yum duplicates problem

for command

Code (Text):

yum update --disableplugin=priorities --enablerepo=remi

copy and paste full output to pastebin.com or gist.github.com and provide link to it here

 

1. how much memory do you have on server ?

Code (Text):

free -m

2. looks like you haven't updated in ages ???

what out put do you get just for

Code (Text):

yum clean all
yum -y update

 

output for

Code (Text):

package-cleanup --dupes

 

once got --dupes output try cleaning up duplicates with command below - copy and paste output of this command too for reference

Code (Text):

package-cleanup --cleandupes

then double check with

Code (Text):

package-cleanup --problems

then try yum update

Code (Text):

yum -y update

 

1st --dupes error log seems funky.. you sure you copied and pasted correct output ?

package-cleanup --cleandupes hit a limit from output

Code (Text):

Error: Depsolving loop limit reached.

seems problem could be systemd package conflict

Code (Text):

Error: systemd conflicts with dracut-033-463.el7_3.2.x86_64

Code (Text):

systemd-219-42.el7_4.1.x86_64 has installed conflicts dracut < ('0', '033', '499'): dracut-033-463.el7_3.2.x86_64

so try raising depsolving loop limit first edit /etc/yum.conf under [main] section add

Code (Text):

depsolve_loop_limit=forever

from CentOS 7.0 - man page for yum.conf (centos section 5) - Unix & Linux Commands

then retry

Code (Text):

package-cleanup --cleandupes

then

Code (Text):

yum -y update

 

what if you try cleandupes excluding NetworkManager packages first ?

Code (Text):

package-cleanup --cleandupes --exclude=NetworkManager --exclude=NetworkManager-libnm

which web host ?

also output for these 2

Code (Text):

yum info NetworkManager

Code (Text):

yum info NetworkManager-libnm

 

seems this thread is the exact same problem you got Something went very wrong - CentOS

so you can do the following within a tmux or screen session so network disconnection doesn't abort the processes

• Sysadmin - [Tutorial] tmux tutorial
• Sysadmin - Who uses Screen for linux ?

Within SSH via screen or tmux session

1. backup yum / rpm databases etc just in case

Code (Text):

cp -a /var/lib/rpm /var/lib/rpm-backup
cp -a /var/lib/yum /var/lib/yum-backup

2. remove the newest package duplicates by first grabbing your duplicates listing and saving to yum-update-dupes.txt file which contains

Code (Text):

