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The server’s system package manager, YUM failed

Discussion in 'EasyApache' started by sreeninair, Jul 1, 2014.

  1. sreeninair

    sreeninair Well-Known Member

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    Hello,


    While running easy apache Yum is giving error

    !! The server’s system package manager, ‘YUM’, failed. !!


    tried the below fixes:

    -----------
    Solution :
    Code:
    # yum clean headers
    
    # yum clean packages
    
    # yum clean metadata
    # yum clean dbcache
    # yum clean all
    Run yum update command, if all above cmds did not resolve the error:
    # yum update

    If yum update failed it may possible that the RPM database is corruption it can be resolved by running below commands

    Code:
    # rm -f /var/lib/rpm/__db.*
    # rpm -vv –rebuilddb
    # yum update
    Code:
    rpm -e --justdb --nodeps openssl.i386
    yum install openssl
    -----------

    Still getting the same error.


    I have also ran upcp , getting this error
    Code:
    ==============================
    
    
    [20140701.104608]      [25848] Error: Package: clamav-0.98.3-1.el5.x86_64 (epel)
    [20140701.104608]      [25848]            Requires: libcurl.so.3()(64bit)
    [20140701.104608]      [25848]  You could try using --skip-broken to work around the problem
    [20140701.104609]      [25848] ** Found 2 pre-existing rpmdb problem(s), 'yum check' output follows:
    [20140701.104609]      [25848] frontpage-2002-SR1.2.i386 has missing requires of libexpat.so.0
    [20140701.104609]      [25848] sendmail-cf-8.14.4-8.el6.noarch has missing requires of sendmail = ('0', '8.14.4', '8.el6')
    [20140701.104609]      [25848] checkyum version 21.1
    
    
    ===========================================


    Code:
    =====================
    # yum check
    Loaded plugins: fastestmirror
    MySQL51-client-5.1.73-1.cp1136.x86_64 is a duplicate with MySQL51-client-5.1.72-2.cp1136.x86_64
    MySQL51-server-5.1.73-1.cp1136.x86_64 is a duplicate with MySQL51-server-5.1.72-2.cp1136.x86_64
    cpanel-ckeditor-4.2.1-2.cp1140.noarch is a duplicate with cpanel-ckeditor-4.2-3.cp1140.noarch
    cpanel-clamav-0.98.1-2.cp1140.x86_64 is a duplicate with cpanel-clamav-0.98-4.cp1140.x86_64
    cpanel-clamav-virusdefs-0.98-4.cp1140.x86_64 is obsoleted by cpanel-clamav-virusdefs-0.98-4.cp1140.x86_64
    cpanel-clamav-virusdefs-0.98-4.cp1140.x86_64 is obsoleted by cpanel-clamav-virusdefs-0.98.1-2.cp1140.x86_64
    cpanel-clamav-virusdefs-0.98.1-2.cp1140.x86_64 is a duplicate with cpanel-clamav-virusdefs-0.98-4.cp1140.x86_64
    cpanel-clamav-virusdefs-0.98.1-2.cp1140.x86_64 is obsoleted by cpanel-clamav-virusdefs-0.98-4.cp1140.x86_64
    cpanel-clamav-virusdefs-0.98.1-2.cp1140.x86_64 is obsoleted by cpanel-clamav-virusdefs-0.98.1-2.cp1140.x86_64
    cpanel-libxml2-2.9.1-1.cp1136.x86_64 is a duplicate with cpanel-libxml2-2.7.7-2.cp1136.x86_64
    cpanel-perl-514-Locale-Maketext-1.23-1.cp1136.x86_64 is a duplicate with cpanel-perl-514-Locale-Maketext-1.22-1.cp1136.x86_64
    cpanel-perl-514-Locales-0.32-1.cp1136.x86_64 is a duplicate with cpanel-perl-514-Locales-0.26-1.cp1136.x86_64
    cpanel-perl-514-Mail-SpamAssassin-3.003002-4.cp1136.x86_64 is a duplicate with cpanel-perl-514-Mail-SpamAssassin-3.003002-3.cp1136.x86_64
    cpanel-perl-514-Module-Want-0.6-1.cp1136.x86_64 is a duplicate with cpanel-perl-514-Module-Want-0.4-1.cp1136.x86_64
    exim-4.82-3.cp1136.x86_64 is a duplicate with exim-4.82-2.cp1136.x86_64
    frontpage-2002-SR1.2.i386 has missing requires of libexpat.so.0
    sendmail-cf-8.14.4-8.el6.noarch has missing requires of sendmail = ('0', '8.14.4', '8.el6')
    Error: check all
    =======================
     
