YUM update error; nss bug

General support questions
DonX
Posts: 33
Joined: 2014/11/05 07:24:54
Location: Michigan
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Re: YUM update error; nss bug

Post by DonX » 2015/01/19 22:03:09

TrevorH - Yes looks like they did that.

Does CentOS come with pre-installed packages like PHP, httpd, etc and if so, are they suppose to be listed when doing: yum list installed ?

Thanks.

gerald_clark
Posts: 10642
Joined: 2005/08/05 15:19:54
Location: Northern Illinois, USA

Re: YUM update error; nss bug

Post by gerald_clark » 2015/01/19 22:07:40

You could check the /var/log/yum.log and re-install all the listed packages.

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TrevorH
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Re: YUM update error; nss bug

Post by TrevorH » 2015/01/19 22:52:49

Running yum list installed should list everything that is installed but it depends on the integrity of the rpm database for its results. Gerald's suggestion of parsing yum.log* sounds like your best bet though I would be wary of making sure you have copies of all your config files first. When you update an already installed rpm that has a config file marked as a config file in the rpm building process then it is careful not to overwrite any changes you may have made to the installed copy but i have no idea if it also does the same thing on initial installation if the same file is already present. It might create a config.file.rpmnew file or it might just overwrite it.
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DonX
Posts: 33
Joined: 2014/11/05 07:24:54
Location: Michigan
Contact:

Re: YUM update error; nss bug

Post by DonX » 2015/01/19 23:36:49

Here is what my yum.log looks like at the moment:

