Requesting Suggestions: System broken after 7.6 Update

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tonybKDE
Posts: 1
Joined: 2018/12/06 01:52:48

Requesting Suggestions: System broken after 7.6 Update

Post by tonybKDE » 2018/12/08 16:24:46

This is a long-ish post asking for help fixing issues that occurred with the CentOS 7.6 (1810) update.
Apologies for the length but I’m trying to give enough information to allow someone to give me some suggestions for what to do next.

I made some errors in updating a CentOS machine to 7.6 and as a result it’s now is very marginally functional. It’s an older Lenovo D30 workstation, very powerful with lots of memory and CPU but with a vintage 2012 NVidia Quadro 2000 card. I am running the NVidia proprietary driver. Within the last three months or so support for my card has lapsed and YUM’s nvidia plug-in has correctly stopped updating the driver and I am still running the 390 legacy version.

My errors were (I think):
  • I was running KDE at the time ofthe upgrade
    I was running NVidia at the time of the upgrade
    I ignored some problems with xorg* packages and excluded them from the update
    I ignored some issues with the centos-sclo repo and excluded it from the update
As best I can reconstruct from my yum history here is the command I ran:

Code: Select all

[tt]Command Line   : update --exclude=filesystem,xorg* --disablerepo=centos-sclo-sclo[/tt]
900+ packages were updated and several, including some GNOME packages, were obsoleted. The only unusual messages I recorded were related to configuration of the “infinality” font package.

Symptoms are
GNOME will no longer start. KDE, xfce, and IceWM will start.

The NVidia driver still functions but nvidia-settings configuration GUI doesn’t work

Code: Select all

[tt]ERROR: /lib64/libcairo.so.2: undefined symbol: FT_Get_Var_Design_Coordinates
       /lib64/libcairo.so.2: undefined symbol: FT_Get_Var_Design_Coordinates
       /lib64/libcairo.so.2: undefined symbol: FT_Get_Var_Design_Coordinates
       /lib64/libcairo.so.2: undefined symbol: FT_Get_Var_Design_Coordinates


ERROR: A problem occured when loading the GUI library. Please check your installation and library path. You may need to specify this library when
       calling nvidia-settings. Please run `nvidia-settings --help` for usage information[/tt].

At least one program, the shutter screensaver, doesn’t work

Code: Select all

[tt]$ shutter
WARNING: Gtk2::AppIndicator is missing --> there will be no icon showing up in the status bar when running Unity!

Fontconfig error: failed reading config file
Fontconfig error: Cannot load config file "infinality/conf.d"


Fontconfig error: Cannot load config file "infinality/conf.d"                                                                                          
GdkPixbuf-LOG **: gdk_pixbuf_from_pixdata() called on: at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.          
GdkPixbuf-LOG **:       Encoding raw at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.                            
GdkPixbuf-LOG **:       Dimensions: 16 x 16 at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.
GdkPixbuf-LOG **:       Rowstride: 64, Length: 1048 at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.
GdkPixbuf-LOG **:       Copy pixels == false at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.
GdkPixbuf-LOG **: gdk_pixbuf_from_pixdata() called on: at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.
GdkPixbuf-LOG **:       Encoding raw at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.
GdkPixbuf-LOG **:       Dimensions: 16 x 16 at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.
GdkPixbuf-LOG **:       Rowstride: 64, Length: 1048 at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.
GdkPixbuf-LOG **:       Copy pixels == false at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.[/tt]
The nedit editor appears to be affected by the infinality font issue. It starts from the command line and runs, but returns the following to the console:

Code: Select all

[tt]Fontconfig error: failed reading config file
Fontconfig error: Cannot load config file "infinality/conf.d"[/tt]
The xorg issues that caused me to exclude the updates persist. Several xorg packages show up in a yum check-update, but trying to actually update them produces the following:

Code: Select all

[tt]sudo yum update xorg*
Loaded plugins: fastestmirror, langpacks, nvidia
Loading mirror speeds from cached hostfile
 * base: distro.ibiblio.org
 * elrepo: dfw.mirror.rackspace.com
 * elrepo-extras: dfw.mirror.rackspace.com
 * elrepo-kernel: dfw.mirror.rackspace.com
 * epel: archive.linux.duke.edu
 * epel-testing: archive.linux.duke.edu
 * extras: mirror.atlanticmetro.net
 * nux-dextop: li.nux.ro
 * updates: centos.mirror.lstn.net
[nvidia]: excluding kmod-nvidia-410.66-1.el7_5.elrepo.x86_64
[nvidia]: excluding kmod-nvidia-410.73-1.el7_5.elrepo.x86_64
[nvidia]: excluding kmod-nvidia-410.73-2.el7_6.elrepo.x86_64
[nvidia]: excluding kmod-nvidia-410.78-1.el7_6.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-410.66-1.el7_5.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-410.73-1.el7_5.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-410.78-1.el7_6.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-410.78-2.el7_6.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-32bit-410.66-1.el7_5.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-32bit-410.73-1.el7_5.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-32bit-410.78-1.el7_6.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-libs-410.78-2.el7_6.elrepo.i686
[nvidia]: excluding nvidia-x11-drv-libs-410.78-2.el7_6.elrepo.x86_64
Resolving Dependencies
--> Running transaction check
---> Package xorg-x11-drv-ati.x86_64 0:7.10.0-1.el7 will be updated
---> Package xorg-x11-drv-ati.x86_64 0:18.0.1-1.el7 will be an update
---> Package xorg-x11-drv-fbdev.x86_64 0:0.4.3-25.el7 will be updated
---> Package xorg-x11-drv-fbdev.x86_64 0:0.5.0-1.el7 will be an update
---> Package xorg-x11-drv-intel.x86_64 0:2.99.917-27.20160929.el7 will be updated
---> Package xorg-x11-drv-intel.x86_64 0:2.99.917-28.20180530.el7 will be an update
---> Package xorg-x11-drv-nouveau.x86_64 1:1.0.13-3.el7 will be updated
---> Package xorg-x11-drv-nouveau.x86_64 1:1.0.15-1.el7 will be an update
---> Package xorg-x11-drv-qxl.x86_64 0:0.1.5-3.el7 will be updated
---> Package xorg-x11-drv-qxl.x86_64 0:0.1.5-4.el7.1 will be an update
---> Package xorg-x11-drv-v4l.x86_64 0:0.2.0-47.el7 will be updated
---> Package xorg-x11-drv-v4l.x86_64 0:0.2.0-49.el7 will be an update
---> Package xorg-x11-drv-vesa.x86_64 0:2.3.2-25.1.el7 will be updated
---> Package xorg-x11-drv-vesa.x86_64 0:2.4.0-1.el7 will be an update
---> Package xorg-x11-drv-vmware.x86_64 0:13.2.1-1.el7 will be updated
---> Package xorg-x11-drv-vmware.x86_64 0:13.2.1-1.el7.1 will be an update
---> Package xorg-x11-server-Xorg.x86_64 0:1.19.5-5.1.el7_5.0.1 will be updated
--> Processing Dependency: xserver-abi(videodrv-23) >= 0 for package: xorg-x11-drv-dummy-0.3.8-1.xpra1.el7_4.x86_64
---> Package xorg-x11-server-Xorg.x86_64 0:1.20.1-5.1.el7 will be an update
--> Finished Dependency Resolution
Error: Package: xorg-x11-drv-dummy-0.3.8-1.xpra1.el7_4.x86_64 (@el7-local)
           Requires: xserver-abi(videodrv-23) >= 0
           Removing: xorg-x11-server-Xorg-1.19.5-5.1.el7_5.0.1.x86_64 (@updates)
               xserver-abi(videodrv-23) = 0
           Updated By: xorg-x11-server-Xorg-1.20.1-5.1.el7.x86_64 (c7-updates)
              ~xserver-abi(videodrv-24) = 0
 You could try using --skip-broken to work around the problem
 You could try running: rpm -Va --nofiles --nodigest[/tt]
If I could do so I would back out this entire update and start over. But with the updates to the kernel, the various kernel modules, and the version change to 7.6 (resulting in back-level versions of many packages being no longer available) I don’t think this is an option.

