Please fill in any relevant information that applies to you: CentOS Version: CentOS 7 64bit Centmin Mod Version Installed: 123.09beta01 Code (Text): $ yum update --disableplugin=priorities --enablerepo=remi Loaded plugins: fastestmirror, versionlock Loading mirror speeds from cached hostfile * epel: my.fedora.ipserverone.com * nux-dextop: mirror.li.nux.ro * remi: mirrors.thzhost.com * rpmforge: kartolo.sby.datautama.net.id Resolving Dependencies --> Running transaction check ---> Package grub2-tools.x86_64 1:2.02-0.65.el7.centos.2 will be obsoleted ---> Package grub2-tools.x86_64 1:2.02-0.76.el7.centos will be obsoleting Removing grub2-tools.x86_64 1:2.02-0.65.el7.centos.2 - od due to obsoletes from installed 1:grub2-tools-extra-2.02-0.76.el7.centos.x86_64 --> Restarting Dependency Resolution with new changes. --> Running transaction check ---> Package grub2-tools.x86_64 1:2.02-0.65.el7.centos.2 will be obsoleted --> Processing Dependency: grub2-common = 1:2.02-0.65.el7.centos.2 for package: 1:grub2-tools-2.02-0.65.el7.centos.2.x86_64 --> Processing Dependency: grub2-tools-minimal = 1:2.02-0.65.el7.centos.2 for package: 1:grub2-tools-2.02-0.65.el7.centos.2.x86_64 --> Finished Dependency Resolution Error: Package: 1:grub2-tools-2.02-0.65.el7.centos.2.x86_64 (@updates) Requires: grub2-tools-minimal = 1:2.02-0.65.el7.centos.2 Installed: 1:grub2-tools-minimal-2.02-0.76.el7.centos.x86_64 (@base) grub2-tools-minimal = 1:2.02-0.76.el7.centos Error: Package: 1:grub2-tools-2.02-0.65.el7.centos.2.x86_64 (@updates) Requires: grub2-common = 1:2.02-0.65.el7.centos.2 Installed: 1:grub2-common-2.02-0.76.el7.centos.noarch (@base) grub2-common = 1:2.02-0.76.el7.centos You could try using --skip-broken to work around the problem ** Found 55 pre-existing rpmdb problem(s), 'yum check' output follows: ... (cropped possible irrelevant problems, mostly missing libglomp.so.1, though if there's a solution to that too, I'm all ears) 1:grub2-pc-2.02-0.76.el7.centos.x86_64 has missing requires of grub2-tools = ('1', '2.02', '0.76.el7.centos') 1:grub2-tools-2.02-0.65.el7.centos.2.x86_64 has missing requires of grub2-common = ('1', '2.02', '0.65.el7.centos.2') 1:grub2-tools-2.02-0.65.el7.centos.2.x86_64 has missing requires of grub2-tools-minimal = ('1', '2.02', '0.65.el7.centos.2') 1:grub2-tools-extra-2.02-0.76.el7.centos.x86_64 has missing requires of grub2-tools = ('1', '2.02', '0.76.el7.centos') ... Any idea how to fix this? My system is mostly being updated by yum-cron, but one day instead of a clean upgrade, I received an email notification about upgrade failing from these packages in particular. Any help would be very much appreciated.
that's tricky one what do you get when you run Code (Text): yum update and Code (Text): rpm -qa 'grub2' and Code (Text): rpm -qa 'grub2*'
I think pretty much the same thing with just bare "yum update": Code (Text): $ yum update Loaded plugins: fastestmirror, priorities, versionlock Loading mirror speeds from cached hostfile * epel: my.fedora.ipserverone.com * nux-dextop: mirror.li.nux.ro * rpmforge: kartolo.sby.datautama.net.id 860 packages excluded due to repository priority protections Resolving Dependencies --> Running transaction check ---> Package grub2-tools.x86_64 1:2.02-0.65.el7.centos.2 will be obsoleted ---> Package grub2-tools.x86_64 1:2.02-0.76.el7.centos will be obsoleting Removing grub2-tools.x86_64 1:2.02-0.65.el7.centos.2 - od due to obsoletes from installed 1:grub2-tools-extra-2.02-0.76.el7.centos.x86_64 --> Restarting Dependency Resolution with new changes. --> Running transaction check ---> Package grub2-tools.x86_64 1:2.02-0.65.el7.centos.2 will be obsoleted --> Processing Dependency: grub2-common = 1:2.02-0.65.el7.centos.2 for package: 1:grub2-tools-2.02-0.65.el7.centos.2.x86_64 --> Processing Dependency: grub2-tools-minimal = 1:2.02-0.65.el7.centos.2 for package: 1:grub2-tools-2.02-0.65.el7.centos.2.x86_64 --> Finished Dependency Resolution Error: Package: 1:grub2-tools-2.02-0.65.el7.centos.2.x86_64 (@updates) Requires: grub2-tools-minimal = 1:2.02-0.65.el7.centos.2 Installed: 1:grub2-tools-minimal-2.02-0.76.el7.centos.x86_64 (@base) grub2-tools-minimal = 1:2.02-0.76.el7.centos Error: Package: 1:grub2-tools-2.02-0.65.el7.centos.2.x86_64 (@updates) Requires: grub2-common = 1:2.02-0.65.el7.centos.2 Installed: 1:grub2-common-2.02-0.76.el7.centos.noarch (@base) grub2-common = 1:2.02-0.76.el7.centos You could try using --skip-broken to work around the problem ** Found 55 pre-existing rpmdb problem(s), 'yum check' output follows: ... (cropped) 1:grub2-pc-2.02-0.76.el7.centos.x86_64 has missing requires of grub2-tools = ('1', '2.02', '0.76.el7.centos') 1:grub2-tools-2.02-0.65.el7.centos.2.x86_64 has missing requires of grub2-common = ('1', '2.02', '0.65.el7.centos.2') 1:grub2-tools-2.02-0.65.el7.centos.2.x86_64 has missing requires of grub2-tools-minimal = ('1', '2.02', '0.65.el7.centos.2') 1:grub2-tools-extra-2.02-0.76.el7.centos.x86_64 has missing requires of grub2-tools = ('1', '2.02', '0.76.el7.centos') ... Code (Text): $ rpm -qa 'grub2' grub2-2.02-0.76.el7.centos.x86_64 Code (Text): rpm -qa 'grub2*' grub2-pc-modules-2.02-0.76.el7.centos.noarch grub2-tools-extra-2.02-0.76.el7.centos.x86_64 grub2-tools-2.02-0.65.el7.centos.2.x86_64 grub2-common-2.02-0.76.el7.centos.noarch grub2-2.02-0.76.el7.centos.x86_64 grub2-tools-minimal-2.02-0.76.el7.centos.x86_64 grub2-pc-2.02-0.76.el7.centos.x86_6 So yeah. It seems the dependencies have higher version than the package that needed those dependencies, somehow. But upgrading the said package would need older dependencies. Truly a mystery.
try backing up rpm/yum directories and removing the newer packages yum database only and leave filesystem installed intact and re-try yum update but as this can potentially break things, if you web host has backup snapshot at VPS level feature, use it to get a backup snapshot first i.e. linode, digitalocean, upcloud etc. Once you have VPS level backup, try the steps Code (Text): cp -a /var/lib/rpm /var/lib/rpm.backup cp -a /var/lib/yum /var/lib/yum.backup rpm -e --nodeps --justdb grub2-pc-2.02-0.76.el7.centos.x86_64 rpm -e --nodeps --justdb grub2-pc-modules-2.02-0.76.el7.centos.noarch rpm -e --nodeps --justdb grub2-tools-extra-2.02-0.76.el7.centos.x86_64 rpm -e --nodeps --justdb grub2-common-2.02-0.76.el7.centos.noarch rpm -e --nodeps --justdb grub2-tools-minimal-2.02-0.76.el7.centos.x86_64 #rpm -e --nodeps --justdb grub2-2.02-0.76.el7.centos.x86_64 yum update edit grub2-2.02-0.76.el7.centos.x86_64 might not need removing so commented it out
Hmm, I suppose it went well? Code (Text): $ yum update Loaded plugins: fastestmirror, priorities, versionlock Loading mirror speeds from cached hostfile * epel: my.fedora.ipserverone.com * nux-dextop: mirror.li.nux.ro * rpmforge: kartolo.sby.datautama.net.id 860 packages excluded due to repository priority protections Resolving Dependencies --> Running transaction check ---> Package grub2-tools.x86_64 1:2.02-0.65.el7.centos.2 will be obsoleted ---> Package grub2-tools.x86_64 1:2.02-0.76.el7.centos will be obsoleting --> Processing Dependency: grub2-common = 1:2.02-0.76.el7.centos for package: 1:grub2-tools-2.02-0.76.el7.centos.x86_64 ---> Package grub2-tools-extra.x86_64 1:2.02-0.76.el7.centos will be obsoleting ---> Package grub2-tools-minimal.x86_64 1:2.02-0.76.el7.centos will be obsoleting --> Running transaction check ---> Package grub2-common.noarch 1:2.02-0.76.el7.centos will be installed --> Finished Dependency Resolution Dependencies Resolved ============================================================================================================= Package Arch Version Repository Size ============================================================================================================= Installing: grub2-tools x86_64 1:2.02-0.76.el7.centos base 1.8 M replacing grub2-tools.x86_64 1:2.02-0.65.el7.centos.2 grub2-tools-extra x86_64 1:2.02-0.76.el7.centos base 995 k replacing grub2-tools.x86_64 1:2.02-0.65.el7.centos.2 grub2-tools-minimal x86_64 1:2.02-0.76.el7.centos base 172 k replacing