  2. cPanelMichael

    cPanelMichael Forums Analyst
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    Hello :)

    The output shows that you are using the EPEL repo with YUM in the /etc/yum.repos.d directory. This is not standard. Are you using this repo for a specific package?

    Thank you.
     
  3. sreeninair

    sreeninair Well-Known Member

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    Hello,

    How can I change it to standard one.

    Now when I execute yum update I get following output.

    ---> Package shared-mime-info.x86_64 0:0.70-4.el6 will be installed
    --> Finished Dependency Resolution
    Error: Package: clamav-0.98.3-1.el5.x86_64 (epel)
    Requires: libcurl.so.3()(64bit)
    You could try using --skip-broken to work around the problem
    ** Found 2 pre-existing rpmdb problem(s), 'yum check' output follows:
    frontpage-2002-SR1.2.i386 has missing requires of libexpat.so.0
    sendmail-cf-8.14.4-8.el6.noarch has missing requires of sendmail = ('0', '8.14.4', '8.el6')
     
  4. sreeninair

    sreeninair Well-Known Member

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    Hello,

    cPanel fixed it.

    ================

    [13:48:04 server root@5176965 ~]cPs# rpm -e --justdb --nodeps libstdc++-4.4.7-3.el6.i686

    Once I did that, I ran /scripts/easyapache --build and it built without error.

    Distilled successfully
    !! Done executing '/scripts/posteasyapache' !!
    !! Verbose logfile is at '/usr/local/cpanel/logs/easy/apache/build.1404247997' !!
    [14:15:57 server root@5176965 ~]cPs#
    ==========
     
  5. cPanelMichael

    cPanelMichael Forums Analyst
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  6. rainbowpower

    rainbowpower Registered

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    I tried to recompile also apache with easyapache and i got the same error
    "The server's system package manager, 'YUM', failed."

    Some details from the console that might help
     
    #6 rainbowpower, Feb 5, 2015
    Last edited by a moderator: Feb 5, 2015
  7. rainbowpower

    rainbowpower Registered

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    Any solution on the issue ? Thanks!
     
  8. cPJacob

    cPJacob cPanel Product Owner
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    Twitter:
    Hi,

    As root on your server, can you run
    Code:
    yum update
    Please paste the output here. This should let us know how Yum failed.
     
