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

Kemal3535
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 ?

Comments

5 comments

Date Votes
  • cPanelMichael
    Hello @Kemal3535, Can you let us know the full output when running the "yum update" command on this system? Thank you.
    0
  • Kemal3535
    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
    Hello @Kemal3535, Can you let us know the full output when running the "yum update" command on this system? Thank you.

    ? have vps i need to quickly upgrade php version 5.6 or 7 can you help me pls ?
    0
  • cPanelMichael
    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: 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: 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.
    0
  • Kemal3535
    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: 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: 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.

    ?m using easyApache 3 and i tried to easyApache4 but Apache is not working when i upgrade to apache 4 For example : "XID (2hks3?) "PHP" its not working " error how can i fix it ?
    0
  • cPanelMichael
    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.
    0

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