What’s the best way to approach this problem?

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TrevorH
Forum Moderator
Posts: 24052
Joined: 2009/09/24 10:40:56
Location: Brighton, UK

Re: Requesting Suggestions: System broken after 7.6 Update

Post by TrevorH » 2018/12/08 18:13:12

FT_Get_Var_Design_Coordinates
Run qpm -qa \*infinality\* and see what packages match that. If those are from the nux-dextop repo then I think you either have to ask him to update those packages (or maybe there are rebuilt versions already in his -testing repo?) or remove them as they're not compatible with the 7.6 version of freetype. That will also fix half the other problems in your post.

I suspect you need newer kmod-nvidia packages but since your cards have been retired, you probably need to switch from the main kmod-nvidia packages to one of the legacy ones, most likely kmod-nvidia390*. That should also let you update the xorg packages too.
CentOS 5 died in March 2017 - migrate NOW!
Full time Geek, part time moderator. Use the FAQ Luke

desertcat
Posts: 479
Joined: 2014/08/07 02:17:29
Location: Tucson, AZ

Re: Requesting Suggestions: System broken after 7.6 Update

Post by desertcat » 2018/12/09 10:49:17

tonybKDE wrote:
2018/12/08 16:24:46
This is a long-ish post asking for help fixing issues that occurred with the CentOS 7.6 (1810) update.
Apologies for the length but I’m trying to give enough information to allow someone to give me some suggestions for what to do next.

I made some errors in updating a CentOS machine to 7.6 and as a result it’s now is very marginally functional. It’s an older Lenovo D30 workstation, very powerful with lots of memory and CPU but with a vintage 2012 NVidia Quadro 2000 card. I am running the NVidia proprietary driver. Within the last three months or so support for my card has lapsed and YUM’s nvidia plug-in has correctly stopped updating the driver and I am still running the 390 legacy version.

My errors were (I think):
  • I was running KDE at the time ofthe upgrade
    I was running NVidia at the time of the upgrade
    I ignored some problems with xorg* packages and excluded them from the update
    I ignored some issues with the centos-sclo repo and excluded it from the update
As best I can reconstruct from my yum history here is the command I ran:

Code: Select all

[tt]Command Line   : update --exclude=filesystem,xorg* --disablerepo=centos-sclo-sclo[/tt]
900+ packages were updated and several, including some GNOME packages, were obsoleted. The only unusual messages I recorded were related to configuration of the “infinality” font package.

Symptoms are
GNOME will no longer start. KDE, xfce, and IceWM will start.

The NVidia driver still functions but nvidia-settings configuration GUI doesn’t work

Code: Select all

[tt]ERROR: /lib64/libcairo.so.2: undefined symbol: FT_Get_Var_Design_Coordinates
       /lib64/libcairo.so.2: undefined symbol: FT_Get_Var_Design_Coordinates
       /lib64/libcairo.so.2: undefined symbol: FT_Get_Var_Design_Coordinates
       /lib64/libcairo.so.2: undefined symbol: FT_Get_Var_Design_Coordinates


ERROR: A problem occured when loading the GUI library. Please check your installation and library path. You may need to specify this library when
       calling nvidia-settings. Please run `nvidia-settings --help` for usage information[/tt].

At least one program, the shutter screensaver, doesn’t work

Code: Select all

[tt]$ shutter
WARNING: Gtk2::AppIndicator is missing --> there will be no icon showing up in the status bar when running Unity!