1:NetworkManager-1.8.0-9.el7.x86_64 is a duplicate with 1:NetworkManager-1.4.0-20.el7_3.x86_64
1:NetworkManager-libnm-1.8.0-9.el7.x86_64 is a duplicate with 1:NetworkManager-libnm-1.4.0-20.el7_3.x86_64
atk-2.22.0-3.el7.x86_64 is a duplicate with atk-2.14.0-1.el7.x86_64
audit-libs-2.7.6-3.el7.x86_64 is a duplicate with audit-libs-2.6.5-3.el7_3.1.x86_64
bash-4.2.46-29.el7_4.x86_64 is a duplicate with bash-4.2.46-21.el7_3.x86_64
32:bind-libs-9.9.4-51.el7.x86_64 is a duplicate with 32:bind-libs-9.9.4-50.el7_3.1.x86_64
32:bind-libs-lite-9.9.4-51.el7.x86_64 is a duplicate with 32:bind-libs-lite-9.9.4-50.el7_3.1.x86_64
32:bind-license-9.9.4-51.el7.noarch is a duplicate with 32:bind-license-9.9.4-50.el7_3.1.noarch
binutils-2.25.1-32.base.el7_4.1.x86_64 is a duplicate with binutils-2.25.1-22.base.el7.x86_64
bluez-libs-5.44-4.el7_4.x86_64 is a duplicate with bluez-libs-5.41-1.el7.x86_64
boost-system-1.53.0-27.el7.x86_64 is a duplicate with boost-system-1.53.0-26.el7.x86_64
boost-thread-1.53.0-27.el7.x86_64 is a duplicate with boost-thread-1.53.0-26.el7.x86_64
ca-certificates-2017.2.14-71.el7.noarch is a duplicate with ca-certificates-2017.2.14-70.1.el7_3.noarch
cairo-1.14.8-2.el7.x86_64 is a duplicate with cairo-1.14.2-1.el7.x86_64
centos-release-7-4.1708.el7.centos.x86_64 is a duplicate with centos-release-7-3.1611.el7.centos.x86_64
chkconfig-1.7.4-1.el7.x86_64 is a duplicate with chkconfig-1.7.2-1.el7_3.1.x86_64
cpio-2.11-25.el7_4.x86_64 is a duplicate with cpio-2.11-24.el7.x86_64
cpp-4.8.5-16.el7.x86_64 is a duplicate with cpp-4.8.5-11.el7.x86_64
cronie-1.4.11-17.el7.x86_64 is a duplicate with cronie-1.4.11-14.el7_2.1.x86_64
cronie-anacron-1.4.11-17.el7.x86_64 is a duplicate with cronie-anacron-1.4.11-14.el7_2.1.x86_64
cryptsetup-libs-1.7.4-3.el7.x86_64 is a duplicate with cryptsetup-libs-1.7.2-1.el7.x86_64
1:cups-libs-1.6.3-29.el7.x86_64 is a duplicate with 1:cups-libs-1.6.3-26.el7.x86_64
curl-7.29.0-42.el7.x86_64 is a duplicate with curl-7.29.0-35.el7.centos.x86_64
cyrus-imapd-utils-2.4.17-13.el7.x86_64 is a duplicate with cyrus-imapd-utils-2.4.17-8.el7_3.1.x86_64
cyrus-sasl-2.1.26-21.el7.x86_64 is a duplicate with cyrus-sasl-2.1.26-20.el7_2.x86_64
cyrus-sasl-devel-2.1.26-21.el7.x86_64 is a duplicate with cyrus-sasl-devel-2.1.26-20.el7_2.x86_64
cyrus-sasl-lib-2.1.26-21.el7.x86_64 is a duplicate with cyrus-sasl-lib-2.1.26-20.el7_2.x86_64
7:device-mapper-1.02.140-8.el7.x86_64 is a duplicate with 7:device-mapper-1.02.135-1.el7_3.5.x86_64
7:device-mapper-libs-1.02.140-8.el7.x86_64 is a duplicate with 7:device-mapper-libs-1.02.135-1.el7_3.5.x86_64
12:dhclient-4.2.5-58.el7.centos.x86_64 is a duplicate with 12:dhclient-4.2.5-47.el7.centos.x86_64
12:dhcp-common-4.2.5-58.el7.centos.x86_64 is a duplicate with 12:dhcp-common-4.2.5-47.el7.centos.x86_64
12:dhcp-libs-4.2.5-58.el7.centos.x86_64 is a duplicate with 12:dhcp-libs-4.2.5-47.el7.centos.x86_64
1:dmidecode-3.0-5.el7.x86_64 is a duplicate with 1:dmidecode-3.0-2.1.el7_3.x86_64
dracut-033-502.el7.x86_64 is a duplicate with dracut-033-463.el7_3.2.x86_64
dracut-network-033-502.el7.x86_64 is a duplicate with dracut-network-033-463.el7_3.2.x86_64
e2fsprogs-1.42.9-10.el7.x86_64 is a duplicate with e2fsprogs-1.42.9-9.el7.x86_64
e2fsprogs-libs-1.42.9-10.el7.x86_64 is a duplicate with e2fsprogs-libs-1.42.9-9.el7.x86_64
elfutils-libelf-0.168-8.el7.x86_64 is a duplicate with elfutils-libelf-0.166-2.el7.x86_64
elfutils-libelf-devel-0.168-8.el7.x86_64 is a duplicate with elfutils-libelf-devel-0.166-2.el7.x86_64
elfutils-libs-0.168-8.el7.x86_64 is a duplicate with elfutils-libs-0.166-2.el7.x86_64
2:ethtool-4.8-1.el7.x86_64 is a duplicate with 2:ethtool-4.5-3.el7.x86_64
fipscheck-1.4.1-6.el7.x86_64 is a duplicate with fipscheck-1.4.1-5.el7.x86_64
fipscheck-lib-1.4.1-6.el7.x86_64 is a duplicate with fipscheck-lib-1.4.1-5.el7.x86_64
fontconfig-2.10.95-11.el7.x86_64 is a duplicate with fontconfig-2.10.95-10.el7.x86_64
freetype-2.4.11-15.el7.x86_64 is a duplicate with freetype-2.4.11-12.el7.x86_64
freetype-devel-2.4.11-15.el7.x86_64 is a duplicate with freetype-devel-2.4.11-12.el7.x86_64
gcc-4.8.5-16.el7.x86_64 is a duplicate with gcc-4.8.5-11.el7.x86_64
gdk-pixbuf2-2.36.5-1.el7.x86_64 is a duplicate with gdk-pixbuf2-2.31.6-3.el7.x86_64
gettext-0.19.8.1-2.el7.x86_64 is a duplicate with gettext-0.18.2.1-4.el7.x86_64
gettext-common-devel-0.19.8.1-2.el7.noarch is a duplicate with gettext-common-devel-0.18.2.1-4.el7.noarch
gettext-libs-0.19.8.1-2.el7.x86_64 is a duplicate with gettext-libs-0.18.2.1-4.el7.x86_64
ghostscript-9.07-28.el7_4.2.x86_64 is a duplicate with ghostscript-9.07-20.el7_3.7.x86_64
git-1.8.3.1-12.el7_4.x86_64 is a duplicate with git-1.8.3.1-6.el7_2.1.x86_64
glib2-2.50.3-3.el7.x86_64 is a duplicate with glib2-2.46.2-4.el7.x86_64
glibc-2.17-196.el7.x86_64 is a duplicate with glibc-2.17-157.el7_3.5.x86_64
glibc-common-2.17-196.el7.x86_64 is a duplicate with glibc-common-2.17-157.el7_3.5.x86_64
glibc-devel-2.17-196.el7.x86_64 is a duplicate with glibc-devel-2.17-157.el7_3.5.x86_64
glibc-headers-2.17-196.el7.x86_64 is a duplicate with glibc-headers-2.17-157.el7_3.5.x86_64
1:gmp-6.0.0-15.el7.x86_64 is a duplicate with 1:gmp-6.0.0-12.el7_1.x86_64
gobject-introspection-1.50.0-1.el7.x86_64 is a duplicate with gobject-introspection-1.42.0-1.el7.x86_64
grep-2.20-3.el7.x86_64 is a duplicate with grep-2.20-2.el7.x86_64
grubby-8.28-23.el7.x86_64 is a duplicate with grubby-8.28-21.el7_3.x86_64
gsettings-desktop-schemas-3.22.0-1.el7.x86_64 is a duplicate with gsettings-desktop-schemas-3.14.2-1.el7.x86_64