Code: Select all

Jan 05 15:26:51 Updated: usermin-1.640-1.noarch
Jan 05 15:27:25 Updated: webmin-1.730-1.noarch
Jan 07 14:41:04 Updated: 1:autofs-5.0.5-109.el6_6.1.x86_64
Jan 07 14:41:19 Updated: 1:dovecot-2.0.9-8.el6_6.4.x86_64
Jan 07 14:42:51 Updated: wbm-virtual-server-4.13.gpl-1.noarch
Jan 11 18:45:41 Updated: glibc-2.12-1.149.el6_6.4.x86_64
Jan 11 18:45:48 Updated: glibc-common-2.12-1.149.el6_6.4.x86_64
Jan 11 18:45:50 Updated: glibc-headers-2.12-1.149.el6_6.4.x86_64
Jan 11 18:45:50 Updated: glibc-devel-2.12-1.149.el6_6.4.x86_64
Jan 11 18:46:21 Updated: wbm-virtual-server-4.13.gpl-2.noarch
Jan 14 17:34:32 Updated: kpartx-0.4.9-80.el6_6.2.x86_64
Jan 14 17:34:47 Updated: nss-softokn-3.14.3-19.el6_6.x86_64
Jan 16 10:04:36 Installed: centos-release-6-6.el6.centos.12.2.x86_64
Jan 16 10:21:13 Installed: centos-release-6-6.el6.centos.12.2.x86_64
Jan 16 10:36:05 Installed: centos-release-6-6.el6.centos.12.2.x86_64
Jan 16 10:38:12 Installed: centos-release-6-6.el6.centos.12.2.x86_64
Jan 16 10:39:02 Installed: centos-release-6-6.el6.centos.12.2.x86_64
Jan 16 10:39:18 Installed: centos-release-6-6.el6.centos.12.2.x86_64
Jan 16 10:55:13 Installed: centos-release-6-6.el6.centos.12.2.x86_64
Jan 16 11:11:24 Installed: setup-2.8.14-20.el6_4.1.noarch
Jan 16 11:11:24 Installed: filesystem-2.4.30-3.el6.x86_64
Jan 16 11:11:25 Installed: basesystem-10.0-4.el6.noarch
Jan 16 11:11:25 Installed: tzdata-2014j-1.el6.noarch
Jan 16 11:11:25 Installed: libgcc-4.4.7-11.el6.x86_64
Jan 16 11:11:25 Installed: ncurses-base-5.7-3.20090208.el6.x86_64
Jan 16 11:11:25 Installed: nss-softokn-freebl-3.14.3-19.el6_6.x86_64
Jan 16 11:11:25 Installed: glibc-common-2.12-1.149.el6_6.4.x86_64
Jan 16 11:11:25 Installed: glibc-2.12-1.149.el6_6.4.x86_64
Jan 16 11:11:26 Installed: ncurses-libs-5.7-3.20090208.el6.x86_64
Jan 16 11:11:26 Installed: bash-4.1.2-29.el6.x86_64
Jan 16 11:11:26 Installed: libattr-2.4.44-7.el6.x86_64
Jan 16 11:11:26 Installed: libcap-2.16-5.5.el6.x86_64
Jan 16 11:11:26 Installed: 1:telnet-0.17-48.el6.x86_64
Jan 16 11:13:05 Installed: setup-2.8.14-20.el6_4.1.noarch
Jan 16 11:13:05 Installed: filesystem-2.4.30-3.el6.x86_64
Jan 16 11:13:05 Installed: basesystem-10.0-4.el6.noarch
Jan 16 11:13:05 Installed: tzdata-2014j-1.el6.noarch
Jan 16 11:13:05 Installed: libgcc-4.4.7-11.el6.x86_64
Jan 16 11:13:06 Installed: ncurses-base-5.7-3.20090208.el6.x86_64
Jan 16 11:13:06 Installed: nss-softokn-freebl-3.14.3-19.el6_6.x86_64
Jan 16 11:13:06 Installed: glibc-common-2.12-1.149.el6_6.4.x86_64
Jan 16 11:13:06 Installed: glibc-2.12-1.149.el6_6.4.x86_64
Jan 16 11:13:06 Installed: ncurses-libs-5.7-3.20090208.el6.x86_64
Jan 16 11:13:06 Installed: bash-4.1.2-29.el6.x86_64
Jan 16 11:13:06 Installed: libattr-2.4.44-7.el6.x86_64
Jan 16 11:13:06 Installed: libcap-2.16-5.5.el6.x86_64
Jan 16 11:13:06 Installed: 1:telnet-0.17-48.el6.x86_64
Jan 16 11:14:16 Installed: centos-release-6-6.el6.centos.12.2.x86_64
Jan 16 11:14:59 Installed: centos-release-6-6.el6.centos.12.2.x86_64
Jan 16 11:20:52 Installed: centos-release-6-6.el6.centos.12.2.x86_64
Jan 16 11:24:58 Installed: centos-release-6-6.el6.centos.12.2.x86_64
Jan 17 19:19:07 Installed: basesystem-10.0-4.el6.noarch
Jan 17 19:19:09 Installed: tzdata-2014j-1.el6.noarch
Jan 17 19:19:09 Installed: libgcc-4.4.7-11.el6.x86_64
Jan 17 19:19:10 Installed: ncurses-base-5.7-3.20090208.el6.x86_64
Jan 17 19:19:10 Installed: nss-softokn-freebl-3.14.3-19.el6_6.x86_64
Jan 17 19:19:18 Installed: glibc-common-2.12-1.149.el6_6.4.x86_64
Jan 17 19:19:24 Installed: glibc-2.12-1.149.el6_6.4.x86_64
Jan 17 19:19:25 Installed: ncurses-libs-5.7-3.20090208.el6.x86_64
Jan 17 19:19:26 Installed: bash-4.1.2-29.el6.x86_64
Jan 17 19:19:26 Installed: libattr-2.4.44-7.el6.x86_64
Jan 17 19:19:27 Installed: libcap-2.16-5.5.el6.x86_64
Jan 17 19:20:58 Installed: zlib-1.2.3-29.el6.x86_64
Jan 17 19:20:59 Installed: info-4.13a-8.el6.x86_64
Jan 17 19:20:59 Installed: nspr-4.10.6-1.el6_5.x86_64
Jan 17 19:21:00 Installed: nss-util-3.16.2.3-2.el6_6.x86_64
Jan 17 19:21:01 Installed: db4-4.7.25-18.el6_4.x86_64
Jan 17 19:21:02 Installed: libcom_err-1.41.12-21.el6.x86_64
Jan 17 19:21:02 Installed: readline-6.0-4.el6.x86_64
Jan 17 19:21:03 Installed: libacl-2.2.49-6.el6.x86_64
Jan 17 19:21:04 Installed: bzip2-libs-1.0.5-7.el6_0.x86_64
Jan 17 19:21:04 Installed: libstdc++-4.4.7-11.el6.x86_64
Jan 17 19:21:05 Installed: popt-1.13-7.el6.x86_64
Jan 17 19:21:06 Installed: chkconfig-1.3.49.3-2.el6_4.1.x86_64
Jan 17 19:21:06 Installed: pcre-7.8-6.el6.x86_64
Jan 17 19:21:07 Installed: grep-2.6.3-6.el6.x86_64
Jan 17 19:21:08 Installed: lua-5.1.4-4.1.el6.x86_64
Jan 17 19:21:08 Installed: libidn-1.18-2.el6.x86_64
Jan 17 19:21:09 Installed: file-libs-5.04-21.el6.x86_64
Jan 17 19:21:10 Installed: elfutils-libelf-0.158-3.2.el6.x86_64
Jan 17 19:21:10 Installed: xz-libs-4.999.9-0.5.beta.20091007git.el6.x86_64
Jan 17 19:21:11 Installed: libtasn1-2.3-6.el6_5.x86_64
Jan 17 19:21:12 Installed: p11-kit-0.18.5-2.el6_5.2.x86_64
Jan 17 19:21:13 Installed: libgpg-error-1.7-4.el6.x86_64
Jan 17 19:21:13 Installed: libgcrypt-1.4.5-11.el6_4.x86_64
Jan 17 19:21:14 Installed: p11-kit-trust-0.18.5-2.el6_5.2.x86_64
Jan 17 19:21:16 Installed: ca-certificates-2014.1.98-65.1.el6.noarch
Jan 17 19:21:16 Installed: pinentry-0.7.6-6.el6.x86_64
Jan 17 19:21:17 Installed: gmp-4.3.1-7.el6_2.2.x86_64
Jan 17 19:21:18 Installed: sqlite-3.6.20-1.el6.x86_64
Jan 17 19:21:18 Installed: nss-softokn-3.14.3-19.el6_6.x86_64
Jan 17 19:21:19 Installed: db4-utils-4.7.25-18.el6_4.x86_64
Jan 17 19:21:19 Installed: cyrus-sasl-lib-2.1.23-15.el6_6.1.x86_64
Jan 17 19:21:20 Installed: 1:make-3.81-20.el6.x86_64
Jan 17 19:21:21 Installed: audit-libs-2.3.7-5.el6.x86_64
Jan 17 19:21:21 Installed: ncurses-5.7-3.20090208.el6.x86_64
Jan 17 19:21:22 Installed: pth-2.0.7-9.3.el6.x86_64
Jan 17 19:21:23 Installed: keyutils-libs-1.4-5.el6.x86_64
Jan 17 19:21:23 Installed: libsepol-2.0.41-4.el6.x86_64
Jan 17 19:21:24 Installed: libselinux-2.0.94-5.8.el6.x86_64
Jan 17 19:21:25 Installed: krb5-libs-1.10.3-33.el6.x86_64
Jan 17 19:21:25 Installed: sed-4.2.1-10.el6.x86_64
Jan 17 19:21:27 Installed: groff-1.18.1.4-21.el6.x86_64
Jan 17 19:21:28 Installed: less-436-13.el6.x86_64
Jan 17 19:21:28 Installed: coreutils-libs-8.4-37.el6.x86_64
Jan 17 19:21:29 Installed: gzip-1.3.12-22.el6.x86_64
Jan 17 19:21:30 Installed: cracklib-2.8.16-4.el6.x86_64
Jan 17 19:21:31 Installed: cracklib-dicts-2.8.16-4.el6.x86_64
Jan 17 19:21:33 Installed: coreutils-8.4-37.el6.x86_64
Jan 17 19:21:34 Installed: pam-1.1.1-20.el6.x86_64