Fontconfig error: failed reading config file
Fontconfig error: Cannot load config file "infinality/conf.d"


Fontconfig error: Cannot load config file "infinality/conf.d"                                                                                          
GdkPixbuf-LOG **: gdk_pixbuf_from_pixdata() called on: at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.          
GdkPixbuf-LOG **:       Encoding raw at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.                            
GdkPixbuf-LOG **:       Dimensions: 16 x 16 at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.
GdkPixbuf-LOG **:       Rowstride: 64, Length: 1048 at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.
GdkPixbuf-LOG **:       Copy pixels == false at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.
GdkPixbuf-LOG **: gdk_pixbuf_from_pixdata() called on: at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.
GdkPixbuf-LOG **:       Encoding raw at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.
GdkPixbuf-LOG **:       Dimensions: 16 x 16 at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.
GdkPixbuf-LOG **:       Rowstride: 64, Length: 1048 at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.
GdkPixbuf-LOG **:       Copy pixels == false at /usr/share/perl5/vendor_perl/Shutter/App/SimpleDialogs.pm line 254, <DATA> line 19.[/tt]
The nedit editor appears to be affected by the infinality font issue. It starts from the command line and runs, but returns the following to the console:

Code: Select all

[tt]Fontconfig error: failed reading config file
Fontconfig error: Cannot load config file "infinality/conf.d"[/tt]
The xorg issues that caused me to exclude the updates persist. Several xorg packages show up in a yum check-update, but trying to actually update them produces the following:

Code: Select all

[tt]sudo yum update xorg*
Loaded plugins: fastestmirror, langpacks, nvidia
Loading mirror speeds from cached hostfile
 * base: distro.ibiblio.org
 * elrepo: dfw.mirror.rackspace.com
 * elrepo-extras: dfw.mirror.rackspace.com
 * elrepo-kernel: dfw.mirror.rackspace.com
 * epel: archive.linux.duke.edu
 * epel-testing: archive.linux.duke.edu
 * extras: mirror.atlanticmetro.net
 * nux-dextop: li.nux.ro
 * updates: centos.mirror.lstn.net
[nvidia]: excluding kmod-nvidia-410.66-1.el7_5.elrepo.x86_64
[nvidia]: excluding kmod-nvidia-410.73-1.el7_5.elrepo.x86_64
[nvidia]: excluding kmod-nvidia-410.73-2.el7_6.elrepo.x86_64
[nvidia]: excluding kmod-nvidia-410.78-1.el7_6.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-410.66-1.el7_5.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-410.73-1.el7_5.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-410.78-1.el7_6.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-410.78-2.el7_6.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-32bit-410.66-1.el7_5.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-32bit-410.73-1.el7_5.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-32bit-410.78-1.el7_6.elrepo.x86_64
[nvidia]: excluding nvidia-x11-drv-libs-410.78-2.el7_6.elrepo.i686
[nvidia]: excluding nvidia-x11-drv-libs-410.78-2.el7_6.elrepo.x86_64
Resolving Dependencies
--> Running transaction check
---> Package xorg-x11-drv-ati.x86_64 0:7.10.0-1.el7 will be updated
---> Package xorg-x11-drv-ati.x86_64 0:18.0.1-1.el7 will be an update
---> Package xorg-x11-drv-fbdev.x86_64 0:0.4.3-25.el7 will be updated
---> Package xorg-x11-drv-fbdev.x86_64 0:0.5.0-1.el7 will be an update
---> Package xorg-x11-drv-intel.x86_64 0:2.99.917-27.20160929.el7 will be updated
---> Package xorg-x11-drv-intel.x86_64 0:2.99.917-28.20180530.el7 will be an update
---> Package xorg-x11-drv-nouveau.x86_64 1:1.0.13-3.el7 will be updated
---> Package xorg-x11-drv-nouveau.x86_64 1:1.0.15-1.el7 will be an update
---> Package xorg-x11-drv-qxl.x86_64 0:0.1.5-3.el7 will be updated
---> Package xorg-x11-drv-qxl.x86_64 0:0.1.5-4.el7.1 will be an update
---> Package xorg-x11-drv-v4l.x86_64 0:0.2.0-47.el7 will be updated
---> Package xorg-x11-drv-v4l.x86_64 0:0.2.0-49.el7 will be an update
---> Package xorg-x11-drv-vesa.x86_64 0:2.3.2-25.1.el7 will be updated
---> Package xorg-x11-drv-vesa.x86_64 0:2.4.0-1.el7 will be an update
---> Package xorg-x11-drv-vmware.x86_64 0:13.2.1-1.el7 will be updated
---> Package xorg-x11-drv-vmware.x86_64 0:13.2.1-1.el7.1 will be an update
---> Package xorg-x11-server-Xorg.x86_64 0:1.19.5-5.1.el7_5.0.1 will be updated
--> Processing Dependency: xserver-abi(videodrv-23) >= 0 for package: xorg-x11-drv-dummy-0.3.8-1.xpra1.el7_4.x86_64
---> Package xorg-x11-server-Xorg.x86_64 0:1.20.1-5.1.el7 will be an update
--> Finished Dependency Resolution
Error: Package: xorg-x11-drv-dummy-0.3.8-1.xpra1.el7_4.x86_64 (@el7-local)
           Requires: xserver-abi(videodrv-23) >= 0
           Removing: xorg-x11-server-Xorg-1.19.5-5.1.el7_5.0.1.x86_64 (@updates)
               xserver-abi(videodrv-23) = 0
           Updated By: xorg-x11-server-Xorg-1.20.1-5.1.el7.x86_64 (c7-updates)
              ~xserver-abi(videodrv-24) = 0
 You could try using --skip-broken to work around the problem
 You could try running: rpm -Va --nofiles --nodigest[/tt]
If I could do so I would back out this entire update and start over. But with the updates to the kernel, the various kernel modules, and the version change to 7.6 (resulting in back-level versions of many packages being no longer available) I don’t think this is an option.

