Resolved Does Update#10 broken other packages?

[raytracy]

I just applied updated#10 to my Centos 7.3, but soon found my yum update report following when I try to update glibc-headers:
=======================
#yum update glibc-headers.x86_64
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
* base: centos.cs.nctu.edu.tw
* extras: centos.cs.nctu.edu.tw
* updates: centos.cs.nctu.edu.tw
Resolving Dependencies
--> Running transaction check
---> Package glibc-headers.x86_64 0:2.17-157.el7_3.2 will be updated
--> Processing Dependency: glibc-headers = 2.17-157.el7_3.2 for package: glibc-devel-2.17-157.el7_3.2.x86_64
---> Package glibc-headers.x86_64 0:2.17-157.el7_3.4 will be an update
--> Finished Dependency Resolution
Error: Package: glibc-devel-2.17-157.el7_3.2.x86_64 (@updates)
Requires: glibc-headers = 2.17-157.el7_3.2
Removing: glibc-headers-2.17-157.el7_3.2.x86_64 (@updates)
glibc-headers = 2.17-157.el7_3.2
Updated By: glibc-headers-2.17-157.el7_3.4.x86_64 (updates)
glibc-headers = 2.17-157.el7_3.4
Available: glibc-headers-2.17-157.el7.x86_64 (base)
glibc-headers = 2.17-157.el7
Available: glibc-headers-2.17-157.el7_3.1.x86_64 (updates)
glibc-headers = 2.17-157.el7_3.1
You could try using --skip-broken to work around the problem
** Found 6 pre-existing rpmdb problem(s), 'yum check' output follows:
glibc-devel-2.17-157.el7_3.2.x86_64 has missing requires of glibc = ('0', '2.17', '157.el7_3.2')
glibc-devel-2.17-157.el7_3.4.x86_64 is a duplicate with glibc-devel-2.17-157.el7_3.2.x86_64
glibc-devel-2.17-157.el7_3.4.x86_64 has missing requires of glibc-headers = ('0', '2.17', '157.el7_3.4')
glibc-headers-2.17-157.el7_3.2.x86_64 has missing requires of glibc = ('0', '2.17', '157.el7_3.2')
plesk-php71-fpm-7.1.5-centos7.17051211.x86_64 has missing requires of plesk-php71 = ('0', '7.1.5', 'centos7.17051211')
plesk-php71-fpm-7.1.6-centos7.17060817.x86_64 is a duplicate with plesk-php71-fpm-7.1.5-centos7.17051211.x86_64
==================================

I have try yum clean all and stop using mirror repository but still got same result.
Does anyone has similar situation and know how to fix it?

 

[Bitpalast]

CentOS 7.3 from Epel repositories and MU #10 --> no issues here on a test system and no issues yet on production servers that have #10 and CentOS 7.3.

With no guarantees for your case, maybe this will help:
# yum clean all
# yum reinstall glibc glibc-common glibc-headers glibc-devel
# yum upgrade

For glibc only. the PHP part is a different thing, I'd first solve the glibc issue, because then everything else can probably be managed by the Plesk functions.

 

[IgorG]

You can try to rebuild rpm database with

# rm -f /var/lib/rpm/__*
# rpm --rebuilddb

after that run

# plesk installer --select-release-current --reinstall-patch --upgrade-installed-components

 

[raytracy]

Neither Peter's nor IgorG's way has luck to solve it.

yum reinstall got the same error and cannot be applied.
rpm --rebuilddb and plesk installer has finished without error, but yum update still show same error as 1st post.

when I yum list glibc glibc-common glibc-headers glibc-devel, I got following info:

Installed Packages
glibc.x86_64 2.17-157.el7_3.4 @updates
glibc-common.x86_64 2.17-157.el7_3.4 @updates
glibc-devel.x86_64 2.17-157.el7_3.2 @updates
glibc-devel.x86_64 2.17-157.el7_3.4 @updates
glibc-headers.x86_64 2.17-157.el7_3.2 @updates

It looks like glibc-devel installed with two difference version: both 3.2 and 3.4.

package-cleanup --dupes
Loaded plugins: fastestmirror
glibc-devel-2.17-157.el7_3.4.x86_64
glibc-devel-2.17-157.el7_3.2.x86_64
plesk-php71-fpm-7.1.5-centos7.17051211.x86_64
plesk-php71-fpm-7.1.6-centos7.17060817.x86_64

Is it safe to remove glibc-devel without disrupt Plesk Onyx? I like ganna try package-cleanup --cleandupes but afraid it will destroy whole production system.....

