The server's system package manager, 'YUM', failed

Kemal3535

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Jun 22, 2018
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Hello I changed my ip adresses and I want to upgrade php version from 5.3 to 5.6 in whm cpanel but yum failed I saw similar threads, but was not sure how exactly to applied it to my current server. I am new to server admin, and learning on the fly. So I apologize in advance if I have ask things a few times.
I was trying to update my server through Easy Apache 3, have a CENTOS 6.9 x86 server. And got the following error message.

!! The server's system package manager, 'YUM', failed. !!

!! direct ensure() call will be used (does not support get_command_arrayref_only): pkglist = 'xorg-x11-devel libtool-ltdl-devel libXpm-dev ca_root_nss gcc zlib1-devel libcap libstdc++-devel libltdl3-devel e2fsprogs-devel libXpm-devel glibc-devel gd ssl-dev autoconf261 sed libopenssl0-dev gettext readline-devel automake cpp libpng-devel make libtool libtool-ltdl libltdl libopenssl0.9.7-devel openssl-dev pam-devel autoconf libopenssl0.9.7-static-devel gmake openssl-devel lex xorg-x11-dev bison glibc-dev expat libssl-dev coreutils libidn expat-dev automake19 zlib libopenssl0 flex libjpeg-dev krb5-devel gcc-c++ openssl libstdc++ libstdc++-dev libz-devel libXpm libtool-libltdl-devel expat-devel lsof zlib-devel libltdl-devel pam-dev libpng-dev libopenssl0-devel libcap-devel patch libX11-devel libstdc++-devel.x86_64 fileutils libidn-devel krb5-dev readline-dev libjpeg-devel' !!

!! Please visit EasyApache FAQ - EasyApache - cPanel Documentation for help with this error. !!

I try to # yum update code from SSH but still is problem issue continue

Can you help me ?
 

cPanelMichael

Administrator
Staff member
Apr 11, 2011
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Hello @Kemal3535,

Can you let us know the full output when running the "yum update" command on this system?

Thank you.
 
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Kemal3535

Registered
Jun 22, 2018
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turkiye
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Code:
[email protected] [~]# yum update
Loaded plugins: fastestmirror
Setting up Update Process
Loading mirror speeds from cached hostfile
 * base: mirror.widexs.nl
 * extras: ams.edge.kernel.org
 * updates: mirror.ipserv.nl
base                                                     | 3.7 kB     00:00
extras                                                   | 3.3 kB     00:00
updates                                                  | 3.4 kB     00:00
vz-base                                                  |  951 B     00:00
vz-updates                                               |  951 B     00:00
Resolving Dependencies
--> Running transaction check
---> Package bind-utils.i686 32:9.8.2-0.30.rc1.el6 will be updated
---> Package bind-utils.i686 32:9.8.2-0.62.rc1.el6_9.5 will be an update
---> Package binutils.i686 0:2.20.51.0.2-5.42.el6 will be updated
---> Package binutils.i686 0:2.20.51.0.2-5.47.el6_9.1 will be an update
---> Package coreutils.i686 0:8.4-37.el6 will be updated
---> Package coreutils.i686 0:8.4-46.el6 will be an update
---> Package db4-utils.i686 0:4.7.25-18.el6_4 will be updated
---> Package db4-utils.i686 0:4.7.25-22.el6 will be an update
---> Package elfutils.i686 0:0.158-3.2.el6 will be updated
---> Package elfutils.i686 0:0.164-2.el6 will be an update
---> Package findutils.i686 1:4.4.2-6.el6 will be updated
---> Package findutils.i686 1:4.4.2-9.el6 will be an update
---> Package initscripts.i686 0:9.03.46-1.el6.centos will be updated
---> Package initscripts.i686 0:9.03.58-1.el6.centos.2 will be an update
---> Package iputils.i686 0:20071127-17.el6_4.2 will be updated
---> Package iputils.i686 0:20071127-24.el6 will be an update
---> Package setup.noarch 0:2.8.14-20.el6_4.1 will be updated
---> Package setup.noarch 0:2.8.14-23.el6 will be an update
---> Package shadow-utils.i686 2:4.1.4.2-19.el6 will be updated
---> Package shadow-utils.i686 2:4.1.5.1-5.el6 will be an update
--> Finished Dependency Resolution

Dependencies Resolved

================================================================================
 Package          Arch       Version                          Repository   Size
================================================================================
Updating:
 bind-utils       i686       32:9.8.2-0.62.rc1.el6_9.5        updates     188 k
 binutils         i686       2.20.51.0.2-5.47.el6_9.1         updates     2.8 M
 coreutils        i686       8.4-46.el6                       base        3.0 M
 db4-utils        i686       4.7.25-22.el6                    base        130 k
 elfutils         i686       0.164-2.el6                      base        255 k
 findutils        i686       1:4.4.2-9.el6                    base        413 k
 initscripts      i686       9.03.58-1.el6.centos.2           updates     949 k
 iputils          i686       20071127-24.el6                  base        119 k
 setup            noarch     2.8.14-23.el6                    base        151 k
 shadow-utils     i686       2:4.1.5.1-5.el6                  base        1.0 M