gzip-1.5-9.el7.x86_64 is a duplicate with gzip-1.5-8.el7.x86_64
harfbuzz-1.3.2-1.el7.x86_64 is a duplicate with harfbuzz-0.9.36-1.el7.x86_64
hwdata-0.252-8.6.el7.x86_64 is a duplicate with hwdata-0.252-8.4.el7.x86_64
initscripts-9.49.39-1.el7.x86_64 is a duplicate with initscripts-9.49.37-1.el7_3.1.x86_64
iproute-3.10.0-87.el7.x86_64 is a duplicate with iproute-3.10.0-74.el7.x86_64
ipset-libs-6.29-1.el7.x86_64 is a duplicate with ipset-libs-6.19-6.el7.x86_64
iptables-1.4.21-18.0.1.el7.centos.x86_64 is a duplicate with iptables-1.4.21-17.el7.x86_64
iputils-20160308-10.el7.x86_64 is a duplicate with iputils-20160308-8.el7.x86_64
jansson-2.10-1.el7.x86_64 is a duplicate with jansson-2.4-6.el7.x86_64
jasper-libs-1.900.1-31.el7.x86_64 is a duplicate with jasper-libs-1.900.1-30.el7_3.x86_64
kbd-legacy-1.15.5-13.el7.noarch is a duplicate with kbd-legacy-1.15.5-12.el7.noarch
kernel-headers-3.10.0-693.2.2.el7.x86_64 is a duplicate with kernel-headers-3.10.0-514.26.2.el7.x86_64
kernel-tools-libs-3.10.0-693.2.2.el7.x86_64 is a duplicate with kernel-tools-libs-3.10.0-514.26.2.el7.x86_64
kmod-20-15.el7_4.2.x86_64 is a duplicate with kmod-20-9.el7.x86_64
kmod-libs-20-15.el7_4.2.x86_64 is a duplicate with kmod-libs-20-9.el7.x86_64
kpartx-0.4.9-111.el7.x86_64 is a duplicate with kpartx-0.4.9-99.el7_3.3.x86_64
krb5-devel-1.15.1-8.el7.x86_64 is a duplicate with krb5-devel-1.14.1-27.el7_3.x86_64
krb5-libs-1.15.1-8.el7.x86_64 is a duplicate with krb5-libs-1.14.1-27.el7_3.x86_64
libICE-1.0.9-9.el7.x86_64 is a duplicate with libICE-1.0.9-2.el7.x86_64
libICE-devel-1.0.9-9.el7.x86_64 is a duplicate with libICE-devel-1.0.9-2.el7.x86_64
libX11-1.6.5-1.el7.x86_64 is a duplicate with libX11-1.6.3-3.el7.x86_64
libX11-common-1.6.5-1.el7.noarch is a duplicate with libX11-common-1.6.3-3.el7.noarch
libX11-devel-1.6.5-1.el7.x86_64 is a duplicate with libX11-devel-1.6.3-3.el7.x86_64
libXcursor-1.1.14-8.el7.x86_64 is a duplicate with libXcursor-1.1.14-2.1.el7.x86_64
libXfixes-5.0.3-1.el7.x86_64 is a duplicate with libXfixes-5.0.1-2.1.el7.x86_64
libXfixes-devel-5.0.3-1.el7.x86_64 is a duplicate with libXfixes-devel-5.0.1-2.1.el7.x86_64
libXi-1.7.9-1.el7.x86_64 is a duplicate with libXi-1.7.4-2.el7.x86_64
libXpm-3.5.12-1.el7.x86_64 is a duplicate with libXpm-3.5.11-3.el7.x86_64
libXrandr-1.5.1-2.el7.x86_64 is a duplicate with libXrandr-1.4.2-2.el7.x86_64
libXrender-0.9.10-1.el7.x86_64 is a duplicate with libXrender-0.9.8-2.1.el7.x86_64
libXt-1.1.5-3.el7.x86_64 is a duplicate with libXt-1.1.4-6.1.el7.x86_64
libXxf86vm-1.1.4-1.el7.x86_64 is a duplicate with libXxf86vm-1.1.3-2.1.el7.x86_64
libXxf86vm-devel-1.1.4-1.el7.x86_64 is a duplicate with libXxf86vm-devel-1.1.3-2.1.el7.x86_64
libblkid-2.23.2-43.el7.x86_64 is a duplicate with libblkid-2.23.2-33.el7_3.2.x86_64
libcap-2.22-9.el7.x86_64 is a duplicate with libcap-2.22-8.el7.x86_64
libcom_err-1.42.9-10.el7.x86_64 is a duplicate with libcom_err-1.42.9-9.el7.x86_64
libcom_err-devel-1.42.9-10.el7.x86_64 is a duplicate with libcom_err-devel-1.42.9-9.el7.x86_64
libcroco-0.6.11-1.el7.x86_64 is a duplicate with libcroco-0.6.8-5.el7.x86_64
libcurl-7.29.0-42.el7.x86_64 is a duplicate with libcurl-7.29.0-35.el7.centos.x86_64
libdb-5.3.21-20.el7.x86_64 is a duplicate with libdb-5.3.21-19.el7.x86_64
libdb-devel-5.3.21-20.el7.x86_64 is a duplicate with libdb-devel-5.3.21-19.el7.x86_64
libdb-utils-5.3.21-20.el7.x86_64 is a duplicate with libdb-utils-5.3.21-19.el7.x86_64
libdrm-2.4.74-1.el7.x86_64 is a duplicate with libdrm-2.4.67-3.el7.x86_64
libdrm-devel-2.4.74-1.el7.x86_64 is a duplicate with libdrm-devel-2.4.67-3.el7.x86_64
libfontenc-1.1.3-3.el7.x86_64 is a duplicate with libfontenc-1.1.2-3.el7.x86_64
libgcc-4.8.5-16.el7.x86_64 is a duplicate with libgcc-4.8.5-11.el7.x86_64
libgcrypt-1.5.3-14.el7.x86_64 is a duplicate with libgcrypt-1.5.3-13.el7_3.1.x86_64
libgnome-keyring-3.12.0-1.el7.x86_64 is a duplicate with libgnome-keyring-3.8.0-3.el7.x86_64
libgomp-4.8.5-16.el7.x86_64 is a duplicate with libgomp-4.8.5-11.el7.x86_64
libibverbs-13-7.el7.x86_64 is a duplicate with libibverbs-1.2.1-1.el7.x86_64
libkadm5-1.15.1-8.el7.x86_64 is a duplicate with libkadm5-1.14.1-27.el7_3.x86_64
libmount-2.23.2-43.el7.x86_64 is a duplicate with libmount-2.23.2-33.el7_3.2.x86_64
libnl3-3.2.28-4.el7.x86_64 is a duplicate with libnl3-3.2.28-3.el7_3.x86_64
1:librados2-0.94.5-2.el7.x86_64 is a duplicate with 1:librados2-0.94.5-1.el7.x86_64
libselinux-2.5-11.el7.x86_64 is a duplicate with libselinux-2.5-6.el7.x86_64
libselinux-devel-2.5-11.el7.x86_64 is a duplicate with libselinux-devel-2.5-6.el7.x86_64
libselinux-utils-2.5-11.el7.x86_64 is a duplicate with libselinux-utils-2.5-6.el7.x86_64
libsemanage-2.5-8.el7.x86_64 is a duplicate with libsemanage-2.5-5.1.el7_3.x86_64
libss-1.42.9-10.el7.x86_64 is a duplicate with libss-1.42.9-9.el7.x86_64
libstdc++-4.8.5-16.el7.x86_64 is a duplicate with libstdc++-4.8.5-11.el7.x86_64
libstdc++-devel-4.8.5-16.el7.x86_64 is a duplicate with libstdc++-devel-4.8.5-11.el7.x86_64
libtasn1-4.10-1.el7.x86_64 is a duplicate with libtasn1-3.8-3.el7.x86_64
libuuid-2.23.2-43.el7.x86_64 is a duplicate with libuuid-2.23.2-33.el7_3.2.x86_64
libwebp-0.3.0-7.el7.x86_64 is a duplicate with libwebp-0.3.0-3.el7.x86_64
libxcb-1.12-1.el7.x86_64 is a duplicate with libxcb-1.11-4.el7.x86_64
libxcb-devel-1.12-1.el7.x86_64 is a duplicate with libxcb-devel-1.11-4.el7.x86_64
linux-firmware-20170606-56.gitc990aae.el7.noarch is a duplicate with linux-firmware-20160830-49.git7534e19.el7.noarch