Jan 17 19:21:35 Installed: nss-sysinit-3.16.2.3-3.el6_6.x86_64
Jan 17 19:21:36 Installed: nss-3.16.2.3-3.el6_6.x86_64
Jan 17 19:21:37 Installed: nss-tools-3.16.2.3-3.el6_6.x86_64
Jan 17 19:21:38 Installed: openssl-1.0.1e-30.el6_6.4.x86_64
Jan 17 19:21:39 Installed: libssh2-1.4.2-1.el6.x86_64
Jan 17 19:21:39 Installed: libcurl-7.19.7-40.el6_6.3.x86_64
Jan 17 19:21:40 Installed: curl-7.19.7-40.el6_6.3.x86_64
Jan 17 19:21:40 Installed: rpm-libs-4.8.0-38.el6_6.x86_64
Jan 17 19:21:41 Installed: rpm-4.8.0-38.el6_6.x86_64
Jan 17 19:21:42 Installed: openldap-2.4.39-8.el6.x86_64
Jan 17 19:21:43 Installed: gnupg2-2.0.14-8.el6.x86_64
Jan 17 19:25:47 Erased: rpm
Jan 17 19:25:48 Erased: rpm-libs
Jan 17 20:19:15 Installed: libgpg-error-devel-1.7-4.el6.x86_64
Jan 17 20:19:16 Installed: gpgme-devel-1.1.8-3.el6.x86_64
Jan 17 20:19:32 Installed: rpm-libs-4.8.0-37.el6.x86_64
Jan 17 20:19:33 Installed: rpm-4.8.0-37.el6.x86_64
Jan 17 20:19:34 Installed: 2:shadow-utils-4.1.4.2-19.el6.x86_64
Jan 17 20:19:35 Installed: 1:dbus-libs-1.2.24-7.el6_3.x86_64
Jan 17 20:19:35 Installed: sysvinit-tools-2.87-5.dsf.el6.x86_64
Jan 17 20:19:36 Installed: libuuid-2.17.2-12.18.el6.x86_64
Jan 17 20:19:37 Installed: gawk-3.1.7-10.el6.x86_64
Jan 17 20:19:37 Installed: 1:pkgconfig-0.23-9.1.el6.x86_64
Jan 17 20:19:38 Installed: expat-2.0.1-11.el6_2.x86_64
Jan 17 20:19:39 Installed: libxml2-2.7.6-17.el6_6.1.x86_64
Jan 17 20:19:39 Installed: logrotate-3.7.8-17.el6.x86_64
Jan 17 20:19:40 Installed: gamin-0.1.10-9.el6.x86_64
Jan 17 20:19:41 Installed: glib2-2.28.8-4.el6.x86_64
Jan 17 20:19:42 Installed: shared-mime-info-0.70-6.el6.x86_64
Jan 17 20:19:43 Installed: dbus-glib-0.86-6.el6.x86_64
Jan 17 20:19:44 Installed: libblkid-2.17.2-12.18.el6.x86_64
Jan 17 20:19:44 Installed: libnih-1.0.1-7.el6.x86_64
Jan 17 20:19:45 Installed: upstart-0.6.5-13.el6_5.3.x86_64
Jan 17 20:19:46 Installed: libutempter-1.1.5-4.1.el6.x86_64
Jan 17 20:19:47 Installed: MAKEDEV-3.24-6.el6.x86_64
Jan 17 20:19:47 Installed: 1:findutils-4.4.2-6.el6.x86_64
Jan 17 20:19:48 Installed: tcp_wrappers-libs-7.6-57.el6.x86_64
Jan 17 20:19:49 Installed: hesiod-3.1.0-19.el6.x86_64
Jan 17 20:19:49 Installed: libffi-3.0.5-3.2.el6.x86_64
Jan 17 20:19:50 Installed: 2:ethtool-3.5-5.el6.x86_64
Jan 17 20:19:50 Installed: mingetty-1.08-5.el6.x86_64
Jan 17 20:19:51 Installed: popt-devel-1.13-7.el6.x86_64
Jan 17 20:19:51 Installed: checkpolicy-2.0.22-1.el6.x86_64
Jan 17 20:19:52 Installed: libusb-0.1.12-23.el6.x86_64
Jan 17 20:19:53 Installed: binutils-2.20.51.0.2-5.42.el6.x86_64
Jan 17 20:19:55 Installed: module-init-tools-3.9-24.el6.x86_64
Jan 17 20:19:55 Installed: hwdata-0.233-11.1.el6.noarch
Jan 17 20:19:56 Installed: net-tools-1.60-110.el6_2.x86_64
Jan 17 20:19:57 Installed: cpio-2.10-12.el6_5.x86_64
Jan 17 20:19:57 Installed: libselinux-utils-2.0.94-5.8.el6.x86_64
Jan 17 20:19:58 Installed: gdbm-1.8.0-36.el6.x86_64
Jan 17 20:19:59 Installed: python-2.6.6-52.el6.x86_64
Jan 17 20:20:02 Installed: python-libs-2.6.6-52.el6.x86_64
Jan 17 20:20:02 Installed: rpm-python-4.8.0-37.el6.x86_64
Jan 17 20:20:03 Installed: yum-metadata-parser-1.1.2-16.el6.x86_64
Jan 17 20:20:04 Installed: pygpgme-0.1-18.20090824bzr68.el6.x86_64
Jan 17 20:20:05 Installed: python-pycurl-7.19.0-8.el6.x86_64
Jan 17 20:20:06 Installed: python-urlgrabber-3.9.1-9.el6.noarch
Jan 17 20:20:06 Installed: python-iniparse-0.3.1-2.1.el6.noarch
Jan 17 20:20:07 Installed: yum-plugin-fastestmirror-1.1.30-30.el6.noarch
Jan 17 20:20:08 Installed: yum-3.2.29-60.el6.centos.noarch
Jan 17 20:20:09 Installed: procmail-3.22-25.1.el6_5.1.x86_64
Jan 17 20:20:09 Installed: diffutils-2.8.1-28.el6.x86_64
Jan 17 20:20:10 Installed: file-5.04-21.el6.x86_64
Jan 17 20:20:11 Installed: file-devel-5.04-21.el6.x86_64
Jan 17 20:20:11 Installed: ustr-1.0.4-9.1.el6.x86_64
Jan 17 20:20:12 Installed: libsemanage-2.0.43-4.2.el6.x86_64
Jan 17 20:20:12 Installed: psmisc-22.6-19.el6_5.x86_64
Jan 17 20:20:13 Installed: procps-3.2.8-30.el6.x86_64
Jan 17 20:20:14 Installed: policycoreutils-2.0.83-19.47.el6_6.1.x86_64
Jan 17 20:20:15 Installed: iptables-1.4.7-14.el6.x86_64
Jan 17 20:20:16 Installed: iproute-2.6.32-33.el6_6.x86_64
Jan 17 20:20:17 Installed: iputils-20071127-17.el6_4.2.x86_64
Jan 17 20:20:19 Installed: util-linux-ng-2.17.2-12.18.el6.x86_64
Jan 17 20:20:20 Installed: initscripts-9.03.46-1.el6.centos.1.x86_64
Jan 17 20:20:21 Installed: udev-147-2.57.el6.x86_64
Jan 17 20:20:22 Installed: cyrus-sasl-2.1.23-15.el6_6.1.x86_64
Jan 17 20:20:24 Installed: sendmail-8.14.4-8.el6.x86_64
Jan 17 20:20:25 Installed: rsyslog-5.8.10-10.el6_6.x86_64
Jan 17 20:20:26 Installed: crontabs-1.10-33.el6.noarch
Jan 17 20:20:27 Installed: cronie-anacron-1.4.4-12.el6.x86_64
Jan 17 20:20:28 Installed: cronie-1.4.4-12.el6.x86_64
Jan 17 20:20:28 Installed: rpm-cron-4.8.0-37.el6.noarch
Jan 17 20:20:29 Installed: rpm-devel-4.8.0-37.el6.x86_64
Jan 17 20:20:30 Installed: rpm-apidocs-4.8.0-37.el6.noarch
Jan 17 20:20:53 Updated: rpm-4.8.0-38.el6_6.x86_64
Jan 17 20:20:53 Updated: rpm-libs-4.8.0-38.el6_6.x86_64
Jan 17 20:20:54 Updated: rpm-devel-4.8.0-38.el6_6.x86_64
Jan 17 20:20:55 Updated: rpm-python-4.8.0-38.el6_6.x86_64
Jan 17 20:20:55 Updated: rpm-cron-4.8.0-38.el6_6.noarch
Jan 17 20:20:56 Updated: rpm-apidocs-4.8.0-38.el6_6.noarch
Jan 17 20:39:13 Installed: 1:telnet-0.17-48.el6.x86_64
Jan 18 16:42:26 Installed: freetype-2.3.11-14.el6_3.1.x86_64
Jan 18 16:42:29 Installed: fontconfig-2.8.0-5.el6.x86_64
Jan 18 16:42:30 Installed: libjpeg-turbo-1.2.1-3.el6_5.x86_64
Jan 18 16:42:31 Installed: 2:libpng-1.2.49-1.el6_2.x86_64
Jan 18 16:42:31 Installed: 1:perl-Pod-Escapes-1.04-136.el6_6.1.x86_64
Jan 18 16:42:32 Installed: 3:perl-version-0.77-136.el6_6.1.x86_64
Jan 18 16:42:32 Installed: 1:perl-Module-Pluggable-3.90-136.el6_6.1.x86_64
Jan 18 16:42:33 Installed: 4:perl-libs-5.10.1-136.el6_6.1.x86_64
Jan 18 16:42:34 Installed: 1:perl-Pod-Simple-3.13-136.el6_6.1.x86_64
Jan 18 16:42:37 Installed: 4:perl-5.10.1-136.el6_6.1.x86_64
Jan 18 16:42:37 Installed: libX11-common-1.6.0-2.2.el6.noarch
Jan 18 16:42:38 Installed: libXau-1.0.6-4.el6.x86_64
Jan 18 16:42:39 Installed: libxcb-1.9.1-2.el6.x86_64
Jan 18 16:42:40 Installed: libX11-1.6.0-2.2.el6.x86_64
Jan 18 16:42:40 Installed: libXpm-3.5.10-2.el6.x86_64
Jan 18 16:42:41 Installed: gd-2.0.35-11.el6.x86_64
Jan 18 16:42:42 Installed: perl-GD-2.44-3.el6.x86_64
Jan 18 16:42:43 Installed: perl-GDTextUtil-0.86-15.el6.noarch
Jan 18 16:42:44 Installed: 1:perl-GDGraph-1.44-7.el6.noarch
Here are my current installed packages displayed via yum list installed:

Installed Packages

Code: Select all

MAKEDEV.x86_64                  3.24-6.el6                       @base          
audit-libs.x86_64               2.3.7-5.el6                      @base          
basesystem.noarch               10.0-4.el6                       @base          
bash.x86_64                     4.1.2-29.el6                     @/bash-4.1.2-29.el6.x86_64
binutils.x86_64                 2.20.51.0.2-5.42.el6             @base          
bzip2-libs.x86_64               1.0.5-7.el6_0                    @base          
ca-certificates.noarch          2014.1.98-65.1.el6               @base          
centos-release.x86_64           6-6.el6.centos.12.2              @base          
checkpolicy.x86_64              2.0.22-1.el6                     @base          
chkconfig.x86_64                1.3.49.3-2.el6_4.1               @base          
coreutils.x86_64                8.4-37.el6                       @base          
coreutils-libs.x86_64           8.4-37.el6                       @base          
cpio.x86_64                     2.10-12.el6_5                    @base          
cracklib.x86_64                 2.8.16-4.el6                     @base          
cracklib-dicts.x86_64           2.8.16-4.el6                     @base          
cronie.x86_64                   1.4.4-12.el6                     @base          
cronie-anacron.x86_64           1.4.4-12.el6                     @base          
crontabs.noarch                 1.10-33.el6                      @base          
curl.x86_64                     7.19.7-40.el6_6.3                @updates       
cyrus-sasl.x86_64               2.1.23-15.el6_6.1                @updates       
cyrus-sasl-lib.x86_64           2.1.23-15.el6_6.1                @updates       
db4.x86_64                      4.7.25-18.el6_4                  @base          
db4-utils.x86_64                4.7.25-18.el6_4                  @base          
dbus-glib.x86_64                0.86-6.el6                       @base          
dbus-libs.x86_64                1:1.2.24-7.el6_3                 @base          
diffutils.x86_64                2.8.1-28.el6                     @base          
elfutils-libelf.x86_64          0.158-3.2.el6                    @base          
ethtool.x86_64                  2:3.5-5.el6                      @base          
expat.x86_64                    2.0.1-11.el6_2                   @base          
file.x86_64                     5.04-21.el6                      @base          
file-devel.x86_64               5.04-21.el6                      @base          
file-libs.x86_64                5.04-21.el6                      @base          
filesystem.x86_64               2.4.30-3.el6                     @anaconda-CentOS-201303020151.x86_64/6.4
findutils.x86_64                1:4.4.2-6.el6                    @base          
fontconfig.x86_64               2.8.0-5.el6                      @base          
freetype.x86_64                 2.3.11-14.el6_3.1                @base          
gamin.x86_64                    0.1.10-9.el6                     @base          
gawk.x86_64                     3.1.7-10.el6                     @base          
gd.x86_64                       2.0.35-11.el6                    @base          
gdbm.x86_64                     1.8.0-36.el6                     @base          
glib2.x86_64                    2.28.8-4.el6                     @base          
glibc.x86_64                    2.12-1.149.el6_6.4               @updates       
glibc-common.x86_64             2.12-1.149.el6_6.4               @updates       
gmp.x86_64                      4.3.1-7.el6_2.2                  @base          
gnupg2.x86_64                   2.0.14-8.el6                     @/gnupg2-2.0.14-8.el6.x86_64
gpgme.x86_64                    1.1.8-3.el6                      @anaconda-CentOS-201303020151.x86_64/6.4
gpgme-devel.x86_64              1.1.8-3.el6                      @/gpgme-devel-1.1.8-3.el6.x86_64
grep.x86_64                     2.6.3-6.el6                      @base          
groff.x86_64                    1.18.1.4-21.el6                  @base          
gzip.x86_64                     1.3.12-22.el6                    @base          
hesiod.x86_64                   3.1.0-19.el6                     @base          
hwdata.noarch                   0.233-11.1.el6                   @base          
info.x86_64                     4.13a-8.el6                      @base          
initscripts.x86_64              9.03.46-1.el6.centos.1           @updates       
iproute.x86_64                  2.6.32-33.el6_6                  @updates       
iptables.x86_64                 1.4.7-14.el6                     @base          
iputils.x86_64                  20071127-17.el6_4.2              @base          
keyutils-libs.x86_64            1.4-5.el6                        @base          
krb5-libs.x86_64                1.10.3-33.el6                    @base          
less.x86_64                     436-13.el6                       @base          
libX11.x86_64                   1.6.0-2.2.el6                    @base          
libX11-common.noarch            1.6.0-2.2.el6                    @base          
libXau.x86_64                   1.0.6-4.el6                      @base          
libXpm.x86_64                   3.5.10-2.el6                     @base          
libacl.x86_64                   2.2.49-6.el6                     @base          
libattr.x86_64                  2.4.44-7.el6                     @base          
libblkid.x86_64                 2.17.2-12.18.el6                 @base          
libcap.x86_64                   2.16-5.5.el6                     @base          
libcom_err.x86_64               1.41.12-21.el6                   @base          
libcurl.x86_64                  7.19.7-40.el6_6.3                @updates       
libffi.x86_64                   3.0.5-3.2.el6                    @base          
libgcc.x86_64                   4.4.7-11.el6                     @base          
libgcrypt.x86_64                1.4.5-11.el6_4                   @base          
libgpg-error.x86_64             1.7-4.el6                        @base          
libgpg-error-devel.x86_64       1.7-4.el6                        @base          
libidn.x86_64                   1.18-2.el6                       @base          
libjpeg-turbo.x86_64            1.2.1-3.el6_5                    @base          
libnih.x86_64                   1.0.1-7.el6                      @base          
libpng.x86_64                   2:1.2.49-1.el6_2                 @base          
libselinux.x86_64               2.0.94-5.8.el6                   @base          
libselinux-utils.x86_64         2.0.94-5.8.el6                   @base          
libsemanage.x86_64              2.0.43-4.2.el6                   @base          
libsepol.x86_64                 2.0.41-4.el6                     @base          
libssh2.x86_64                  1.4.2-1.el6                      @base          
libstdc++.x86_64                4.4.7-11.el6                     @base          
libtasn1.x86_64                 2.3-6.el6_5                      @base          
libusb.x86_64                   0.1.12-23.el6                    @base          
libutempter.x86_64              1.1.5-4.1.el6                    @base          
libuuid.x86_64                  2.17.2-12.18.el6                 @base          
libxcb.x86_64                   1.9.1-2.el6                      @base          
libxml2.x86_64                  2.7.6-17.el6_6.1                 @updates       
logrotate.x86_64                3.7.8-17.el6                     @base          
lua.x86_64                      5.1.4-4.1.el6                    @base          
make.x86_64                     1:3.81-20.el6                    @base          
mingetty.x86_64                 1.08-5.el6                       @base          
module-init-tools.x86_64        3.9-24.el6                       @base          
ncurses.x86_64                  5.7-3.20090208.el6               @base          
ncurses-base.x86_64             5.7-3.20090208.el6               @base          
ncurses-libs.x86_64             5.7-3.20090208.el6               @base          
net-tools.x86_64                1.60-110.el6_2                   @base          
nspr.x86_64                     4.10.6-1.el6_5                   @base          
nss.x86_64                      3.16.2.3-3.el6_6                 @updates       
nss-softokn.x86_64              3.14.3-19.el6_6                  @updates       
nss-softokn-freebl.x86_64       3.14.3-19.el6_6                  @updates       
nss-sysinit.x86_64              3.16.2.3-3.el6_6                 @updates       
nss-tools.x86_64                3.16.2.3-3.el6_6                 @updates       
nss-util.x86_64                 3.16.2.3-2.el6_6                 @updates       
openldap.x86_64                 2.4.39-8.el6                     @base          
openssl.x86_64                  1.0.1e-30.el6_6.4                @updates       
p11-kit.x86_64                  0.18.5-2.el6_5.2                 @base          
p11-kit-trust.x86_64            0.18.5-2.el6_5.2                 @base          
pam.x86_64                      1.1.1-20.el6                     @base          
pcre.x86_64                     7.8-6.el6                        @base          
perl.x86_64                     4:5.10.1-136.el6_6.1             @updates       
perl-GD.x86_64                  2.44-3.el6                       @base          
perl-GDGraph.noarch             1:1.44-7.el6                     @base          
perl-GDTextUtil.noarch          0.86-15.el6                      @base          
perl-Module-Pluggable.x86_64    1:3.90-136.el6_6.1               @updates       
perl-Pod-Escapes.x86_64         1:1.04-136.el6_6.1               @updates       
perl-Pod-Simple.x86_64          1:3.13-136.el6_6.1               @updates       
perl-libs.x86_64                4:5.10.1-136.el6_6.1             @updates       
perl-version.x86_64             3:0.77-136.el6_6.1               @updates       
pinentry.x86_64                 0.7.6-6.el6                      @base          
pkgconfig.x86_64                1:0.23-9.1.el6                   @base          
policycoreutils.x86_64          2.0.83-19.47.el6_6.1             @updates       
popt.x86_64                     1.13-7.el6                       @base          
popt-devel.x86_64               1.13-7.el6                       @base          
procmail.x86_64                 3.22-25.1.el6_5.1                @base          
procps.x86_64                   3.2.8-30.el6                     @base          
psmisc.x86_64                   22.6-19.el6_5                    @base          
pth.x86_64                      2.0.7-9.3.el6                    @base          
pygpgme.x86_64                  0.1-18.20090824bzr68.el6         @/pygpgme-0.1-18.20090824bzr68.el6.x86_64
python.x86_64                   2.6.6-52.el6                     @base          
python-iniparse.noarch          0.3.1-2.1.el6                    @/python-iniparse-0.3.1-2.1.el6.noarch
python-libs.x86_64              2.6.6-52.el6                     @base          
python-pycurl.x86_64            7.19.0-8.el6                     @/python-pycurl-7.19.0-8.el6.x86_64
python-urlgrabber.noarch        3.9.1-9.el6                      @/python-urlgrabber-3.9.1-9.el6.noarch
readline.x86_64                 6.0-4.el6                        @base          
rpm.x86_64                      4.8.0-38.el6_6                   @updates       
rpm-apidocs.noarch              4.8.0-38.el6_6                   @updates       
rpm-cron.noarch                 4.8.0-38.el6_6                   @updates       
rpm-devel.x86_64                4.8.0-38.el6_6                   @updates       
rpm-libs.x86_64                 4.8.0-38.el6_6                   @updates       
rpm-python.x86_64               4.8.0-38.el6_6                   @updates       
rsyslog.x86_64                  5.8.10-10.el6_6                  @updates       
sed.x86_64                      4.2.1-10.el6                     @base          
sendmail.x86_64                 8.14.4-8.el6                     @base          
setup.noarch                    2.8.14-20.el6_4.1                @updates       
shadow-utils.x86_64             2:4.1.4.2-19.el6                 @base          
shared-mime-info.x86_64         0.70-6.el6                       @base          
sqlite.x86_64                   3.6.20-1.el6                     @base          
sysvinit-tools.x86_64           2.87-5.dsf.el6                   @base          
tcp_wrappers-libs.x86_64        7.6-57.el6                       @base          
telnet.x86_64                   1:0.17-48.el6                    @base          
tzdata.noarch                   2014j-1.el6                      @updates       
udev.x86_64                     147-2.57.el6                     @base          
upstart.x86_64                  0.6.5-13.el6_5.3                 @base          
ustr.x86_64                     1.0.4-9.1.el6                    @base          
util-linux-ng.x86_64            2.17.2-12.18.el6                 @base          
xz-libs.x86_64                  4.999.9-0.5.beta.20091007git.el6 @base          
yum.noarch                      3.2.29-60.el6.centos             @/yum-3.2.29-60.el6.centos.noarch
yum-metadata-parser.x86_64      1.1.2-16.el6                     @/yum-metadata-parser-1.1.2-16.el6.x86_64
yum-plugin-fastestmirror.noarch 1.1.30-30.el6                    @/yum-plugin-fastestmirror-1.1.30-30.el6.noarch
zlib.x86_64                     1.2.3-29.el6                     @base    
From you can tell from the list of installed packages, packages like php, httpd are not listed and they actually are on the server if for example I would do php-v gives me:

Code: Select all

PHP 5.3.3 (cli) (built: Oct 30 2014 20:12:53) 
Copyright (c) 1997-2010 The PHP Group
Zend Engine v2.3.0, Copyright (c) 1998-2010 Zend Technologies
Will running the command rpm --rebuilddb possibly rebuild the database and have all actual packages that are installed on the system by displayed when doing yum list installed?

Thanks guys, really appreciate your help. :)

User avatar
TrevorH
Forum Moderator
Posts: 25847
Joined: 2009/09/24 10:40:56
Location: Brighton, UK

Re: YUM update error; nss bug

Post by TrevorH » 2015/01/19 23:41:26

No. You need to parse yum.log and extract the package names from it without the version numbers etc. The compare that list with the currently installed rpms using e.g rpm -qa --qf '%{name}\n' and get a list of the ones in yum.log that are missing from the installed system. Then you can do, for example, rpm -qc httpd to get a list of the config files it provides and back those up before you reinstall it.
CentOS 5 died in March 2017 - migrate NOW!
Full time Geek, part time moderator. Use the FAQ Luke

User avatar
avij
Forum Moderator
Posts: 2965
Joined: 2010/12/01 19:25:52
Location: Helsinki, Finland
Contact:

Re: YUM update error; nss bug

Post by avij » 2015/01/20 01:29:11

WARNING -- untested commands ahead -- WARNING
WARNING -- make a backup of ALL files you care about before trying this -- WARNING


First make sure you have actually fixed the nss-softokn problem so that the system has the required libfreeblpriv3.* files in the correct location.

At this stage you can try rpm -qa to see if it lists a few pages of installed packages. If it does, congratulations, your rpm database is most probably fine and you can stop here.

If you have tried to rebuild the rpm database WITHOUT first copying the libfreeblpriv3.* files to their proper location, it's possible that your rpm database is now empty. Sorry. The rpm database is the place where the system keeps track of which packages have been installed. If that database is damaged, there is no (certain) way to determine which packages you have installed, and thus fully automatic recovery is not feasible.

You can start the recovery by adding the centos-release package to the database. It will (probably) make yum work again, which can help with the next tasks. For x86_64, run curl -O http://mirror.centos.org/centos/6/os/x8 ... x86_64.rpm to download the centos-release file. For i386, use http://mirror.centos.org/centos/6/os/i3 ... 2.i686.rpm instead. After you have downloaded the file, run rpm -i --nodeps --noscripts --notriggers --excludepath / centos-release-6-6.el6.centos.12.2.*.rpm to add centos-release to the rpm database. --nodeps means it ignores any errors about missing dependencies, --noscripts means it won't execute any installation scripts in the package and --notriggers disables any commands that are normally executed before or after package installation. --excludepath / (notice the slash at the end) will make rpm not create any pathnames that start with a /, ie. all files.

You can use the next steps to determine which packages you may have installed in the past or during initial install. However, this method does not tell you which version of the package you have installed. If you have kept your system mostly up-to-date and were running CentOS 6.6, you can start with 6.6 GA versions of the packages (ie. those that reside in 'os', not 'updates') and then finally install the updates. Edit /etc/yum.repos.d/CentOS-Base.repo and add/change enabled=0 to the [updates] section.

At this stage you should be able to run yum whatprovides /bin/bash to see that the file is provided by a package named "bash". For subsequent queries you can add the -C parameter to run entirely from cache. This may speed up the process a bit.

Now that you know which package you need to add (like bash in this example), run yum install --setopt=tsflags=justdb bash to download bash and any of its dependencies, and with the magic of the setopt=tsflags=justdb option, the change is made only to the rpm database and not to files on filesystem.

Rinse and repeat. Finally edit /etc/yum.repos.d/CentOS-Base.repo again and re-enable [updates], then run yum update to (re)install the updates. You can also use rpm -Va to check that your rpm database matches the installed files on your system.

Please note that this process works relatively OK for CentOS without any third party repositories. Repositories which do not overwrite CentOS files (such as EPEL) should not cause that much headache either. If you have used EPEL, you can reinstall the EPEL repository with yum install --setopt=tsflags=justdb epel-release.

Third-party repositories which overwrite CentOS packages will be problematic. For example, if your MySQL package was not provided by CentOS, your MySQL database may end up getting totally *cked up if you install an incorrect version of MySQL. But fortunately you made a backup of all the files you care about, right? I told you to do that at the beginning of this message. The same goes for PHP and Apache. Many users using "web control panels" are in this situation. If you are even a little bit unsure about this, ASK your provider first if it's OK to follow these instructions, or tell them to fix the situation for you.

I know these instructions are not complete. I did not write these to cover all possible cases that you might run into. Some independent thinking will be required.

I have not tried these instructions myself. I only looked up the manual pages of the appropriate commands and came up with these instructions. Anybody else could have done that (that's the "community" aspect). Hopefully these will be of help to someone, but I (or the CentOS Linux Project) will not be held liable if there are errors in these instructions, causing your corporation billions of damages or the loss of your pet boa constrictor.

DonX
Posts: 33
Joined: 2014/11/05 07:24:54
Location: Michigan
Contact:

Re: YUM update error; nss bug

Post by DonX » 2015/01/20 08:06:25

Wow! a huge thank you to avij for the very helpful and informative post and of course to TrevorH and gerald_clark for their help!