grub2-tools.x86_64 1:2.02-0.65.el7.centos.2 Installing for dependencies: grub2-common noarch 1:2.02-0.76.el7.centos base 728 k Transaction Summary ============================================================================================================= Install 3 Packages (+1 Dependent package) Total download size: 3.6 M Is this ok [y/d/N]: y Downloading packages: (1/4): grub2-common-2.02-0.76.el7.centos.noarch.rpm | 728 kB 00:00:01 (2/4): grub2-tools-2.02-0.76.el7.centos.x86_64.rpm | 1.8 MB 00:00:02 (3/4): grub2-tools-minimal-2.02-0.76.el7.centos.x86_64.rpm | 172 kB 00:00:00 (4/4): grub2-tools-extra-2.02-0.76.el7.centos.x86_64.rpm | 995 kB 00:00:00 ------------------------------------------------------------------------------------------------------------- Total 1.5 MB/s | 3.6 MB 00:00:02 Running transaction check Running transaction test Transaction test succeeded Running transaction Warning: RPMDB altered outside of yum. ** Found 51 pre-existing rpmdb problem(s), 'yum check' output follows: ... (cropped) ... Installing : 1:grub2-common-2.02-0.76.el7.centos.noarch 1/5 Installing : 1:grub2-tools-minimal-2.02-0.76.el7.centos.x86_64 2/5 Installing : 1:grub2-tools-2.02-0.76.el7.centos.x86_64 3/5 Installing : 1:grub2-tools-extra-2.02-0.76.el7.centos.x86_64 4/5 Cleanup : 1:grub2-tools-2.02-0.65.el7.centos.2.x86_64 5/5 Verifying : 1:grub2-tools-minimal-2.02-0.76.el7.centos.x86_64 1/5 Verifying : 1:grub2-tools-2.02-0.76.el7.centos.x86_64 2/5 Verifying : 1:grub2-tools-extra-2.02-0.76.el7.centos.x86_64 3/5 Verifying : 1:grub2-common-2.02-0.76.el7.centos.noarch 4/5 Verifying : 1:grub2-tools-2.02-0.65.el7.centos.2.x86_64 5/5 Installed: grub2-tools.x86_64 1:2.02-0.76.el7.centos grub2-tools-extra.x86_64 1:2.02-0.76.el7.centos grub2-tools-minimal.x86_64 1:2.02-0.76.el7.centos Dependency Installed: grub2-common.noarch 1:2.02-0.76.el7.centos Replaced: grub2-tools.x86_64 1:2.02-0.65.el7.centos.2 Complete! Turns out VPS level backup isn't available for mine (OVH SG), not even as a purchasable extra (heck, it doesn't even have extra storage, so much regret). Anyways, I tried doing "yum update" again afterwards and there were no errors and no packages marked as update, so I think it's working well. Thank you very much! By the way, do I have to concern myself with all these RPMDB problems relating to missing libgomp.so.1? I tried to google around but couldn't really find anything relevant. ImageMagick was one of the packages with the missing libgomp.so.1.
Whoops, I didn't do this one. Literally did all the commands you listed as-is. But it worked so I guess it was fine?
Oh, lookie Code (Text): $ rpm -qa 'grub2*' grub2-tools-extra-2.02-0.76.el7.centos.x86_64 grub2-common-2.02-0.76.el7.centos.noarch grub2-tools-minimal-2.02-0.76.el7.centos.x86_64 grub2-tools-2.02-0.76.el7.centos.x86_64 As opposed to one time I ran it before, 3 packages went missing (especially to be concerned with is "grub2", I suppose). Should I be concerned? Is it better if I just install them manually?
some yum package builds don't cleaning install/remove/update stuff so it doesn't happen though i haven't seen that one yeah guess it worked you can confirm which versions installed via command Code (Text): rpm -qa 'grub2*' and compare with yes install them again Code (Text): yum install grub2 grub2-pc grub2-pc-modules edited instructions at Yum update error for future folks as grub2 might not need removing
Alright, installation went smoothly for the said 3 packages, and I can confirm they're all the same version through rpm -qa 'grub2*'. Phew finally. I've been having this issue for at least a week by now. Tried to google around for solution but I always ended up giving up. Once again many thanks!
Geez, I wonder what was on my mind back then. I mean, it was very straightforward, I just had to install libgomp package. Anyways, no more RPMDB problems on my end. It was just some missing dependencies that I could all install manually with yum. Not sure what caused them to be missing in the first place, but it's all good now.