logrotate-3.8.6-14.el7.x86_64 is a duplicate with logrotate-3.8.6-12.el7.x86_64
lsscsi-0.27-6.el7.x86_64 is a duplicate with lsscsi-0.27-4.el7.x86_64
mesa-libEGL-17.0.1-6.20170307.el7.x86_64 is a duplicate with mesa-libEGL-11.2.2-2.20160614.el7.x86_64
mesa-libGL-17.0.1-6.20170307.el7.x86_64 is a duplicate with mesa-libGL-11.2.2-2.20160614.el7.x86_64
mesa-libgbm-17.0.1-6.20170307.el7.x86_64 is a duplicate with mesa-libgbm-11.2.2-2.20160614.el7.x86_64
mesa-libglapi-17.0.1-6.20170307.el7.x86_64 is a duplicate with mesa-libglapi-11.2.2-2.20160614.el7.x86_64
ncurses-base-5.9-14.20130511.el7_4.noarch is a duplicate with ncurses-base-5.9-13.20130511.el7.noarch
ncurses-devel-5.9-14.20130511.el7_4.x86_64 is a duplicate with ncurses-devel-5.9-13.20130511.el7.x86_64
ncurses-libs-5.9-14.20130511.el7_4.x86_64 is a duplicate with ncurses-libs-5.9-13.20130511.el7.x86_64
1:net-snmp-agent-libs-5.7.2-28.el7.x86_64 is a duplicate with 1:net-snmp-agent-libs-5.7.2-24.el7_3.2.x86_64
1:net-snmp-libs-5.7.2-28.el7.x86_64 is a duplicate with 1:net-snmp-libs-5.7.2-24.el7_3.2.x86_64
nss-softokn-3.28.3-8.el7_4.x86_64 is a duplicate with nss-softokn-3.16.2.3-14.4.el7.x86_64
nss-softokn-freebl-3.28.3-8.el7_4.x86_64 is a duplicate with nss-softokn-freebl-3.16.2.3-14.4.el7.x86_64
nss-util-3.28.4-3.el7.x86_64 is a duplicate with nss-util-3.28.4-1.0.el7_3.x86_64
openldap-2.4.44-5.el7.x86_64 is a duplicate with openldap-2.4.40-13.el7.x86_64
openssh-7.4p1-12.el7_4.x86_64 is a duplicate with openssh-6.6.1p1-35.el7_3.x86_64
openssh-clients-7.4p1-12.el7_4.x86_64 is a duplicate with openssh-clients-6.6.1p1-35.el7_3.x86_64
1:openssl-1.0.2k-8.el7.x86_64 is a duplicate with 1:openssl-1.0.1e-60.el7_3.1.x86_64
1:openssl-devel-1.0.2k-8.el7.x86_64 is a duplicate with 1:openssl-devel-1.0.1e-60.el7_3.1.x86_64
1:openssl-libs-1.0.2k-8.el7.x86_64 is a duplicate with 1:openssl-libs-1.0.1e-60.el7_3.1.x86_64
p11-kit-0.23.5-3.el7.x86_64 is a duplicate with p11-kit-0.20.7-3.el7.x86_64
p11-kit-trust-0.23.5-3.el7.x86_64 is a duplicate with p11-kit-trust-0.20.7-3.el7.x86_64
pango-1.40.4-1.el7.x86_64 is a duplicate with pango-1.36.8-2.el7.x86_64
pciutils-3.5.1-2.el7.x86_64 is a duplicate with pciutils-3.5.1-1.el7.x86_64
pciutils-libs-3.5.1-2.el7.x86_64 is a duplicate with pciutils-libs-3.5.1-1.el7.x86_64
pcre-8.32-17.el7.x86_64 is a duplicate with pcre-8.32-15.el7_2.1.x86_64
pcre-devel-8.32-17.el7.x86_64 is a duplicate with pcre-devel-8.32-15.el7_2.1.x86_64
4:perl-5.16.3-292.el7.x86_64 is a duplicate with 4:perl-5.16.3-291.el7.x86_64
perl-ExtUtils-Install-1.58-292.el7.noarch is a duplicate with perl-ExtUtils-Install-1.58-291.el7.noarch
1:perl-ExtUtils-ParseXS-3.18-3.el7.noarch is a duplicate with 1:perl-ExtUtils-ParseXS-3.18-2.el7.noarch
perl-Git-1.8.3.1-12.el7_4.noarch is a duplicate with perl-Git-1.8.3.1-6.el7_2.1.noarch
perl-Net-SSLeay-1.55-6.el7.x86_64 is a duplicate with perl-Net-SSLeay-1.55-4.el7.x86_64
4:perl-devel-5.16.3-292.el7.x86_64 is a duplicate with 4:perl-devel-5.16.3-291.el7.x86_64
4:perl-libs-5.16.3-292.el7.x86_64 is a duplicate with 4:perl-libs-5.16.3-291.el7.x86_64
4:perl-macros-5.16.3-292.el7.x86_64 is a duplicate with 4:perl-macros-5.16.3-291.el7.x86_64
policycoreutils-2.5-17.1.el7.x86_64 is a duplicate with policycoreutils-2.5-11.el7_3.x86_64
procps-ng-3.3.10-16.el7.x86_64 is a duplicate with procps-ng-3.3.10-10.el7.x86_64
python-2.7.5-58.el7.x86_64 is a duplicate with python-2.7.5-48.el7.x86_64
python-libs-2.7.5-58.el7.x86_64 is a duplicate with python-libs-2.7.5-48.el7.x86_64
python-perf-3.10.0-693.2.2.el7.x86_64 is a duplicate with python-perf-3.10.0-514.26.2.el7.x86_64
readline-6.2-10.el7.x86_64 is a duplicate with readline-6.2-9.el7.x86_64
rpm-4.11.3-25.el7.x86_64 is a duplicate with rpm-4.11.3-21.el7.x86_64
rpm-build-libs-4.11.3-25.el7.x86_64 is a duplicate with rpm-build-libs-4.11.3-21.el7.x86_64
rpm-devel-4.11.3-25.el7.x86_64 is a duplicate with rpm-devel-4.11.3-21.el7.x86_64
rpm-libs-4.11.3-25.el7.x86_64 is a duplicate with rpm-libs-4.11.3-21.el7.x86_64
rpm-python-4.11.3-25.el7.x86_64 is a duplicate with rpm-python-4.11.3-21.el7.x86_64
rsync-3.0.9-18.el7.x86_64 is a duplicate with rsync-3.0.9-17.el7.x86_64
shared-mime-info-1.8-3.el7.x86_64 is a duplicate with shared-mime-info-1.1-9.el7.x86_64
subversion-libs-1.7.14-11.el7_4.x86_64 is a duplicate with subversion-libs-1.7.14-10.el7.x86_64
systemd-219-42.el7_4.1.x86_64 has installed conflicts dracut < ('0', '033', '499'): dracut-033-463.el7_3.2.x86_64
systemd-219-42.el7_4.1.x86_64 is a duplicate with systemd-219-30.el7_3.9.x86_64
systemd-libs-219-42.el7_4.1.x86_64 is a duplicate with systemd-libs-219-30.el7_3.9.x86_64
systemd-sysv-219-42.el7_4.1.x86_64 is a duplicate with systemd-sysv-219-30.el7_3.9.x86_64
systemtap-sdt-devel-3.1-3.el7.x86_64 is a duplicate with systemtap-sdt-devel-3.0-7.el7.x86_64
2:tar-1.26-32.el7.x86_64 is a duplicate with 2:tar-1.26-31.el7.x86_64
util-linux-2.23.2-43.el7.x86_64 is a duplicate with util-linux-2.23.2-33.el7_3.2.x86_64
2:vim-minimal-7.4.160-2.el7.x86_64 is a duplicate with 2:vim-minimal-7.4.160-1.el7_3.1.x86_64
virt-what-1.13-10.el7.x86_64 is a duplicate with virt-what-1.13-8.el7.x86_64
1:wpa_supplicant-2.6-5.el7.x86_64 is a duplicate with 1:wpa_supplicant-2.0-21.el7_3.x86_64
xorg-x11-proto-devel-7.7-20.el7.noarch is a duplicate with xorg-x11-proto-devel-7.7-13.el7.noarch
yum-3.4.3-154.el7.centos.noarch is a duplicate with yum-3.4.3-150.el7.centos.noarch
yum-plugin-fastestmirror-1.1.31-42.el7.noarch is a duplicate with yum-plugin-fastestmirror-1.1.31-40.el7.noarch