  9. Alaa Tubasi

    Alaa Tubasi Registered

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    Hello ,

    i have an error with easyapache when i want to customize profile or bulid

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

    I tried to use this solution
    - Removed link, threads merged -

    but i got same problem

    Code:
    root@server [~]# yum update
    Loaded plugins: fastestmirror
    Setting up Update Process
    Loading mirror speeds from cached hostfile
    * base: mirror.san.fastserv.com
    * updates: centos.unixheads.org
    Resolving Dependencies
    --> Running transaction check
    ---> Package gcc.x86_64 0:4.4.7-11.el6 will be updated
    ---> Package gcc.x86_64 0:4.4.7-16.el6 will be an update
    ---> Package gcc-c++.x86_64 0:4.4.7-11.el6 will be updated
    ---> Package gcc-c++.x86_64 0:4.4.7-16.el6 will be an update
    ---> Package glibc.i686 0:2.12-1.149.el6_6.9 will be updated
    ---> Package glibc.i686 0:2.12-1.166.el6_7.1 will be an update
    ---> Package glibc-common.x86_64 0:2.12-1.149.el6_6.9 will be updated
    ---> Package glibc-common.x86_64 0:2.12-1.166.el6_7.1 will be an update
    ---> Package libstdc++.i686 0:4.4.7-11.el6 will be updated
    ---> Package libstdc++.i686 0:4.4.7-16.el6 will be an update
    ---> Package libstdc++-devel.x86_64 0:4.4.7-11.el6 will be updated
    ---> Package libstdc++-devel.x86_64 0:4.4.7-16.el6 will be an update
    ---> Package libxml2.i686 0:2.7.6-17.el6_6.1 will be updated
    ---> Package libxml2.i686 0:2.7.6-20.el6 will be an update
    ---> Package ncurses-libs.i686 0:5.7-3.20090208.el6 will be updated
    ---> Package ncurses-libs.i686 0:5.7-4.20090207.el6 will be an update
    ---> Package python-libs.x86_64 0:2.6.6-52.el6 will be updated
    ---> Package python-libs.x86_64 0:2.6.6-64.el6 will be an update
    ---> Package rpm.x86_64 0:4.8.0-38.el6_6 will be updated
    ---> Package rpm.x86_64 0:4.8.0-47.el6 will be an update
    ---> Package yum.noarch 0:3.2.29-60.el6.centos will be updated
    ---> Package yum.noarch 0:3.2.29-69.el6.centos will be an update
    --> Finished Dependency Resolution
    
    Dependencies Resolved
    
    ================================================================================
    Package              Arch        Version                    Repository    Size
    ================================================================================
    Updating:
    gcc                  x86_64      4.4.7-16.el6               base          10 M
    gcc-c++              x86_64      4.4.7-16.el6               base         4.7 M
    glibc                i686        2.12-1.166.el6_7.1         updates      4.3 M
    glibc-common         x86_64      2.12-1.166.el6_7.1         updates       14 M
    libstdc++            i686        4.4.7-16.el6               base         302 k
    libstdc++-devel      x86_64      4.4.7-16.el6               base         1.6 M
    libxml2              i686        2.7.6-20.el6               base         801 k
    ncurses-libs         i686        5.7-4.20090207.el6         base         249 k
    python-libs          x86_64      2.6.6-64.el6               base         5.3 M
    rpm                  x86_64      4.8.0-47.el6               base         904 k
    yum                  noarch      3.2.29-69.el6.centos       base         1.0 M
    
    Transaction Summary
    ================================================================================
    Upgrade      11 Package(s)
    
