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Cpanel update / up2date and yum problem

Discussion in 'General Discussion' started by X22, Jun 28, 2005.

  1. X22

    X22 Member

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    Im not sure whats happened here however when i run cpanel update i get the following log:

    [snip]Updated: openssh-server 3.6.1p2-33.30.4.i386 bind-devel 20:9.2.4-7_EL3.i386 openssl-devel 0.9.7a-33.15.i386 gcc 3.2.3-52.i386 bind 20:9.2.4-7_EL3.i386 XFree86-devel 4.3.0-81.EL.i386 openssh-clients 3.6.1p2-33.30.4.i386 openssl 0.9.7a-33.15.i686 bind-utils 20:9.2.4-7_EL3.i386 sharutils 4.2.1-16.2.i386 XFree86-libs 4.3.0-81.EL.i386 openssh 3.6.1p2-33.30.4.i386 wget 1.9.1-16.EL3.1.i386
    Dep Installed: libgcc 3.2.3-52.i386 XFree86-libs-data 4.3.0-81.EL.i386 XFree86-xfs 4.3.0-81.EL.i386 libf2c 3.2.3-52.i386 gcc-g77 3.2.3-52.i386 gcc-java 3.2.3-52.i386 cpp 3.2.3-52.i386 libobjc 3.2.3-52.i386 gcc-objc 3.2.3-52.i386 gcc-c++ 3.2.3-52.i386 gcc-gnat 3.2.3-52.i386 libgnat 3.2.3-52.i386
    Transaction(s) Complete
    gd is installed and is the latest version.
    gd-devel is installed and is the latest version.
    gd-progs is installed and is the latest version.
    expect is installed and is the latest version.
    freetype is installed and is the latest version.
    freetype-devel is installed and is the latest version.
    gnupg is installed and is the latest version.
    lynx is installed and is the latest version.
    perl-CPAN is installed and is the latest version.
    error: db4 error(13) from db->close: Permission denied
    error: db4 error(13) from db->close: Permission denied
    error: db4 error(13) from db->close: Permission denied
    error: db4 error(13) from db->close: Permission denied
    error: db4 error(13) from db->close: Permission denied
    error: db4 error(13) from db->close: Permission denied
    error: db4 error(13) from db->close: Permission denied
    error: db4 error(13) from db->close: Permission denied
    error: db4 error(13) from db->close: Permission denied
    error: db4 error(13) from db->close: Permission denied
    error: db4 error(13) from db->close: Permission denied
    error: db4 error(13) from db->close: Permission denied
    error: db4 error(13) from db->close: Permission denied
    error: db4 error(13) from db->close: Permission denied
    error: db4 error(13) from db->close: Permission denied
    error: cannot open Packages index using db3 - Permission denied (13)
    error: cannot open Packages database in /var/lib/rpm