then parse that text file for the newest packages listed on the 1st field of each line

filter yum-update-dupes.txt and parse for lines with X: in front where X is an integer

Code (Text):

grep ':' yum-update-dupes.txt | grep duplicate | awk -F ":" '{print $2}' | awk '{print $1}'

Code (Text):

grep ':' yum-update-dupes.txt | grep duplicate | awk -F ":" '{print $2}' | awk '{print $1}'
NetworkManager-1.8.0-9.el7.x86_64
NetworkManager-libnm-1.8.0-9.el7.x86_64
bind-libs-9.9.4-51.el7.x86_64
bind-libs-lite-9.9.4-51.el7.x86_64
bind-license-9.9.4-51.el7.noarch
cups-libs-1.6.3-29.el7.x86_64
device-mapper-1.02.140-8.el7.x86_64
device-mapper-libs-1.02.140-8.el7.x86_64
dhclient-4.2.5-58.el7.centos.x86_64
dhcp-common-4.2.5-58.el7.centos.x86_64
dhcp-libs-4.2.5-58.el7.centos.x86_64
dmidecode-3.0-5.el7.x86_64
ethtool-4.8-1.el7.x86_64
gmp-6.0.0-15.el7.x86_64
librados2-0.94.5-2.el7.x86_64
net-snmp-agent-libs-5.7.2-28.el7.x86_64
net-snmp-libs-5.7.2-28.el7.x86_64
openssl-1.0.2k-8.el7.x86_64
openssl-devel-1.0.2k-8.el7.x86_64
openssl-libs-1.0.2k-8.el7.x86_64
perl-5.16.3-292.el7.x86_64
perl-ExtUtils-ParseXS-3.18-3.el7.noarch
perl-devel-5.16.3-292.el7.x86_64
perl-libs-5.16.3-292.el7.x86_64
perl-macros-5.16.3-292.el7.x86_64
tar-1.26-32.el7.x86_64
vim-minimal-7.4.160-2.el7.x86_64
wpa_supplicant-2.6-5.el7.x86_64

filter yum-update-dupes.txt and parse for lines without X: in front where X is an integer

Code (Text):

grep -v ':' yum-update-dupes.txt | grep duplicate | awk '{print $1}'

Code (Text):

