kernel-headers.x86_64 4.0.7-300.fc22 @System kernel-modules.x86_64 4.0.5-300.fc22 @System kernel-modules.x86_64 4.0.6-300.fc22 @System kernel-modules.x86_64 4.0.7-300.fc22 @System kernel-modules-extra.x86_64 4.0.5-300.fc22 @System kernel-modules-extra.x86_64 4.0.6-300.fc22 @System kernel-modules-extra.x86_64 4.0.7-300.fc22 @System Available Packages kernel.x86_64 4.0.8-300.fc22 updates-testing kernel-core.x86_64 4.0.8-300.fc22 updates-testing kernel-debug.x86_64 4.0.8-300.fc22 updates-testing kernel-debug-core.x86_64 4.0.8-300.fc22 updates-testing kernel-debug-devel.x86_64 4.0.8-300.fc22 updates-testing kernel-debug-modules.x86_64 4.0.8-300.fc22 updates-testing kernel-debug-modules-extra.x86_64 4.0.8-300.fc22 updates-testing kernel-devel.x86_64 4.0.8-300.fc22 updates-testing kernel-headers.x86_64 4.0.8-300.fc22 updates-testing kernel-modules.x86_64 4.0.8-300.fc22 updates-testing kernel-modules-extra.x86_64 4.0.8-300.fc22 updates-testing kernel-rpm-macros.noarch 28-1.fc22 updates kernel-tools.x86_64 4.0.8-300.fc22 updates-testing kernel-tools-libs.i686 4.0.8-300.fc22 updates-testing kernel-tools-libs.x86_64 4.0.8-300.fc22 updates-testing kernel-tools-libs-devel.i686 4.0.8-300.fc22 updates-testing kernel-tools-libs-devel.x86_64 4.0.8-300.fc22 updates-testing kernelshark.x86_64 2.2.1-5.fc22 fedora
Created attachment 1053050 [details] distro-sync with --setopt=clean_requirements_on_remove=0 The same happens with --setopt=clean_requirements_on_remove=0.
Created attachment 1053060 [details] minimal debug data from dnf --debugsolver I tried to update everything except kernel, and the minimal case really seems to be orphan packages + kernel update: Last metadata expiration check performed 1:07:19 ago on Fri Jul 17 13:09:21 2015. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: kernel x86_64 4.0.8-300.fc22 updates-testing 67 k kernel-core x86_64 4.0.8-300.fc22 updates-testing 19 M kernel-modules x86_64 4.0.8-300.fc22 updates-testing 18 M kernel-modules-extra x86_64 4.0.8-300.fc22 updates-testing 2.2 M Upgrading: kernel-headers x86_64 4.0.8-300.fc22 updates-testing 996 k Removing: atom x86_64 1.0.0-0.1.fc21 @System 198 M hamster-applet x86_64 2.32.1-3.fc17 @System 2.2 M kernel x86_64 4.0.5-300.fc22 @System 0 kernel-core x86_64 4.0.5-300.fc22 @System 41 M kernel-modules x86_64 4.0.5-300.fc22 @System 17 M kernel-modules-extra x86_64 4.0.5-300.fc22 @System 2.1 M skype i586 4.3.0.37-fc16 @System 42 M Transaction Summary ================================================================================ Install 4 Packages Upgrade 1 Package Remove 7 Packages Total download size: 40 M Attaching new debug data, just for this minimal case.
The same case with `dnf update` is absolutely fine: $ sudo dnf update Last metadata expiration check performed 1:10:51 ago on Fri Jul 17 13:09:21 2015. Dependencies resolved. ================================================================================================================================== Package Arch Version Repository Size ================================================================================================================================== Installing: kernel x86_64 4.0.8-300.fc22 updates-testing 67 k kernel-core x86_64 4.0.8-300.fc22 updates-testing 19 M kernel-modules x86_64 4.0.8-300.fc22 updates-testing 18 M kernel-modules-extra x86_64 4.0.8-300.fc22 updates-testing 2.2 M Upgrading: kernel-headers x86_64 4.0.8-300.fc22 updates-testing 996 k Removing: kernel x86_64 4.0.5-300.fc22 @System 0 kernel-core x86_64 4.0.5-300.fc22 @System 41 M kernel-modules x86_64 4.0.5-300.fc22 @System 17 M kernel-modules-extra x86_64 4.0.5-300.fc22 @System 2.1 M Transaction Summary ================================================================================================================================== Install 4 Packages Upgrade 1 Package Remove 4 Packages Total download size: 40 M
I see exactly the same problem on a different machine as well. Once there is a kernel update, it wants to remove 'atom'. This does not seem to be a rare issue.
How does `dnf distro-sync -x <all orphaned pkgs>` work? Maybe we can add switch to distro-sync to preserve orphans.