(I am sorry to ask here since it may not related to Plesk, but I have no one can help me).

 

[raytracy]

OK, it seems solved. Here is my steps:

package-cleanup --cleandupes
Removed:
glibc-devel.x86_64 0:2.17-157.el7_3.2 plesk-php71-fpm.x86_64 0:7.1.5-centos7.17051211
Complete!

yum check dependencies
Loaded plugins: fastestmirror
glibc-devel-2.17-157.el7_3.4.x86_64 has missing requires of glibc-headers = ('0', '2.17', '157.el7_3.4')
glibc-headers-2.17-157.el7_3.2.x86_64 has missing requires of glibc = ('0', '2.17', '157.el7_3.2')
Error: check ['dependencies']

yum update glibc-headers
plesk installer --select-release-current --reinstall-patch --upgrade-installed-components

Now yum update report with no error.

Thanks a lot for both of you.

 

[raytracy]

Ohhh!!!....No.....that's no good!!

After fixed yum update, I found the data disk has crashed.

I have rollback to the snapshot before I fix the glibc, try to fix it again.
And found that after fix the glibc to latest version, the data disk will show an XFS error and lost data.

Jun 23 02:44:08 psa-fbb kernel: XFS (dm-2): metadata I/O error: block 0x12c0afc8 ("xfs_trans_read_buf_map") error 74 numblks 8
Jun 23 02:44:08 psa-fbb kernel: XFS (dm-2): Metadata CRC error detected at xfs_dir3_block_read_verify+0x5e/0x110 [xfs], xfs_dir3_block block 0x12c0afc8
Jun 23 02:44:08 psa-fbb kernel: XFS (dm-2): Unmount and run xfs_repair
Jun 23 02:44:08 psa-fbb kernel: XFS (dm-2): First 64 bytes of corrupted metadata buffer:
Jun 23 02:44:08 psa-fbb kernel: ffff88027837c000: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ................
Jun 23 02:44:08 psa-fbb kernel: ffff88027837c010: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ................
Jun 23 02:44:08 psa-fbb kernel: ffff88027837c020: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ................
Jun 23 02:44:08 psa-fbb kernel: ffff88027837c030: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ................
Jun 23 02:44:08 psa-fbb kernel: XFS (dm-2): metadata I/O error: block 0x12c0afc8 ("xfs_trans_read_buf_map") error 74 numblks 8
Jun 23 02:44:08 psa-fbb kernel: XFS (dm-2): Metadata CRC error detected at xfs_dir3_block_read_verify+0x5e/0x110 [xfs], xfs_dir3_block block 0x12c0afc8
Jun 23 02:44:08 psa-fbb kernel: XFS (dm-2): Unmount and run xfs_repair
Jun 23 02:44:08 psa-fbb kernel: XFS (dm-2): First 64 bytes of corrupted metadata buffer:
Jun 23 02:44:08 psa-fbb kernel: ffff88027837c000: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ................
Jun 23 02:44:08 psa-fbb kernel: ffff88027837c010: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ................
Jun 23 02:44:08 psa-fbb kernel: ffff88027837c020: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ................
Jun 23 02:44:08 psa-fbb kernel: ffff88027837c030: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ................
Jun 23 02:44:08 psa-fbb kernel: XFS (dm-2): metadata I/O error: block 0x12c0afc8 ("xfs_trans_read_buf_map") error 74 numblks 8

I am still try to fix it....

 

[raytracy]

OK, I am back, the steps in above has no problem.
Disk failure was caused by other event, not related to yum operation.

Thanks guys!!

 

[Bart_NL]

Got the same issue,

How did you fix?