grep -v ':' yum-update-dupes.txt | grep duplicate | awk '{print $1}'                       
atk-2.22.0-3.el7.x86_64
audit-libs-2.7.6-3.el7.x86_64
bash-4.2.46-29.el7_4.x86_64
binutils-2.25.1-32.base.el7_4.1.x86_64
bluez-libs-5.44-4.el7_4.x86_64
boost-system-1.53.0-27.el7.x86_64
boost-thread-1.53.0-27.el7.x86_64
ca-certificates-2017.2.14-71.el7.noarch
cairo-1.14.8-2.el7.x86_64
centos-release-7-4.1708.el7.centos.x86_64
chkconfig-1.7.4-1.el7.x86_64
cpio-2.11-25.el7_4.x86_64
cpp-4.8.5-16.el7.x86_64
cronie-1.4.11-17.el7.x86_64
cronie-anacron-1.4.11-17.el7.x86_64
cryptsetup-libs-1.7.4-3.el7.x86_64
curl-7.29.0-42.el7.x86_64
cyrus-imapd-utils-2.4.17-13.el7.x86_64
cyrus-sasl-2.1.26-21.el7.x86_64
cyrus-sasl-devel-2.1.26-21.el7.x86_64
cyrus-sasl-lib-2.1.26-21.el7.x86_64
dracut-033-502.el7.x86_64
dracut-network-033-502.el7.x86_64
e2fsprogs-1.42.9-10.el7.x86_64
e2fsprogs-libs-1.42.9-10.el7.x86_64
elfutils-libelf-0.168-8.el7.x86_64
elfutils-libelf-devel-0.168-8.el7.x86_64
elfutils-libs-0.168-8.el7.x86_64
fipscheck-1.4.1-6.el7.x86_64
fipscheck-lib-1.4.1-6.el7.x86_64
fontconfig-2.10.95-11.el7.x86_64
freetype-2.4.11-15.el7.x86_64
freetype-devel-2.4.11-15.el7.x86_64
gcc-4.8.5-16.el7.x86_64
gdk-pixbuf2-2.36.5-1.el7.x86_64
gettext-0.19.8.1-2.el7.x86_64
gettext-common-devel-0.19.8.1-2.el7.noarch
gettext-libs-0.19.8.1-2.el7.x86_64
ghostscript-9.07-28.el7_4.2.x86_64
git-1.8.3.1-12.el7_4.x86_64
glib2-2.50.3-3.el7.x86_64
glibc-2.17-196.el7.x86_64
glibc-common-2.17-196.el7.x86_64
glibc-devel-2.17-196.el7.x86_64
glibc-headers-2.17-196.el7.x86_64
gobject-introspection-1.50.0-1.el7.x86_64
grep-2.20-3.el7.x86_64
grubby-8.28-23.el7.x86_64
gsettings-desktop-schemas-3.22.0-1.el7.x86_64
gzip-1.5-9.el7.x86_64
harfbuzz-1.3.2-1.el7.x86_64
hwdata-0.252-8.6.el7.x86_64
initscripts-9.49.39-1.el7.x86_64
iproute-3.10.0-87.el7.x86_64
ipset-libs-6.29-1.el7.x86_64
iptables-1.4.21-18.0.1.el7.centos.x86_64
iputils-20160308-10.el7.x86_64
jansson-2.10-1.el7.x86_64
jasper-libs-1.900.1-31.el7.x86_64
kbd-legacy-1.15.5-13.el7.noarch
kernel-headers-3.10.0-693.2.2.el7.x86_64
kernel-tools-libs-3.10.0-693.2.2.el7.x86_64
kmod-20-15.el7_4.2.x86_64
kmod-libs-20-15.el7_4.2.x86_64
kpartx-0.4.9-111.el7.x86_64
krb5-devel-1.15.1-8.el7.x86_64
krb5-libs-1.15.1-8.el7.x86_64
libICE-1.0.9-9.el7.x86_64
libICE-devel-1.0.9-9.el7.x86_64
libX11-1.6.5-1.el7.x86_64
libX11-common-1.6.5-1.el7.noarch
libX11-devel-1.6.5-1.el7.x86_64
libXcursor-1.1.14-8.el7.x86_64
libXfixes-5.0.3-1.el7.x86_64
libXfixes-devel-5.0.3-1.el7.x86_64
libXi-1.7.9-1.el7.x86_64
libXpm-3.5.12-1.el7.x86_64
libXrandr-1.5.1-2.el7.x86_64
libXrender-0.9.10-1.el7.x86_64
libXt-1.1.5-3.el7.x86_64
libXxf86vm-1.1.4-1.el7.x86_64
libXxf86vm-devel-1.1.4-1.el7.x86_64
libblkid-2.23.2-43.el7.x86_64
libcap-2.22-9.el7.x86_64
libcom_err-1.42.9-10.el7.x86_64
libcom_err-devel-1.42.9-10.el7.x86_64
libcroco-0.6.11-1.el7.x86_64
libcurl-7.29.0-42.el7.x86_64
libdb-5.3.21-20.el7.x86_64
libdb-devel-5.3.21-20.el7.x86_64
libdb-utils-5.3.21-20.el7.x86_64
libdrm-2.4.74-1.el7.x86_64
libdrm-devel-2.4.74-1.el7.x86_64
libfontenc-1.1.3-3.el7.x86_64
libgcc-4.8.5-16.el7.x86_64
libgcrypt-1.5.3-14.el7.x86_64
libgnome-keyring-3.12.0-1.el7.x86_64
libgomp-4.8.5-16.el7.x86_64
libibverbs-13-7.el7.x86_64
libkadm5-1.15.1-8.el7.x86_64
libmount-2.23.2-43.el7.x86_64
libnl3-3.2.28-4.el7.x86_64
libselinux-2.5-11.el7.x86_64
libselinux-devel-2.5-11.el7.x86_64
libselinux-utils-2.5-11.el7.x86_64
libsemanage-2.5-8.el7.x86_64
libss-1.42.9-10.el7.x86_64
libstdc++-4.8.5-16.el7.x86_64
libstdc++-devel-4.8.5-16.el7.x86_64
libtasn1-4.10-1.el7.x86_64
libuuid-2.23.2-43.el7.x86_64
libwebp-0.3.0-7.el7.x86_64
libxcb-1.12-1.el7.x86_64
libxcb-devel-1.12-1.el7.x86_64
linux-firmware-20170606-56.gitc990aae.el7.noarch
logrotate-3.8.6-14.el7.x86_64
lsscsi-0.27-6.el7.x86_64
mesa-libEGL-17.0.1-6.20170307.el7.x86_64
mesa-libGL-17.0.1-6.20170307.el7.x86_64
mesa-libgbm-17.0.1-6.20170307.el7.x86_64
mesa-libglapi-17.0.1-6.20170307.el7.x86_64
ncurses-base-5.9-14.20130511.el7_4.noarch
ncurses-devel-5.9-14.20130511.el7_4.x86_64
ncurses-libs-5.9-14.20130511.el7_4.x86_64
nss-softokn-3.28.3-8.el7_4.x86_64
nss-softokn-freebl-3.28.3-8.el7_4.x86_64
nss-util-3.28.4-3.el7.x86_64
openldap-2.4.44-5.el7.x86_64
openssh-7.4p1-12.el7_4.x86_64
openssh-clients-7.4p1-12.el7_4.x86_64
p11-kit-0.23.5-3.el7.x86_64
p11-kit-trust-0.23.5-3.el7.x86_64
pango-1.40.4-1.el7.x86_64
pciutils-3.5.1-2.el7.x86_64
pciutils-libs-3.5.1-2.el7.x86_64
pcre-8.32-17.el7.x86_64
pcre-devel-8.32-17.el7.x86_64
perl-ExtUtils-Install-1.58-292.el7.noarch
perl-Git-1.8.3.1-12.el7_4.noarch
perl-Net-SSLeay-1.55-6.el7.x86_64
policycoreutils-2.5-17.1.el7.x86_64
procps-ng-3.3.10-16.el7.x86_64
python-2.7.5-58.el7.x86_64
python-libs-2.7.5-58.el7.x86_64
python-perf-3.10.0-693.2.2.el7.x86_64
readline-6.2-10.el7.x86_64
rpm-4.11.3-25.el7.x86_64
rpm-build-libs-4.11.3-25.el7.x86_64
rpm-devel-4.11.3-25.el7.x86_64
rpm-libs-4.11.3-25.el7.x86_64
rpm-python-4.11.3-25.el7.x86_64
rsync-3.0.9-18.el7.x86_64
shared-mime-info-1.8-3.el7.x86_64
subversion-libs-1.7.14-11.el7_4.x86_64
systemd-219-42.el7_4.1.x86_64
systemd-libs-219-42.el7_4.1.x86_64
systemd-sysv-219-42.el7_4.1.x86_64
systemtap-sdt-devel-3.1-3.el7.x86_64
util-linux-2.23.2-43.el7.x86_64
virt-what-1.13-10.el7.x86_64
xorg-x11-proto-devel-7.7-20.el7.noarch
yum-3.4.3-154.el7.centos.noarch
yum-plugin-fastestmirror-1.1.31-42.el7.noarch

combine the parsed newest yum packages reported as being duplicate so you can pipe them into a listnew-pkgs.txt file