    Total download size: 43 M
    Is this ok [y/N]: y
    Downloading Packages:
    (1/11): gcc-4.4.7-16.el6.x86_64.rpm                      |  10 MB     00:00
    (2/11): gcc-c++-4.4.7-16.el6.x86_64.rpm                  | 4.7 MB     00:00
    (3/11): glibc-2.12-1.166.el6_7.1.i686.rpm                | 4.3 MB     00:00
    (4/11): glibc-common-2.12-1.166.el6_7.1.x86_64.rpm       |  14 MB     00:01
    (5/11): libstdc++-4.4.7-16.el6.i686.rpm                  | 302 kB     00:00
    (6/11): libstdc++-devel-4.4.7-16.el6.x86_64.rpm          | 1.6 MB     00:00
    (7/11): libxml2-2.7.6-20.el6.i686.rpm                    | 801 kB     00:00
    (8/11): ncurses-libs-5.7-4.20090207.el6.i686.rpm         | 249 kB     00:00
    (9/11): python-libs-2.6.6-64.el6.x86_64.rpm              | 5.3 MB     00:00
    (10/11): rpm-4.8.0-47.el6.x86_64.rpm                     | 904 kB     00:00
    (11/11): yum-3.2.29-69.el6.centos.noarch.rpm             | 1.0 MB     00:00
    --------------------------------------------------------------------------------
    Total                                            11 MB/s |  43 MB     00:04
    Running rpm_check_debug
    Running Transaction Test
    Transaction Test Succeeded
    Running Transaction
      Updating   : libstdc++-devel-4.4.7-16.el6.x86_64                         1/22
    Error unpacking rpm package libstdc++-devel-4.4.7-16.el6.x86_64
    error: unpacking of archive failed on file /usr/lib/gcc: cpio: chown
      Updating   : glibc-common-2.12-1.166.el6_7.1.x86_64                      2/22
    Error unpacking rpm package glibc-common-2.12-1.166.el6_7.1.x86_64
    error: unpacking of archive failed on file /usr/lib/locale/locale-archive.tmpl;55da10e4: cpio: open
      Updating   : glibc-2.12-1.166.el6_7.1.i686                               3/22
    Error unpacking rpm package glibc-2.12-1.166.el6_7.1.i686
    error: unpacking of archive failed on file /usr/lib/gconv: cpio: chown
      Updating   : rpm-4.8.0-47.el6.x86_64                                     4/22
    Error unpacking rpm package rpm-4.8.0-47.el6.x86_64
    error: unpacking of archive failed on file /usr/lib/rpm: cpio: chown
      Updating   : gcc-4.4.7-16.el6.x86_64                                     5/22
    Error unpacking rpm package gcc-4.4.7-16.el6.x86_64
    error: unpacking of archive failed on file /usr/lib/gcc: cpio: chown
      Updating   : libstdc++-4.4.7-16.el6.i686                                 6/22
    Error unpacking rpm package libstdc++-4.4.7-16.el6.i686
    error: unpacking of archive failed on file /usr/lib/libstdc++.so.6.0.13: cpio: rename
      Updating   : gcc-c++-4.4.7-16.el6.x86_64                                 7/22
    Error unpacking rpm package gcc-c++-4.4.7-16.el6.x86_64
    error: unpacking of archive failed on file /usr/lib/gcc: cpio: chown
      Updating   : yum-3.2.29-69.el6.centos.noarch                             8/22
    Error unpacking rpm package yum-3.2.29-69.el6.centos.noarch
    error: unpacking of archive failed on file /usr/lib/yum-plugins: cpio: chown
      Updating   : python-libs-2.6.6-64.el6.x86_64                             9/22
    Error unpacking rpm package python-libs-2.6.6-64.el6.x86_64
    error: unpacking of archive failed on file /usr/lib/python2.6: cpio: chown
      Updating   : libxml2-2.7.6-20.el6.i686                                  10/22
    Error unpacking rpm package libxml2-2.7.6-20.el6.i686
    error: unpacking of archive failed on file /usr/lib/libxml2.so.2.7.6: cpio: rename
      Updating   : ncurses-libs-5.7-4.20090207.el6.i686                       11/22
    Error unpacking rpm package ncurses-libs-5.7-4.20090207.el6.i686
    error: unpacking of archive failed on file /usr/lib/libform.so.5.7: cpio: rename
      Verifying  : gcc-c++-4.4.7-16.el6.x86_64                                 1/22
    libstdc++-devel-4.4.7-11.el6.x86_64 was supposed to be removed but is not!
      Verifying  : libstdc++-devel-4.4.7-11.el6.x86_64                         2/22
    glibc-2.12-1.149.el6_6.9.i686 was supposed to be removed but is not!
      Verifying  : glibc-2.12-1.149.el6_6.9.i686                               3/22
      Verifying  : glibc-2.12-1.166.el6_7.1.i686                               4/22
    python-libs-2.6.6-52.el6.x86_64 was supposed to be removed but is not!
      Verifying  : python-libs-2.6.6-52.el6.x86_64                             5/22
      Verifying  : python-libs-2.6.6-64.el6.x86_64                             6/22
      Verifying  : libxml2-2.7.6-20.el6.i686                                   7/22
      Verifying  : libstdc++-4.4.7-16.el6.i686                                 8/22
    ncurses-libs-5.7-3.20090208.el6.i686 was supposed to be removed but is not!
      Verifying  : ncurses-libs-5.7-3.20090208.el6.i686                        9/22
      Verifying  : rpm-4.8.0-47.el6.x86_64                                    10/22
    gcc-c++-4.4.7-11.el6.x86_64 was supposed to be removed but is not!
      Verifying  : gcc-c++-4.4.7-11.el6.x86_64                                11/22
      Verifying  : gcc-4.4.7-16.el6.x86_64                                    12/22
      Verifying  : glibc-common-2.12-1.166.el6_7.1.x86_64                     13/22
      Verifying  : yum-3.2.29-69.el6.centos.noarch                            14/22
    libxml2-2.7.6-17.el6_6.1.i686 was supposed to be removed but is not!
      Verifying  : libxml2-2.7.6-17.el6_6.1.i686                              15/22
      Verifying  : libstdc++-devel-4.4.7-16.el6.x86_64                        16/22
    libstdc++-4.4.7-11.el6.i686 was supposed to be removed but is not!
      Verifying  : libstdc++-4.4.7-11.el6.i686                                17/22
    rpm-4.8.0-38.el6_6.x86_64 was supposed to be removed but is not!
      Verifying  : rpm-4.8.0-38.el6_6.x86_64                                  18/22
    gcc-4.4.7-11.el6.x86_64 was supposed to be removed but is not!
      Verifying  : gcc-4.4.7-11.el6.x86_64                                    19/22
    glibc-common-2.12-1.149.el6_6.9.x86_64 was supposed to be removed but is not!
      Verifying  : glibc-common-2.12-1.149.el6_6.9.x86_64                     20/22
      Verifying  : ncurses-libs-5.7-4.20090207.el6.i686                       21/22
    yum-3.2.29-60.el6.centos.noarch was supposed to be removed but is not!
      Verifying  : yum-3.2.29-60.el6.centos.noarch                            22/22
    