I was able to get php, httpd and mysql back into the rpm db list:

rpm -qa output: (new packages at the bottom. Well not necessarily "new" but back in the rpm db :D )

Code: Select all

setup-2.8.14-20.el6_4.1.noarch
gpg-pubkey-c105b9de-4e0fd3a3
tzdata-2014j-1.el6.noarch
ncurses-base-5.7-3.20090208.el6.x86_64
glibc-common-2.12-1.149.el6_6.4.x86_64
ncurses-libs-5.7-3.20090208.el6.x86_64
libattr-2.4.44-7.el6.x86_64
zlib-1.2.3-29.el6.x86_64
nspr-4.10.6-1.el6_5.x86_64
db4-4.7.25-18.el6_4.x86_64
readline-6.0-4.el6.x86_64
bzip2-libs-1.0.5-7.el6_0.x86_64
popt-1.13-7.el6.x86_64
pcre-7.8-6.el6.x86_64
lua-5.1.4-4.1.el6.x86_64
file-libs-5.04-21.el6.x86_64
xz-libs-4.999.9-0.5.beta.20091007git.el6.x86_64
p11-kit-0.18.5-2.el6_5.2.x86_64
libgcrypt-1.4.5-11.el6_4.x86_64
ca-certificates-2014.1.98-65.1.el6.noarch
gmp-4.3.1-7.el6_2.2.x86_64
nss-softokn-3.14.3-19.el6_6.x86_64
cyrus-sasl-lib-2.1.23-15.el6_6.1.x86_64
audit-libs-2.3.7-5.el6.x86_64
pth-2.0.7-9.3.el6.x86_64
libsepol-2.0.41-4.el6.x86_64
krb5-libs-1.10.3-33.el6.x86_64
groff-1.18.1.4-21.el6.x86_64
coreutils-libs-8.4-37.el6.x86_64
cracklib-2.8.16-4.el6.x86_64
coreutils-8.4-37.el6.x86_64
nss-sysinit-3.16.2.3-3.el6_6.x86_64
nss-tools-3.16.2.3-3.el6_6.x86_64
libssh2-1.4.2-1.el6.x86_64
curl-7.19.7-40.el6_6.3.x86_64
gnupg2-2.0.14-8.el6.x86_64
libgpg-error-devel-1.7-4.el6.x86_64
shadow-utils-4.1.4.2-19.el6.x86_64
sysvinit-tools-2.87-5.dsf.el6.x86_64
gawk-3.1.7-10.el6.x86_64
expat-2.0.1-11.el6_2.x86_64
logrotate-3.7.8-17.el6.x86_64
glib2-2.28.8-4.el6.x86_64
dbus-glib-0.86-6.el6.x86_64
libnih-1.0.1-7.el6.x86_64
libutempter-1.1.5-4.1.el6.x86_64
findutils-4.4.2-6.el6.x86_64
hesiod-3.1.0-19.el6.x86_64
ethtool-3.5-5.el6.x86_64
popt-devel-1.13-7.el6.x86_64
libusb-0.1.12-23.el6.x86_64
module-init-tools-3.9-24.el6.x86_64
net-tools-1.60-110.el6_2.x86_64
libselinux-utils-2.0.94-5.8.el6.x86_64
python-2.6.6-52.el6.x86_64
pygpgme-0.1-18.20090824bzr68.el6.x86_64
python-urlgrabber-3.9.1-9.el6.noarch
yum-plugin-fastestmirror-1.1.30-30.el6.noarch
procmail-3.22-25.1.el6_5.1.x86_64
file-5.04-21.el6.x86_64
ustr-1.0.4-9.1.el6.x86_64
psmisc-22.6-19.el6_5.x86_64
policycoreutils-2.0.83-19.47.el6_6.1.x86_64
iproute-2.6.32-33.el6_6.x86_64
util-linux-ng-2.17.2-12.18.el6.x86_64
udev-147-2.57.el6.x86_64
sendmail-8.14.4-8.el6.x86_64
crontabs-1.10-33.el6.noarch
cronie-1.4.4-12.el6.x86_64
rpm-4.8.0-38.el6_6.x86_64
rpm-devel-4.8.0-38.el6_6.x86_64
rpm-cron-4.8.0-38.el6_6.noarch
telnet-0.17-48.el6.x86_64
fontconfig-2.8.0-5.el6.x86_64
libpng-1.2.49-1.el6_2.x86_64
perl-version-0.77-136.el6_6.1.x86_64
perl-libs-5.10.1-136.el6_6.1.x86_64
perl-5.10.1-136.el6_6.1.x86_64
libXau-1.0.6-4.el6.x86_64
libX11-1.6.0-2.2.el6.x86_64
gd-2.0.35-11.el6.x86_64
perl-GDTextUtil-0.86-15.el6.noarch
apr-1.3.9-5.el6_2.x86_64
apr-util-ldap-1.3.9-3.el6_0.1.x86_64
redhat-logos-60.0.14-12.el6.centos.noarch
libedit-2.11-4.20080712cvs.1.el6.x86_64
php-cli-5.3.3-40.el6_6.x86_64
mysql-libs-5.1.73-3.el6_5.x86_64
centos-release-6-6.el6.centos.12.2.x86_64
filesystem-2.4.30-3.el6.x86_64
basesystem-10.0-4.el6.noarch
libgcc-4.4.7-11.el6.x86_64
nss-softokn-freebl-3.14.3-19.el6_6.x86_64
glibc-2.12-1.149.el6_6.4.x86_64
bash-4.1.2-29.el6.x86_64
libcap-2.16-5.5.el6.x86_64
info-4.13a-8.el6.x86_64
nss-util-3.16.2.3-2.el6_6.x86_64
libcom_err-1.41.12-21.el6.x86_64
libacl-2.2.49-6.el6.x86_64
libstdc++-4.4.7-11.el6.x86_64
chkconfig-1.3.49.3-2.el6_4.1.x86_64
grep-2.6.3-6.el6.x86_64
libidn-1.18-2.el6.x86_64
elfutils-libelf-0.158-3.2.el6.x86_64
libtasn1-2.3-6.el6_5.x86_64
libgpg-error-1.7-4.el6.x86_64
p11-kit-trust-0.18.5-2.el6_5.2.x86_64
pinentry-0.7.6-6.el6.x86_64
sqlite-3.6.20-1.el6.x86_64
db4-utils-4.7.25-18.el6_4.x86_64
make-3.81-20.el6.x86_64
ncurses-5.7-3.20090208.el6.x86_64
keyutils-libs-1.4-5.el6.x86_64
libselinux-2.0.94-5.8.el6.x86_64
sed-4.2.1-10.el6.x86_64
less-436-13.el6.x86_64
gzip-1.3.12-22.el6.x86_64
cracklib-dicts-2.8.16-4.el6.x86_64
pam-1.1.1-20.el6.x86_64
nss-3.16.2.3-3.el6_6.x86_64
openssl-1.0.1e-30.el6_6.4.x86_64
libcurl-7.19.7-40.el6_6.3.x86_64
openldap-2.4.39-8.el6.x86_64
gpgme-1.1.8-3.el6.x86_64
gpgme-devel-1.1.8-3.el6.x86_64
dbus-libs-1.2.24-7.el6_3.x86_64
libuuid-2.17.2-12.18.el6.x86_64
pkgconfig-0.23-9.1.el6.x86_64
libxml2-2.7.6-17.el6_6.1.x86_64
gamin-0.1.10-9.el6.x86_64
shared-mime-info-0.70-6.el6.x86_64
libblkid-2.17.2-12.18.el6.x86_64
upstart-0.6.5-13.el6_5.3.x86_64
MAKEDEV-3.24-6.el6.x86_64
tcp_wrappers-libs-7.6-57.el6.x86_64
libffi-3.0.5-3.2.el6.x86_64
mingetty-1.08-5.el6.x86_64
checkpolicy-2.0.22-1.el6.x86_64
binutils-2.20.51.0.2-5.42.el6.x86_64
hwdata-0.233-11.1.el6.noarch
cpio-2.10-12.el6_5.x86_64
gdbm-1.8.0-36.el6.x86_64
python-libs-2.6.6-52.el6.x86_64
yum-metadata-parser-1.1.2-16.el6.x86_64
python-pycurl-7.19.0-8.el6.x86_64
python-iniparse-0.3.1-2.1.el6.noarch
yum-3.2.29-60.el6.centos.noarch
diffutils-2.8.1-28.el6.x86_64
file-devel-5.04-21.el6.x86_64
libsemanage-2.0.43-4.2.el6.x86_64
procps-3.2.8-30.el6.x86_64
iptables-1.4.7-14.el6.x86_64
iputils-20071127-17.el6_4.2.x86_64
initscripts-9.03.46-1.el6.centos.1.x86_64
cyrus-sasl-2.1.23-15.el6_6.1.x86_64
rsyslog-5.8.10-10.el6_6.x86_64
cronie-anacron-1.4.4-12.el6.x86_64
rpm-libs-4.8.0-38.el6_6.x86_64
rpm-python-4.8.0-38.el6_6.x86_64
rpm-apidocs-4.8.0-38.el6_6.noarch
freetype-2.3.11-14.el6_3.1.x86_64
libjpeg-turbo-1.2.1-3.el6_5.x86_64
perl-Pod-Escapes-1.04-136.el6_6.1.x86_64
perl-Module-Pluggable-3.90-136.el6_6.1.x86_64
perl-Pod-Simple-3.13-136.el6_6.1.x86_64
libX11-common-1.6.0-2.2.el6.noarch
libxcb-1.9.1-2.el6.x86_64
libXpm-3.5.10-2.el6.x86_64
perl-GD-2.44-3.el6.x86_64
perl-GDGraph-1.44-7.el6.noarch
apr-util-1.3.9-3.el6_0.1.x86_64
httpd-tools-2.2.15-39.el6.centos.x86_64
mailcap-2.1.31-2.el6.noarch
httpd-2.2.15-39.el6.centos.x86_64
php-common-5.3.3-40.el6_6.x86_64
php-5.3.3-40.el6_6.x86_64
mysql-5.1.73-3.el6_5.x86_64
yum list installed output:

Code: Select all

MAKEDEV.x86_64                  3.24-6.el6                       @base          
apr.x86_64                      1.3.9-5.el6_2                    @base          
apr-util.x86_64                 1.3.9-3.el6_0.1                  @base          
apr-util-ldap.x86_64            1.3.9-3.el6_0.1                  @base          
audit-libs.x86_64               2.3.7-5.el6                      @base          
basesystem.noarch               10.0-4.el6                       @base          
bash.x86_64                     4.1.2-29.el6                     @/bash-4.1.2-29.el6.x86_64
binutils.x86_64                 2.20.51.0.2-5.42.el6             @base          
bzip2-libs.x86_64               1.0.5-7.el6_0                    @base          
ca-certificates.noarch          2014.1.98-65.1.el6               @base          
centos-release.x86_64           6-6.el6.centos.12.2              @base          
checkpolicy.x86_64              2.0.22-1.el6                     @base          
chkconfig.x86_64                1.3.49.3-2.el6_4.1               @base          
coreutils.x86_64                8.4-37.el6                       @base          
coreutils-libs.x86_64           8.4-37.el6                       @base          
cpio.x86_64                     2.10-12.el6_5                    @base          
cracklib.x86_64                 2.8.16-4.el6                     @base          
cracklib-dicts.x86_64           2.8.16-4.el6                     @base          
cronie.x86_64                   1.4.4-12.el6                     @base          
cronie-anacron.x86_64           1.4.4-12.el6                     @base          
crontabs.noarch                 1.10-33.el6                      @base          
curl.x86_64                     7.19.7-40.el6_6.3                @updates       
cyrus-sasl.x86_64               2.1.23-15.el6_6.1                @updates       
cyrus-sasl-lib.x86_64           2.1.23-15.el6_6.1                @updates       
db4.x86_64                      4.7.25-18.el6_4                  @base          
db4-utils.x86_64                4.7.25-18.el6_4                  @base          
dbus-glib.x86_64                0.86-6.el6                       @base          
dbus-libs.x86_64                1:1.2.24-7.el6_3                 @base          
diffutils.x86_64                2.8.1-28.el6                     @base          
elfutils-libelf.x86_64          0.158-3.2.el6                    @base          
ethtool.x86_64                  2:3.5-5.el6                      @base          
expat.x86_64                    2.0.1-11.el6_2                   @base          
file.x86_64                     5.04-21.el6                      @base          
file-devel.x86_64               5.04-21.el6                      @base          
file-libs.x86_64                5.04-21.el6                      @base          
filesystem.x86_64               2.4.30-3.el6                     @anaconda-CentOS-201303020151.x86_64/6.4
findutils.x86_64                1:4.4.2-6.el6                    @base          
fontconfig.x86_64               2.8.0-5.el6                      @base          
freetype.x86_64                 2.3.11-14.el6_3.1                @base          
gamin.x86_64                    0.1.10-9.el6                     @base          
gawk.x86_64                     3.1.7-10.el6                     @base          
gd.x86_64                       2.0.35-11.el6                    @base          
gdbm.x86_64                     1.8.0-36.el6                     @base          
glib2.x86_64                    2.28.8-4.el6                     @base          
glibc.x86_64                    2.12-1.149.el6_6.4               @updates       
glibc-common.x86_64             2.12-1.149.el6_6.4               @updates       
gmp.x86_64                      4.3.1-7.el6_2.2                  @base          
gnupg2.x86_64                   2.0.14-8.el6                     @/gnupg2-2.0.14-8.el6.x86_64
gpgme.x86_64                    1.1.8-3.el6                      @anaconda-CentOS-201303020151.x86_64/6.4
gpgme-devel.x86_64              1.1.8-3.el6                      @/gpgme-devel-1.1.8-3.el6.x86_64
grep.x86_64                     2.6.3-6.el6                      @base          
groff.x86_64                    1.18.1.4-21.el6                  @base          
gzip.x86_64                     1.3.12-22.el6                    @base          
hesiod.x86_64                   3.1.0-19.el6                     @base          
httpd.x86_64                    2.2.15-39.el6.centos             @base          
httpd-tools.x86_64              2.2.15-39.el6.centos             @base          
hwdata.noarch                   0.233-11.1.el6                   @base          
info.x86_64                     4.13a-8.el6                      @base          
initscripts.x86_64              9.03.46-1.el6.centos.1           @updates       
iproute.x86_64                  2.6.32-33.el6_6                  @updates       
iptables.x86_64                 1.4.7-14.el6                     @base          
iputils.x86_64                  20071127-17.el6_4.2              @base          
keyutils-libs.x86_64            1.4-5.el6                        @base          
krb5-libs.x86_64                1.10.3-33.el6                    @base          
less.x86_64                     436-13.el6                       @base          
libX11.x86_64                   1.6.0-2.2.el6                    @base          
libX11-common.noarch            1.6.0-2.2.el6                    @base          
libXau.x86_64                   1.0.6-4.el6                      @base          
libXpm.x86_64                   3.5.10-2.el6                     @base          
libacl.x86_64                   2.2.49-6.el6                     @base          
libattr.x86_64                  2.4.44-7.el6                     @base          
libblkid.x86_64                 2.17.2-12.18.el6                 @base          
libcap.x86_64                   2.16-5.5.el6                     @base          
libcom_err.x86_64               1.41.12-21.el6                   @base          
libcurl.x86_64                  7.19.7-40.el6_6.3                @updates       
libedit.x86_64                  2.11-4.20080712cvs.1.el6         @base          
libffi.x86_64                   3.0.5-3.2.el6                    @base          
libgcc.x86_64                   4.4.7-11.el6                     @base          
libgcrypt.x86_64                1.4.5-11.el6_4                   @base          
libgpg-error.x86_64             1.7-4.el6                        @base          
libgpg-error-devel.x86_64       1.7-4.el6                        @base          
libidn.x86_64                   1.18-2.el6                       @base          
libjpeg-turbo.x86_64            1.2.1-3.el6_5                    @base          
libnih.x86_64                   1.0.1-7.el6                      @base          
libpng.x86_64                   2:1.2.49-1.el6_2                 @base          
libselinux.x86_64               2.0.94-5.8.el6                   @base          
libselinux-utils.x86_64         2.0.94-5.8.el6                   @base          
libsemanage.x86_64              2.0.43-4.2.el6                   @base          
libsepol.x86_64                 2.0.41-4.el6                     @base          
libssh2.x86_64                  1.4.2-1.el6                      @base          
libstdc++.x86_64                4.4.7-11.el6                     @base          
libtasn1.x86_64                 2.3-6.el6_5                      @base          
libusb.x86_64                   0.1.12-23.el6                    @base          
libutempter.x86_64              1.1.5-4.1.el6                    @base          
libuuid.x86_64                  2.17.2-12.18.el6                 @base          
libxcb.x86_64                   1.9.1-2.el6                      @base          
libxml2.x86_64                  2.7.6-17.el6_6.1                 @updates       
logrotate.x86_64                3.7.8-17.el6                     @base          
lua.x86_64                      5.1.4-4.1.el6                    @base          
mailcap.noarch                  2.1.31-2.el6                     @base          
make.x86_64                     1:3.81-20.el6                    @base          
mingetty.x86_64                 1.08-5.el6                       @base          
module-init-tools.x86_64        3.9-24.el6                       @base          
mysql.x86_64                    5.1.73-3.el6_5                   @base          
mysql-libs.x86_64               5.1.73-3.el6_5                   @base          
ncurses.x86_64                  5.7-3.20090208.el6               @base          
ncurses-base.x86_64             5.7-3.20090208.el6               @base          
ncurses-libs.x86_64             5.7-3.20090208.el6               @base          
net-tools.x86_64                1.60-110.el6_2                   @base          
nspr.x86_64                     4.10.6-1.el6_5                   @base          
nss.x86_64                      3.16.2.3-3.el6_6                 @updates       
nss-softokn.x86_64              3.14.3-19.el6_6                  @updates       
nss-softokn-freebl.x86_64       3.14.3-19.el6_6                  @updates       
nss-sysinit.x86_64              3.16.2.3-3.el6_6                 @updates       
nss-tools.x86_64                3.16.2.3-3.el6_6                 @updates       
nss-util.x86_64                 3.16.2.3-2.el6_6                 @updates       
openldap.x86_64                 2.4.39-8.el6                     @base          
openssl.x86_64                  1.0.1e-30.el6_6.4                @updates       
p11-kit.x86_64                  0.18.5-2.el6_5.2                 @base          
p11-kit-trust.x86_64            0.18.5-2.el6_5.2                 @base          
pam.x86_64                      1.1.1-20.el6                     @base          
pcre.x86_64                     7.8-6.el6                        @base          
perl.x86_64                     4:5.10.1-136.el6_6.1             @updates       
perl-GD.x86_64                  2.44-3.el6                       @base          
perl-GDGraph.noarch             1:1.44-7.el6                     @base          
perl-GDTextUtil.noarch          0.86-15.el6                      @base          
perl-Module-Pluggable.x86_64    1:3.90-136.el6_6.1               @updates       
perl-Pod-Escapes.x86_64         1:1.04-136.el6_6.1               @updates       
perl-Pod-Simple.x86_64          1:3.13-136.el6_6.1               @updates       
perl-libs.x86_64                4:5.10.1-136.el6_6.1             @updates       
perl-version.x86_64             3:0.77-136.el6_6.1               @updates       
php.x86_64                      5.3.3-40.el6_6                   @updates       
php-cli.x86_64                  5.3.3-40.el6_6                   @updates       
php-common.x86_64               5.3.3-40.el6_6                   @updates       
pinentry.x86_64                 0.7.6-6.el6                      @base          
pkgconfig.x86_64                1:0.23-9.1.el6                   @base          
policycoreutils.x86_64          2.0.83-19.47.el6_6.1             @updates       
popt.x86_64                     1.13-7.el6                       @base          
popt-devel.x86_64               1.13-7.el6                       @base          
procmail.x86_64                 3.22-25.1.el6_5.1                @base          
procps.x86_64                   3.2.8-30.el6                     @base          
psmisc.x86_64                   22.6-19.el6_5                    @base          
pth.x86_64                      2.0.7-9.3.el6                    @base          
pygpgme.x86_64                  0.1-18.20090824bzr68.el6         @/pygpgme-0.1-18.20090824bzr68.el6.x86_64
python.x86_64                   2.6.6-52.el6                     @base          
python-iniparse.noarch          0.3.1-2.1.el6                    @/python-iniparse-0.3.1-2.1.el6.noarch
python-libs.x86_64              2.6.6-52.el6                     @base          
python-pycurl.x86_64            7.19.0-8.el6                     @/python-pycurl-7.19.0-8.el6.x86_64
python-urlgrabber.noarch        3.9.1-9.el6                      @/python-urlgrabber-3.9.1-9.el6.noarch
readline.x86_64                 6.0-4.el6                        @base          
redhat-logos.noarch             60.0.14-12.el6.centos            @base          
rpm.x86_64                      4.8.0-38.el6_6                   @updates       
rpm-apidocs.noarch              4.8.0-38.el6_6                   @updates       
rpm-cron.noarch                 4.8.0-38.el6_6                   @updates       
rpm-devel.x86_64                4.8.0-38.el6_6                   @updates       
rpm-libs.x86_64                 4.8.0-38.el6_6                   @updates       
rpm-python.x86_64               4.8.0-38.el6_6                   @updates       
rsyslog.x86_64                  5.8.10-10.el6_6                  @updates       
sed.x86_64                      4.2.1-10.el6                     @base          
sendmail.x86_64                 8.14.4-8.el6                     @base          
setup.noarch                    2.8.14-20.el6_4.1                @updates       
shadow-utils.x86_64             2:4.1.4.2-19.el6                 @base          
shared-mime-info.x86_64         0.70-6.el6                       @base          
sqlite.x86_64                   3.6.20-1.el6                     @base          
sysvinit-tools.x86_64           2.87-5.dsf.el6                   @base          
tcp_wrappers-libs.x86_64        7.6-57.el6                       @base          
telnet.x86_64                   1:0.17-48.el6                    @base          
tzdata.noarch                   2014j-1.el6                      @updates       
udev.x86_64                     147-2.57.el6                     @base          
upstart.x86_64                  0.6.5-13.el6_5.3                 @base          
ustr.x86_64                     1.0.4-9.1.el6                    @base          
util-linux-ng.x86_64            2.17.2-12.18.el6                 @base          
xz-libs.x86_64                  4.999.9-0.5.beta.20091007git.el6 @base          
yum.noarch                      3.2.29-60.el6.centos             @/yum-3.2.29-60.el6.centos.noarch
yum-metadata-parser.x86_64      1.1.2-16.el6                     @/yum-metadata-parser-1.1.2-16.el6.x86_64
yum-plugin-fastestmirror.noarch 1.1.30-30.el6                    @/yum-plugin-fastestmirror-1.1.30-30.el6.noarch
zlib.x86_64                     1.2.3-29.el6                     @base          
Once again, thanks everyone for their help. Really appreciate it! Hopefully others who experienced the same issue with their rpm database because of the nss-softn will find this thread helpful!