Code (Text):

grep ':' yum-update-dupes.txt | grep duplicate | awk -F ":" '{print $2}' | awk '{print $1}' >> listnew-pkgs.txt

Code (Text):

grep -v ':' yum-update-dupes.txt | grep duplicate | awk '{print $1}' >> listnew-pkgs.txt 

Then sort and list listnew-pkgs.txt contents

Code (Text):

sort listnew-pkgs.txt

Code (Text):

sort listnew-pkgs.txt
atk-2.22.0-3.el7.x86_64
audit-libs-2.7.6-3.el7.x86_64
bash-4.2.46-29.el7_4.x86_64
bind-libs-9.9.4-51.el7.x86_64
bind-libs-lite-9.9.4-51.el7.x86_64
bind-license-9.9.4-51.el7.noarch
binutils-2.25.1-32.base.el7_4.1.x86_64
bluez-libs-5.44-4.el7_4.x86_64
boost-system-1.53.0-27.el7.x86_64
boost-thread-1.53.0-27.el7.x86_64
ca-certificates-2017.2.14-71.el7.noarch
cairo-1.14.8-2.el7.x86_64
centos-release-7-4.1708.el7.centos.x86_64
chkconfig-1.7.4-1.el7.x86_64
cpio-2.11-25.el7_4.x86_64
cpp-4.8.5-16.el7.x86_64
cronie-1.4.11-17.el7.x86_64
cronie-anacron-1.4.11-17.el7.x86_64
cryptsetup-libs-1.7.4-3.el7.x86_64
cups-libs-1.6.3-29.el7.x86_64
curl-7.29.0-42.el7.x86_64
cyrus-imapd-utils-2.4.17-13.el7.x86_64
cyrus-sasl-2.1.26-21.el7.x86_64
cyrus-sasl-devel-2.1.26-21.el7.x86_64
cyrus-sasl-lib-2.1.26-21.el7.x86_64
device-mapper-1.02.140-8.el7.x86_64
device-mapper-libs-1.02.140-8.el7.x86_64
dhclient-4.2.5-58.el7.centos.x86_64
dhcp-common-4.2.5-58.el7.centos.x86_64
dhcp-libs-4.2.5-58.el7.centos.x86_64
dmidecode-3.0-5.el7.x86_64
dracut-033-502.el7.x86_64
dracut-network-033-502.el7.x86_64
e2fsprogs-1.42.9-10.el7.x86_64
e2fsprogs-libs-1.42.9-10.el7.x86_64
elfutils-libelf-0.168-8.el7.x86_64
elfutils-libelf-devel-0.168-8.el7.x86_64
elfutils-libs-0.168-8.el7.x86_64
ethtool-4.8-1.el7.x86_64
fipscheck-1.4.1-6.el7.x86_64
fipscheck-lib-1.4.1-6.el7.x86_64
fontconfig-2.10.95-11.el7.x86_64
freetype-2.4.11-15.el7.x86_64
freetype-devel-2.4.11-15.el7.x86_64
gcc-4.8.5-16.el7.x86_64
gdk-pixbuf2-2.36.5-1.el7.x86_64
gettext-0.19.8.1-2.el7.x86_64
gettext-common-devel-0.19.8.1-2.el7.noarch
gettext-libs-0.19.8.1-2.el7.x86_64
ghostscript-9.07-28.el7_4.2.x86_64
git-1.8.3.1-12.el7_4.x86_64
glib2-2.50.3-3.el7.x86_64
glibc-2.17-196.el7.x86_64
glibc-common-2.17-196.el7.x86_64
glibc-devel-2.17-196.el7.x86_64
glibc-headers-2.17-196.el7.x86_64
gmp-6.0.0-15.el7.x86_64
gobject-introspection-1.50.0-1.el7.x86_64
grep-2.20-3.el7.x86_64
grubby-8.28-23.el7.x86_64
gsettings-desktop-schemas-3.22.0-1.el7.x86_64
gzip-1.5-9.el7.x86_64
harfbuzz-1.3.2-1.el7.x86_64
hwdata-0.252-8.6.el7.x86_64
initscripts-9.49.39-1.el7.x86_64
iproute-3.10.0-87.el7.x86_64
ipset-libs-6.29-1.el7.x86_64
iptables-1.4.21-18.0.1.el7.centos.x86_64
iputils-20160308-10.el7.x86_64
jansson-2.10-1.el7.x86_64
jasper-libs-1.900.1-31.el7.x86_64
kbd-legacy-1.15.5-13.el7.noarch
kernel-headers-3.10.0-693.2.2.el7.x86_64
kernel-tools-libs-3.10.0-693.2.2.el7.x86_64
kmod-20-15.el7_4.2.x86_64
kmod-libs-20-15.el7_4.2.x86_64
kpartx-0.4.9-111.el7.x86_64
krb5-devel-1.15.1-8.el7.x86_64
krb5-libs-1.15.1-8.el7.x86_64
libblkid-2.23.2-43.el7.x86_64
libcap-2.22-9.el7.x86_64
libcom_err-1.42.9-10.el7.x86_64
libcom_err-devel-1.42.9-10.el7.x86_64
libcroco-0.6.11-1.el7.x86_64
libcurl-7.29.0-42.el7.x86_64
libdb-5.3.21-20.el7.x86_64
libdb-devel-5.3.21-20.el7.x86_64
libdb-utils-5.3.21-20.el7.x86_64
libdrm-2.4.74-1.el7.x86_64
libdrm-devel-2.4.74-1.el7.x86_64
libfontenc-1.1.3-3.el7.x86_64
libgcc-4.8.5-16.el7.x86_64
libgcrypt-1.5.3-14.el7.x86_64
libgnome-keyring-3.12.0-1.el7.x86_64
libgomp-4.8.5-16.el7.x86_64
libibverbs-13-7.el7.x86_64
libICE-1.0.9-9.el7.x86_64
libICE-devel-1.0.9-9.el7.x86_64
libkadm5-1.15.1-8.el7.x86_64
libmount-2.23.2-43.el7.x86_64
libnl3-3.2.28-4.el7.x86_64
librados2-0.94.5-2.el7.x86_64
libselinux-2.5-11.el7.x86_64
libselinux-devel-2.5-11.el7.x86_64
libselinux-utils-2.5-11.el7.x86_64
libsemanage-2.5-8.el7.x86_64
libss-1.42.9-10.el7.x86_64
libstdc++-4.8.5-16.el7.x86_64
libstdc++-devel-4.8.5-16.el7.x86_64
libtasn1-4.10-1.el7.x86_64
libuuid-2.23.2-43.el7.x86_64
libwebp-0.3.0-7.el7.x86_64
libX11-1.6.5-1.el7.x86_64
libX11-common-1.6.5-1.el7.noarch
libX11-devel-1.6.5-1.el7.x86_64
libxcb-1.12-1.el7.x86_64
libxcb-devel-1.12-1.el7.x86_64
libXcursor-1.1.14-8.el7.x86_64
libXfixes-5.0.3-1.el7.x86_64
libXfixes-devel-5.0.3-1.el7.x86_64
libXi-1.7.9-1.el7.x86_64
libXpm-3.5.12-1.el7.x86_64
libXrandr-1.5.1-2.el7.x86_64
libXrender-0.9.10-1.el7.x86_64
libXt-1.1.5-3.el7.x86_64
libXxf86vm-1.1.4-1.el7.x86_64
libXxf86vm-devel-1.1.4-1.el7.x86_64
linux-firmware-20170606-56.gitc990aae.el7.noarch
logrotate-3.8.6-14.el7.x86_64
lsscsi-0.27-6.el7.x86_64
mesa-libEGL-17.0.1-6.20170307.el7.x86_64
mesa-libgbm-17.0.1-6.20170307.el7.x86_64
mesa-libGL-17.0.1-6.20170307.el7.x86_64
mesa-libglapi-17.0.1-6.20170307.el7.x86_64
ncurses-base-5.9-14.20130511.el7_4.noarch
ncurses-devel-5.9-14.20130511.el7_4.x86_64
ncurses-libs-5.9-14.20130511.el7_4.x86_64
net-snmp-agent-libs-5.7.2-28.el7.x86_64
net-snmp-libs-5.7.2-28.el7.x86_64
NetworkManager-1.8.0-9.el7.x86_64
NetworkManager-libnm-1.8.0-9.el7.x86_64
nss-softokn-3.28.3-8.el7_4.x86_64
nss-softokn-freebl-3.28.3-8.el7_4.x86_64
nss-util-3.28.4-3.el7.x86_64
openldap-2.4.44-5.el7.x86_64
openssh-7.4p1-12.el7_4.x86_64
openssh-clients-7.4p1-12.el7_4.x86_64
openssl-1.0.2k-8.el7.x86_64
openssl-devel-1.0.2k-8.el7.x86_64
openssl-libs-1.0.2k-8.el7.x86_64
p11-kit-0.23.5-3.el7.x86_64
p11-kit-trust-0.23.5-3.el7.x86_64
pango-1.40.4-1.el7.x86_64
pciutils-3.5.1-2.el7.x86_64
pciutils-libs-3.5.1-2.el7.x86_64
pcre-8.32-17.el7.x86_64
pcre-devel-8.32-17.el7.x86_64
perl-5.16.3-292.el7.x86_64
perl-devel-5.16.3-292.el7.x86_64
perl-ExtUtils-Install-1.58-292.el7.noarch
perl-ExtUtils-ParseXS-3.18-3.el7.noarch
perl-Git-1.8.3.1-12.el7_4.noarch
perl-libs-5.16.3-292.el7.x86_64
perl-macros-5.16.3-292.el7.x86_64
perl-Net-SSLeay-1.55-6.el7.x86_64
policycoreutils-2.5-17.1.el7.x86_64
procps-ng-3.3.10-16.el7.x86_64
python-2.7.5-58.el7.x86_64
python-libs-2.7.5-58.el7.x86_64
python-perf-3.10.0-693.2.2.el7.x86_64
readline-6.2-10.el7.x86_64
rpm-4.11.3-25.el7.x86_64
rpm-build-libs-4.11.3-25.el7.x86_64
rpm-devel-4.11.3-25.el7.x86_64
rpm-libs-4.11.3-25.el7.x86_64
rpm-python-4.11.3-25.el7.x86_64
rsync-3.0.9-18.el7.x86_64
shared-mime-info-1.8-3.el7.x86_64
subversion-libs-1.7.14-11.el7_4.x86_64
systemd-219-42.el7_4.1.x86_64
systemd-libs-219-42.el7_4.1.x86_64
systemd-sysv-219-42.el7_4.1.x86_64
systemtap-sdt-devel-3.1-3.el7.x86_64
tar-1.26-32.el7.x86_64
util-linux-2.23.2-43.el7.x86_64
vim-minimal-7.4.160-2.el7.x86_64
virt-what-1.13-10.el7.x86_64
wpa_supplicant-2.6-5.el7.x86_64
xorg-x11-proto-devel-7.7-20.el7.noarch
yum-3.4.3-154.el7.centos.noarch
yum-plugin-fastestmirror-1.1.31-42.el7.noarch