(In reply to Jan Silhan from comment #8) > How does `dnf distro-sync -x <all orphaned pkgs>` work? That doesn't help. Only excluding kernel helps. > Maybe we can add > switch to distro-sync to preserve orphans. I don't follow. Distro-sync always did, and still does preserve orphans. The only bug is when kernel is in the set (and probably wants to remove an older one), in this case it regressed, and behaves like remove-or-distro-sync (which is available for repository-packages command). I suggest this could deserve a higher priority in the Devel Whiteboard. It is basically a scenario resulting in user data loss. Many people using updates-testing are used to running distro-sync instead of update, because it is a must in that case. If they don't read the installation summary properly every time, or have it run automatically, this will remove important packages from their system.
I want to ring the alarm bell when it's still time - this bug might be very problematic during system upgrade. Because fedup got converted into a dnf plugin, this bug now affects system upgrade as well, if it runs in distro-sync mode (which is not yet the default, but I'm trying to push to have it as the default [1]). Because there is always a kernel update during system upgrade, this is always going to affect system upgrade. And the result is that due to this bug, all packages not found in the FN+1 repository will be simply erased from the system. The user can't work around it, except for disabling distro-sync mode, which is problematic for other reasons (when upgrade path is not satisfied for critical packages, it will only half-upgrade your system and potentially break it completely). So, this means that all user third-party packages (without repos, or without functional FN+1 repos) will be missing from the upgraded system. I.e. skype gone, steam gone, dropbox gone, atom gone, etc. This seems to violate our upgrade criteria: " The upgraded system must include all packages that would be present on the system after a default installation from install media, plus any packages the user previously had (minus any obsolete content). " https://fedoraproject.org/wiki/Fedora_23_Beta_Release_Criteria#Upgrade_requirements Once dnf-plugin-system-upgrade switches to distro-sync mode, I'm going to propose this as a blocker. [1] https://github.com/rpm-software-management/dnf-plugin-system-upgrade/issues/10
Fair argument -> raising priority. With combination with bug 1259175 the system upgrades would be even funnier.
FESCo decided distro-sync will be the default upgrade behavior [1] and it will get implemented as part of bug 1263677. I'm therefore proposing this as a final blocker, due to reasons stated in comment 10. [1] https://fedorahosted.org/fesco/ticket/1481
Discussed at 2015-10-05 blocker review meeting: https://meetbot-raw.fedoraproject.org/fedora-blocker-review/2015-10-05/f23-blocker-review.2015-10-05-16.00.html . Accepted as a Final blocker, on the assumption that this will affect pretty much all dnf-system-upgrade runs once it's adjusted to default to distro-sync behaviour.
*** Bug 1253825 has been marked as a duplicate of this bug. ***
This bug was fixed in libsolv-0.6.14-1 which was build for F23 and F24 (we will add it to updates along with DNF). Do we need the build for F22 and F21 too?
(In reply to Jan Silhan from comment #15) > This bug was fixed in libsolv-0.6.14-1 which was build for F23 and F24 (we > will add it to updates along with DNF). Do we need the build for F22 and F21 > too? Does system-upgrade for F22->F23 use F22 libraries or F23 libraries during the offline upgrade? If F22 ones, we need to fix F22. Even if it used F23 libraries during the actual upgrade, system-upgrade still displays the upgrade summary (which packages are going to get upgraded and which packages are going to get skipped or removed) on a F22 system, so this summary would be incorrect and might unnecessarily scare the user (we would claim we're going to remove packages which we wouldn't afterwards). So even in this case, F22 fix would be appropriate. As for F21, I don't know what the official plans for system-upgrade are. If system-upgrade is intended to work only for F22 upwards (and people should use fedup to go F21->F22), we don't need F21 fixed. But since system-upgrade package is present in F21 updates-testing (still not pushed stable, though), I assume the opposite is the case, and in that case we need the same approach for F21 as we do for F22.
dnf-1.1.3-1.fc23 dnf-plugins-core-0.1.13-1.fc23 dnf-plugins-extras-0.0.11-1.fc23 hawkey-0.6.2-1.fc23 libsolv-0.6.14-2.fc23 has been submitted as an update to Fedora 23. https://bodhi.fedoraproject.org/updates/FEDORA-2015-a011ac001a
* It was fixed in libsolv-0.6.14-2. builds for f21+ has been made.
dnf-1.1.3-1.fc23, dnf-plugins-core-0.1.13-1.fc23, dnf-plugins-extras-0.0.11-1.fc23, hawkey-0.6.2-1.fc23, libsolv-0.6.14-2.fc23 has been pushed to the Fedora 23 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with $ su -c 'dnf --enablerepo=updates-testing update hawkey dnf-plugins-core dnf-plugins-extras dnf libsolv' You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2015-a011ac001a
I have tested this with F22, the problem seems to be fixed. Thanks.
dnf-1.1.3-1.fc23, dnf-plugins-core-0.1.13-1.fc23, dnf-plugins-extras-0.0.11-1.fc23, hawkey-0.6.2-1.fc23, libsolv-0.6.14-2.fc23 has been pushed to the Fedora 23 stable repository. If problems still persist, please make note of it in this bug report.
*** Bug 1259175 has been marked as a duplicate of this bug. ***