Transaction Summary
================================================================================
Upgrade      10 Package(s)

Total download size: 9.0 M
Is this ok [y/N]: Y
Downloading Packages:
(1/10): bind-utils-9.8.2-0.62.rc1.el6_9.5.i686.rpm       | 188 kB     00:00
(2/10): binutils-2.20.51.0.2-5.47.el6_9.1.i686.rpm       | 2.8 MB     00:00
(3/10): coreutils-8.4-46.el6.i686.rpm                    | 3.0 MB     00:00
(4/10): db4-utils-4.7.25-22.el6.i686.rpm                 | 130 kB     00:00
(5/10): elfutils-0.164-2.el6.i686.rpm                    | 255 kB     00:00
(6/10): findutils-4.4.2-9.el6.i686.rpm                   | 413 kB     00:00
(7/10): initscripts-9.03.58-1.el6.centos.2.i686.rpm      | 949 kB     00:00
(8/10): iputils-20071127-24.el6.i686.rpm                 | 119 kB     00:00
(9/10): setup-2.8.14-23.el6.noarch.rpm                   | 151 kB     00:00
(10/10): shadow-utils-4.1.5.1-5.el6.i686.rpm             | 1.0 MB     00:00
--------------------------------------------------------------------------------
Total                                           7.2 MB/s | 9.0 MB     00:01
Running rpm_check_debug
Running Transaction Test
Transaction Test Succeeded
Running Transaction
  Updating   : coreutils-8.4-46.el6.i686                                   1/20
Error unpacking rpm package coreutils-8.4-46.el6.i686
error: unpacking of archive failed on file /bin/cat: cpio: rename
  Updating   : setup-2.8.14-23.el6.noarch                                  2/20
Error unpacking rpm package setup-2.8.14-23.el6.noarch
warning: /etc/bashrc created as /etc/bashrc.rpmnew
error: unpacking of archive failed on file /etc/csh.cshrc: cpio: rename
  Updating   : 2:shadow-utils-4.1.5.1-5.el6.i686                           3/20
Error unpacking rpm package 2:shadow-utils-4.1.5.1-5.el6.i686
error: unpacking of archive failed on file /usr/bin/chage: cpio: rename
  Updating   : 1:findutils-4.4.2-9.el6.i686                                4/20
Error unpacking rpm package 1:findutils-4.4.2-9.el6.i686
error: unpacking of archive failed on file /bin/find: cpio: rename
  Updating   : initscripts-9.03.58-1.el6.centos.2.i686                     5/20
Error unpacking rpm package initscripts-9.03.58-1.el6.centos.2.i686
error: unpacking of archive failed on file /bin/ipcalc: cpio: rename
  Updating   : iputils-20071127-24.el6.i686                                6/20
Error unpacking rpm package iputils-20071127-24.el6.i686
error: unpacking of archive failed on file /bin/ping: cpio: rename
  Updating   : db4-utils-4.7.25-22.el6.i686                                7/20
Error unpacking rpm package db4-utils-4.7.25-22.el6.i686
error: unpacking of archive failed on file /usr/bin/berkeley_db_svc: cpio: rename
  Updating   : elfutils-0.164-2.el6.i686                                   8/20
Error unpacking rpm package elfutils-0.164-2.el6.i686
error: unpacking of archive failed on file /usr/bin/eu-addr2line: cpio: rename
  Updating   : 32:bind-utils-9.8.2-0.62.rc1.el6_9.5.i686                   9/20
Error unpacking rpm package 32:bind-utils-9.8.2-0.62.rc1.el6_9.5.i686
error: unpacking of archive failed on file /usr/bin/dig: cpio: rename
  Updating   : binutils-2.20.51.0.2-5.47.el6_9.1.i686                     10/20
Error unpacking rpm package binutils-2.20.51.0.2-5.47.el6_9.1.i686
error: unpacking of archive failed on file /usr/bin/addr2line: cpio: rename
setup-2.8.14-20.el6_4.1.noarch was supposed to be removed but is not!
  Verifying  : setup-2.8.14-20.el6_4.1.noarch                              1/20
initscripts-9.03.46-1.el6.centos.i686 was supposed to be removed but is not!
  Verifying  : initscripts-9.03.46-1.el6.centos.i686                       2/20
  Verifying  : binutils-2.20.51.0.2-5.47.el6_9.1.i686                      3/20
  Verifying  : iputils-20071127-24.el6.i686                                4/20
2:shadow-utils-4.1.4.2-19.el6.i686 was supposed to be removed but is not!
  Verifying  : 2:shadow-utils-4.1.4.2-19.el6.i686                          5/20
db4-utils-4.7.25-18.el6_4.i686 was supposed to be removed but is not!
  Verifying  : db4-utils-4.7.25-18.el6_4.i686                              6/20
  Verifying  : 2:shadow-utils-4.1.5.1-5.el6.i686                           7/20
elfutils-0.158-3.2.el6.i686 was supposed to be removed but is not!
  Verifying  : elfutils-0.158-3.2.el6.i686                                 8/20
  Verifying  : initscripts-9.03.58-1.el6.centos.2.i686                     9/20
  Verifying  : 1:findutils-4.4.2-9.el6.i686                               10/20
  Verifying  : coreutils-8.4-46.el6.i686                                  11/20
binutils-2.20.51.0.2-5.42.el6.i686 was supposed to be removed but is not!
  Verifying  : binutils-2.20.51.0.2-5.42.el6.i686                         12/20
  Verifying  : 32:bind-utils-9.8.2-0.62.rc1.el6_9.5.i686                  13/20
coreutils-8.4-37.el6.i686 was supposed to be removed but is not!
  Verifying  : coreutils-8.4-37.el6.i686                                  14/20
  Verifying  : elfutils-0.164-2.el6.i686                                  15/20
  Verifying  : db4-utils-4.7.25-22.el6.i686                               16/20
iputils-20071127-17.el6_4.2.i686 was supposed to be removed but is not!
  Verifying  : iputils-20071127-17.el6_4.2.i686                           17/20
32:bind-utils-9.8.2-0.30.rc1.el6.i686 was supposed to be removed but is not!
  Verifying  : 32:bind-utils-9.8.2-0.30.rc1.el6.i686                      18/20
  Verifying  : setup-2.8.14-23.el6.noarch                                 19/20
1:findutils-4.4.2-6.el6.i686 was supposed to be removed but is not!
  Verifying  : 1:findutils-4.4.2-6.el6.i686                               20/20