    Gathering header information file(s) from server(s)
    Server: Centos-3 - i386/i686 - Addons
    Server: Centos-3 - i386/i686 - Base
    Server: Centos-3 - i386/i686 - Extras
    Server: Centos-3 - i386/i686 - Updates
    Finding updated packages
    Downloading needed headers
    Resolving dependencies
    Dependencies resolved
    I will do the following:
    [install: kernel 2.4.21-32.0.1.EL.i686]
    [update: openssh-clients 3.6.1p2-33.30.4.i386]
    [update: hotplug 3:2002_04_01-20.4.i386]
    [update: glibc-utils 2.3.2-95.33.i386]
    [update: devlabel 0.48.03-10.i386]
    [update: util-linux 2.11y-31.6.i386]
    [update: rpm 4.2.3-21_nonptl.i386]
    [update: binutils 2.14.90.0.4-37.i386]
    [update: openssh-server 3.6.1p2-33.30.4.i386]
    [update: nscd 2.3.2-95.33.i386]
    [update: XFree86-Mesa-libGLU 4.3.0-81.EL.i386]
    [update: initscripts 7.31.22.EL-2.centos.i386]
    [update: bind-devel 20:9.2.4-7_EL3.i386]
    [update: libstdc++-devel 3.2.3-52.i386]
    [update: rh-postgresql-devel 7.3.10-1.i386]
    [update: openssl-devel 0.9.7a-33.15.i386]
    [update: gcc 3.2.3-52.i386]
    [update: libgcc 3.2.3-52.i386]
    [update: rpmdb-redhat 3.5-0.20050526.i386]
    [update: losetup 2.11y-31.6.i386]
    [update: libgcj 3.2.3-52.i386]
    [update: vixie-cron 3.0.1-76_EL3.i386]
    [update: raidtools 1.00.3-8.EL3.i386]
    [update: quota 1:3.10-7.i386]
    [update: curl-devel 7.10.6-6.rhel3.i386]
    [update: glibc-profile 2.3.2-95.33.i386]
    [update: ipsec-tools 0.2.5-0.7.i386]
    [update: procps 2.0.17-13.7.i386]
    [update: XFree86-libs-data 4.3.0-81.EL.i386]
    [update: XFree86-xfs 4.3.0-81.EL.i386]
    [update: krb5-workstation 1.2.7-44.i386]
    [update: mkinitrd 3.5.13.3-1.i386]
    [update: libf2c 3.2.3-52.i386]
    [update: iscsi-initiator-utils 3.6.2-7.i386]
    [update: pam-devel 0.75-64.i386]
    [update: bind 20:9.2.4-7_EL3.i386]
    [update: man-pages-ja 20041215-1.EL3.noarch]
    [update: net-snmp-libs 5.0.9-2.30E.15.i386]
    [update: usermode 1.68-5E.3.i386]
    [update: ntsysv 1.3.13.2-0.3.i386]
    [update: centos-release 3:3-5.3.i386]
    [update: glibc 2.3.2-95.33.i686]
    [update: comps 3.5centos.0-0.20040916.i386]
    [update: XFree86-devel 4.3.0-81.EL.i386]
    [update: mount 2.11y-31.6.i386]
    [update: kudzu-devel 1.1.22.11-1.centos.0.i386]
    [update: kernel-utils 1:2.4-8.37.12.i386]
    [update: hwdata 0.101.17-1.noarch]
    [update: rpm-devel 4.2.3-21_nonptl.i386]
    [update: kudzu 1.1.22.11-1.centos.0.i386]
    [update: gtk2 2.2.4-15.i386]
    [update: net-snmp-devel 5.0.9-2.30E.15.i386]
    [update: gdb 6.3.0.0-0.30.1.i386]
    [update: rpm-libs 4.2.3-21_nonptl.i386]
    [update: grep 2.5.1-24.4.i386]
    [update: authconfig 4.3.7-3.i386]
    [update: mailx 8.1.1-31.EL3.i386]
    [update: sysklogd 1.4.1-26_EL3.i386]
    [update: rmt 0.4b37-1E.i386]
    [update: laus 0.1-70RHEL3.i386]
    [update: libstdc++ 3.2.3-52.i386]
    [update: pstack 1.2-3.EL.2.i386]
    [update: chkconfig 1.3.13.2-0.3.i386]
    [update: psmisc 21.3-2.i386]
    [update: gcc-g77 3.2.3-52.i386]
    [update: gcc-java 3.2.3-52.i386]
    [update: jpackage-utils 1.5.38-1jpp_5rh.noarch]
    [update: telnet 1:0.17-26.EL3.3.i386]
    [update: openssl096b 0.9.6b-16.22.3.i386]
    [update: dump 0.4b37-1E.i386]
    [update: lvm 1.0.8-12.2.i386]
    [update: popt 1.8.2-21_nonptl.i386]
    [update: openssl 0.9.7a-33.15.i686]
    [update: ltrace 0.3.36-2.EL3.i386]
    [update: libgcj-devel 3.2.3-52.i386]
    [update: glibc-devel 2.3.2-95.33.i386]
    [update: net-tools 1.60-20E.7.i386]
    [update: db4 4.1.25-8.1.i386]
    [update: bzip2 1.0.2-11.EL3.4.i386]
    [update: ncurses-devel 5.3-9.4.i386]
    [update: db4-devel 4.1.25-8.1.i386]
    [update: glibc-common 2.3.2-95.33.i386]
    [update: bonobo-activation 2.2.2-1.2E.i386]
    [update: bind-utils 20:9.2.4-7_EL3.i386]
    [update: nss_ldap 207-15.i386]
    [update: nptl-devel 2.3.2-95.33.i686]
    [update: mktemp 1.5-18.2.i386]
    [update: cvs 1.11.2-27.i386]
    [update: gzip 1.3.3-12.rhel3.i386]
    [update: sharutils 4.2.1-16.2.i386]
    [update: strace 4.5.9-2.EL3.i386]
    [update: bind-libs 20:9.2.4-7_EL3.i386]
    [update: cpp 3.2.3-52.i386]
    [update: laus-libs 0.1-70RHEL3.i386]
    [update: rh-postgresql-libs 7.3.10-1.i386]
    [update: gnome-vfs2 2.2.5-2E.3.2.i386]
    [update: XFree86-Mesa-libGL 4.3.0-81.EL.i386]
    [update: tcpdump 14:3.7.2-7.E3.5.i386]
    [update: net-snmp 5.0.9-2.30E.15.i386]
    [update: lsof 4.63-4.1.i386]
    [update: tzdata 2005f-1.EL3.noarch]
    [update: parted 1.6.3-29.5.i386]
    [update: openmotif 2.2.3-5.RHEL3.2.i386]
    [update: redhat-config-securitylevel-tui 1.2.9.2-1.i386]
    [update: libobjc 3.2.3-52.i386]
    [update: ncurses 5.3-9.4.i386]
    [update: netdump 0.7.7-2.i386]
    [update: crash 3.10-10.centos.0.i386]
    [update: sysreport 1.3.7.2-6.noarch]
    [update: gcc-objc 3.2.3-52.i386]
    [/snip]