DonX
Posts: 33
Joined: 2014/11/05 07:24:54
Location: Michigan
Contact:

Re: YUM update error; nss bug

Post by DonX » 2015/01/21 00:44:27

Hey guys I was wondering since I obviously have more installed on my system than indicated by my rpm database at the moment, in order to get the rpm back to the way it was, would it be a good idea to create a virtualbox of centOS6.6, install all updates,(virtualmin/webmin etc) as was my original system prior to the nss bug and then take the centos6.6 virtualbox rpm directory to my actual server?

I was just wondering if that is possible or a good idea? Came to mind as I was checking out virtualbox.

Thanks.

User avatar
TrevorH
Forum Moderator
Posts: 25847
Joined: 2009/09/24 10:40:56
Location: Brighton, UK

Re: YUM update error; nss bug

Post by TrevorH » 2015/01/21 09:11:03

The trouble is that you have a chicken and egg situation. You don't know what packages you had installed before so you cannot install the same packages on your VB instance. To get the VB rpm database correct you would need to know what packages were installed before.

If you want to correct this properly I think you are going to need to write yourself a script to do it. The basic outlines are: get a list of all files on the system, query rpm to see if $file is currently owned by an installed rpm and if so then skip it, if not then query yum provides to find out if a yum package that is available supplies it and if so then install that package from the base repo (not from updates) without updating the filesystem, just the database. Repeat for all files on the system or at least under /usr and /lib{,64}. Once that process is complete, run yum update with updates enabled to pull down the latest version of all packages.
CentOS 5 died in March 2017 - migrate NOW!
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DonX
Posts: 33
Joined: 2014/11/05 07:24:54
Location: Michigan
Contact:

Re: YUM update error; nss bug

Post by DonX » 2015/01/22 07:20:34

Thank you TrevorH. I actually found all the yum logs on the server. They go back when I got on the server since mid 2013. Every install and update is there. I combined the files into one file base based of "Installed" and now I have a list of what has been "Installed" on my server since I got on the server. I was thinking per Gerald's suggestion, would it be okay to go ahead now and (re)install each package one by one? And if so, is it okay to simply just install the packages or do I have to go about it the way avij posted?

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