Failed:
  bind-utils.i686 32:9.8.2-0.30.rc1.el6
  bind-utils.i686 32:9.8.2-0.62.rc1.el6_9.5
  binutils.i686 0:2.20.51.0.2-5.42.el6
  binutils.i686 0:2.20.51.0.2-5.47.el6_9.1
  coreutils.i686 0:8.4-37.el6
  coreutils.i686 0:8.4-46.el6
  db4-utils.i686 0:4.7.25-18.el6_4
  db4-utils.i686 0:4.7.25-22.el6
  elfutils.i686 0:0.158-3.2.el6
  elfutils.i686 0:0.164-2.el6
  findutils.i686 1:4.4.2-6.el6
  findutils.i686 1:4.4.2-9.el6
  initscripts.i686 0:9.03.46-1.el6.centos
  initscripts.i686 0:9.03.58-1.el6.centos.2
  iputils.i686 0:20071127-17.el6_4.2
  iputils.i686 0:20071127-24.el6
  setup.noarch 0:2.8.14-20.el6_4.1
  setup.noarch 0:2.8.14-23.el6
  shadow-utils.i686 2:4.1.4.2-19.el6
  shadow-utils.i686 2:4.1.5.1-5.el6

Complete!
I need to upgrade php version to 5.6 if there is another way to upgrade php version I can try it

Hello @Kemal3535,

Can you let us know the full output when running the "yum update" command on this system?

Thank you.
İ have vps i need to quickly upgrade php version 5.6 or 7 can you help me pls ?
 
Last edited by a moderator:

cPanelMichael

Administrator
Staff member
Apr 11, 2011
47,913
2,241
363
Hello @Kemal3535,

It looks like YUM is unable to overwrite multiple system files (e.g. /bin/cat, /bin/find). For example:

error: unpacking of archive failed on file /bin/cat: cpio: rename
error: unpacking of archive failed on file /etc/csh.cshrc: cpio: rename
error: unpacking of archive failed on file /bin/find: cpio: rename
Check to see if these files are assigned the immutable attribute with a command such as this:

Code:
lsattr /bin/cat
If so (the output will show the letter "i"), you'll need to remove that attribute so that YUM can overwrite the file. EX:

Code:
chattr -i /bin/cat
You'd need to do this for every file referenced in the errors from the "yum update" output. Additionally, you may want to check with your provider or a system administrator to verify why all of those files were configured with the immutable attribute if that turns out to be the reason why they are not changeable.

Thank you.
 

Kemal3535

Registered
Jun 22, 2018
3
0
1
turkiye
cPanel Access Level
Root Administrator
Hello @Kemal3535,

It looks like YUM is unable to overwrite multiple system files (e.g. /bin/cat, /bin/find). For example:







Check to see if these files are assigned the immutable attribute with a command such as this:

Code:
lsattr /bin/cat
If so (the output will show the letter "i"), you'll need to remove that attribute so that YUM can overwrite the file. EX:

Code:
chattr -i /bin/cat
You'd need to do this for every file referenced in the errors from the "yum update" output. Additionally, you may want to check with your provider or a system administrator to verify why all of those files were configured with the immutable attribute if that turns out to be the reason why they are not changeable.

Thank you.

İm using easyApache 3 and i tried to easyApache4 but Apache is not working when i upgrade to apache 4 For example : "XID (2hks3ı) "PHP" its not working " error how can i fix it ?
 
Last edited by a moderator:

cPanelMichael

Administrator
Staff member
Apr 11, 2011
47,913
2,241
363
Hello,

You'd face the same issue in EasyApache 4 because YUM will need to update successfully before EasyApache updates will succeed. Can you verify that "yum update" completes successfully?

Thank you.