    I have highlighted the area in bold which is causing a problem.

    any ideas as to why this is happening?
     
  2. mctDarren

    mctDarren Well-Known Member

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    Tried rpm --rebuild, then reup cp?
     
  3. X22

    X22 Member

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    root@equinox [~]# rpm --rebuild
    --rebuild: unknown option

    any other ideas?
     
  4. webignition

    webignition Well-Known Member

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    Rebuilding the rpm database would definitely be a good place to start.

    You can do this from within WHM if you are not sure how to do this from shell.
     
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  5. chirpy

    chirpy Well-Known Member

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    Shell would be:

    rpm --rebuilddb -v -v
     
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  6. X22

    X22 Member

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    I get this error using the RPM rebuild commant:

    error: failed to replace old database with new database!
    error: replace files in /var/lib/rpm with files from /var/lib/rpmrebuilddb.6082 to recoverD: removing directory /var/lib/rpmrebuilddb.6082
    error: failed to remove directory /var/lib/rpmrebuilddb.6082: Directory not empty
    error: db4 error(13) from db->close: Permission denied
     
  7. chirpy

    chirpy Well-Known Member

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    Did you check that there were no outstanding locks on the rpm database before rebuilding the database?
     
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  8. X22

    X22 Member

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    not sure how i would check this....
     
  9. chirpy

    chirpy Well-Known Member

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  10. X22

    X22 Member

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    I tried:
    lsof | grep /var/lib/rpm

    rm -fv /var/lib/rpms/__*

    rpm --rebuilddb -v -v

    And still get the following error:

    error: failed to replace old database with new database!
    error: replace files in /var/lib/rpm with files from /var/lib/rpmrebuilddb.24164 to recoverD: removing directory /var/lib/rpmrebuilddb.24164
    error: failed to remove directory /var/lib/rpmrebuilddb.24164: Directory not empty
    error: db4 error(13) from db->close: Permission denied
    D: closed db index /var/lib/rpm/Pubkeys
    D: closed db index /var/lib/rpm/Packages
    D: closed db environment /var/lib/rpm/Packages
     
  11. internetfab

    internetfab Well-Known Member
    PartnerNOC

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    *EDIT*
    Solved my problem at least - the __db files had root as owner. Chowned them to rpm:rpm and I could now finish the installation.

    The rpmrebuild directories are root:root as well - think they should be rpm if you want to rebuild them.

    This was on CentOS 4.1
    *EDIT*


    Same here..

    Tried both solutions - reboot and the other..

    error: failed to replace old database with new database!
    error: replace files in /var/lib/rpm with files from /var/lib/rpmrebuilddb.5293 to recoverD: removing directory /var/lib/rpmrebuilddb.5293
    error: failed to remove directory /var/lib/rpmrebuilddb.5293: Directory not empty
    D: closed db index /var/lib/rpm/Pubkeys
    D: closed db index /var/lib/rpm/Packages
    D: closed db environment /var/lib/rpm/Packages
     
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    #11 internetfab, Jul 9, 2005
    Last edited: Jul 9, 2005
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