What’s the best way to approach this problem?
OK is this too dumb a time to ask if you have BACKED UP YOUR DRIVE?!? Both 7.5. and 7.6 have not been too kind to me, but I had BACKED UP MY Drive and even though I toasted my machine I was able to restore 95+% (or at least as far back as 10 Nov) pus I have specific directories that are were less than a week old.

IF you have a BACKUP simply roll the machine back. Simple as that.

OK what IF you DID NOT BACKUP your machine? The odds go way up that you are partially if not totally hosed. IF you still have access to a konsole try doing this: as su run the command yum group list. That will tell you what groups are available to you. From there run yum group install "[name of group]" One of the group that should be listed is GNOME Desktop. If so run yum group install "GNOME Desktop". If you are lucky it might update all the Packages and Dependencies needed by GNOME. If so login as either GNOME or GNOME Classic and be on your merry way.

OK what if you get some message saying in effect that all packages are the most most recent. "Nothing to do."

Here is where you need to make a decision -- run as KDE (or MATE, Xfce, etc.). You might as well go for broke and simply run yum update. But before you can do that you need to deal with that ERROR message:

Error: Package: xorg-x11-drv-dummy-0.3.8-1.xpra1.el7_4.x86_64 (@el7-local). It *may* be simply safe to remove this package as it refers to CentOS 7.4 [ xorg-x11-drv-dummy-0.3.8-1.xpra1.el7_4.x86_64, then unless there is some mad reason simply run yum update and remove the "--exclude=..." options. With LUCK it will then go out and fix all the broken parts, including GNOME.

If after this you are probably 95% hosed. First BACKUP your /home directory. Second download a copy of the CentOS-7.6-1810 DVD.iso burn it to a CD, check the checksum to make sure you got a clean download and burn. Then simply do a fresh re-install. Giant PITA. Just did it myself after I sincerely toasted my test machine. I toasted my workstation TWICE, first by overconfidence and missed something, the second time on purpose to eliminate any source of conflict. BUT... I HAD A BACKUP which I rolled the machine back to. Even as we speak I am still sitting at 7.5. If worse comes to worse before the end of the year I'll simply update the machine and deal with the BUG, as I discovered a workaround -- it still would be a Giant PITA, but I could live with it if need be. Doing a complete reinstall would be a major bummer, but that might be your only option. Just make sure you backup your entire /home directory.

For your sake I hope you backup the machine. It might take a couple hours to roll it back, compared to the other options which could take DAYS!! A few hours is not such a bad thing.

Wishing you a Happy Holiday Season, and a Safe and Prosperous New Year.

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