Loaded plugins: fastestmirror
PHP52_17                                                                                                                                                                             | 2.9 kB  00:00:00
PHP53_17                                                                                                                                                                             | 2.9 kB  00:00:00
PLESK_17_5_3-extras                                                                                                                                                                  | 2.9 kB  00:00:00
PLESK_17_PHP54                                                                                                                                                                       | 2.9 kB  00:00:00
PLESK_17_PHP55                                                                                                                                                                       | 2.9 kB  00:00:00
PLESK_17_PHP56                                                                                                                                                                       | 2.9 kB  00:00:00
PLESK_17_PHP70                                                                                                                                                                       | 2.9 kB  00:00:00
PLESK_17_PHP71                                                                                                                                                                       | 2.9 kB  00:00:00
Loading mirror speeds from cached hostfile
 * base: ftp.nluug.nl
 * epel: nl.mirror.babylon.network
 * extras: ftp.nluug.nl
 * updates: ftp.nluug.nl
Resolving Dependencies
--> Running transaction check
---> Package compat-libtidy.x86_64 0:0.99.0-37.20091203.el7 will be obsoleting
---> Package glibc-headers.x86_64 0:2.17-157.el7_3.4 will be updated
--> Processing Dependency: glibc-headers = 2.17-157.el7_3.4 for package: glibc-devel-2.17-157.el7_3.4.x86_64
---> Package glibc-headers.x86_64 0:2.17-157.el7_3.5 will be an update
---> Package libopendkim.x86_64 0:2.11.0-0.1.el6 will be updated
---> Package libopendkim.x86_64 0:2.11.0-0.1.el7 will be an update
---> Package libtidy.x86_64 0:0.99.0-31.20091203.el7 will be obsoleted
---> Package log4cplus.x86_64 0:1.1.2-centos7.16071418 will be updated
---> Package log4cplus.x86_64 0:1.1.3-0.4.rc3.el7 will be an update
---> Package perl-JSON-XS.x86_64 0:3.01-centos7.17031417 will be updated
---> Package perl-JSON-XS.x86_64 1:3.01-2.el7 will be an update
---> Package php-imap.x86_64 0:5.4.16-2.el7 will be updated
---> Package php-imap.x86_64 0:5.4.16-7.el7 will be an update
---> Package pigz.x86_64 0:2.3.3-1.el7.centos will be updated
---> Package pigz.x86_64 0:2.3.4-1.el7 will be an update
--> Finished Dependency Resolution
Error: Package: glibc-devel-2.17-157.el7_3.4.x86_64 (@updates)
           Requires: glibc-headers = 2.17-157.el7_3.4
           Removing: glibc-headers-2.17-157.el7_3.4.x86_64 (@updates)
               glibc-headers = 2.17-157.el7_3.4
           Updated By: glibc-headers-2.17-157.el7_3.5.x86_64 (updates)
               glibc-headers = 2.17-157.el7_3.5
           Available: glibc-headers-2.17-157.el7.x86_64 (base)
               glibc-headers = 2.17-157.el7
           Available: glibc-headers-2.17-157.el7_3.1.x86_64 (updates)
               glibc-headers = 2.17-157.el7_3.1
           Available: glibc-headers-2.17-157.el7_3.2.x86_64 (updates)
               glibc-headers = 2.17-157.el7_3.2
 You could try using --skip-broken to work around the problem
** Found 4 pre-existing rpmdb problem(s), 'yum check' output follows:
glibc-devel-2.17-157.el7_3.4.x86_64 has missing requires of glibc = ('0', '2.17', '157.el7_3.4')
glibc-devel-2.17-157.el7_3.5.x86_64 is a duplicate with glibc-devel-2.17-157.el7_3.4.x86_64
glibc-devel-2.17-157.el7_3.5.x86_64 has missing requires of glibc-headers = ('0', '2.17', '157.el7_3.5')
glibc-headers-2.17-157.el7_3.4.x86_64 has missing requires of glibc = ('0', '2.17', '157.el7_3.4')

 

[raytracy]

The #5 steps solved issue:
Does Update#10 broken other packages?

Please ignore my disk crash incident, it is not related to this issue.

 

[Bart_NL]

The #5 steps solved issue:
Does Update#10 broken other packages?

Please ignore my disk crash incident, it is not related to this issue.

Oke, how did you execute the first command? When I run it, it says command not found?! It's also not a yum command

[root@EU-PLESK01 ~]#  package-cleanup --cleandupes
-bash: package-cleanup: command not found
[root@EU-PLESK01 ~]# yum package-cleanup --cleandupes
Command line error: no such option: --cleandupes

 

[Bart_NL]

Fixed it you need the yum-utils package before runing that command.

yum install -y yum-utils
package-cleanup --cleandupes
yum update

That did the trick for me, Thanks!