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

Discussion in 'EasyApache' started by Kemal3535, Jun 22, 2018.

  1. Kemal3535

    Kemal3535 Registered

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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 ?
     
  2. cPanelMichael

    cPanelMichael Technical Support Community Manager
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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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  3. Kemal3535

    Kemal3535 Registered

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    Code:
    root@server [~]# 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

    İ have vps i need to quickly upgrade php version 5.6 or 7 can you help me pls ?
     
    #3 Kemal3535, Jun 23, 2018
    Last edited by a moderator: Jun 25, 2018
  4. cPanelMichael

    cPanelMichael Technical Support Community Manager
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    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.
     
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  5. Kemal3535

    Kemal3535 Registered

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    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 ?
     
    #5 Kemal3535, Jun 25, 2018
    Last edited by a moderator: Jun 25, 2018
  6. cPanelMichael

    cPanelMichael Technical Support Community Manager
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    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.
     
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