    Failed:
      gcc.x86_64 0:4.4.7-11.el6
      gcc.x86_64 0:4.4.7-16.el6
      gcc-c++.x86_64 0:4.4.7-11.el6
      gcc-c++.x86_64 0:4.4.7-16.el6
      glibc.i686 0:2.12-1.149.el6_6.9
      glibc.i686 0:2.12-1.166.el6_7.1
      glibc-common.x86_64 0:2.12-1.149.el6_6.9
      glibc-common.x86_64 0:2.12-1.166.el6_7.1
      libstdc++.i686 0:4.4.7-11.el6
      libstdc++.i686 0:4.4.7-16.el6
      libstdc++-devel.x86_64 0:4.4.7-11.el6
      libstdc++-devel.x86_64 0:4.4.7-16.el6
      libxml2.i686 0:2.7.6-17.el6_6.1
      libxml2.i686 0:2.7.6-20.el6
      ncurses-libs.i686 0:5.7-3.20090208.el6
      ncurses-libs.i686 0:5.7-4.20090207.el6
      python-libs.x86_64 0:2.6.6-52.el6
      python-libs.x86_64 0:2.6.6-64.el6
      rpm.x86_64 0:4.8.0-38.el6_6
      rpm.x86_64 0:4.8.0-47.el6
      yum.noarch 0:3.2.29-60.el6.centos
      yum.noarch 0:3.2.29-69.el6.centos
    
    Complete!
     
    #9 Alaa Tubasi, Aug 23, 2015
    Last edited by a moderator: Aug 23, 2015
  10. cPanelMichael

    cPanelMichael Forums Analyst
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    Hello :)

    It's possible that part of the problem is with immutable or append-only attributes assigned to some of the files in your /usr/lib directory. Try running the lsattr command on some of the files referenced in the YUM error output to see if that's the case. EX:

    Code:
    lsattr /usr/lib/gcc
    On a test system, it shows the following output:

    Code:
    # lsattr /usr/lib/gcc
    ---------------- /usr/lib/gcc/x86_64-redhat-linux
    
    What do you see on your system?

    Thank you.
     
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