Then just remove them from rpm database via rpm -e --justdb --nodeps by piping sorted output through a while read loop to output the commands you need to run

Code (Text):

sort listnew-pkgs.txt | while read p; do echo "rpm -e --justdb --nodeps $p"; done

output would be as follows for each command needed to remove newer duplicate yum package from database only

Code (Text):

sort listnew-pkgs.txt | while read p; do echo "rpm -e --justdb --nodeps $p"; done
rpm -e --justdb --nodeps atk-2.22.0-3.el7.x86_64
rpm -e --justdb --nodeps audit-libs-2.7.6-3.el7.x86_64
rpm -e --justdb --nodeps bash-4.2.46-29.el7_4.x86_64
rpm -e --justdb --nodeps bind-libs-9.9.4-51.el7.x86_64
rpm -e --justdb --nodeps bind-libs-lite-9.9.4-51.el7.x86_64
rpm -e --justdb --nodeps bind-license-9.9.4-51.el7.noarch
rpm -e --justdb --nodeps binutils-2.25.1-32.base.el7_4.1.x86_64
rpm -e --justdb --nodeps bluez-libs-5.44-4.el7_4.x86_64
rpm -e --justdb --nodeps boost-system-1.53.0-27.el7.x86_64
rpm -e --justdb --nodeps boost-thread-1.53.0-27.el7.x86_64
rpm -e --justdb --nodeps ca-certificates-2017.2.14-71.el7.noarch
rpm -e --justdb --nodeps cairo-1.14.8-2.el7.x86_64
rpm -e --justdb --nodeps centos-release-7-4.1708.el7.centos.x86_64
rpm -e --justdb --nodeps chkconfig-1.7.4-1.el7.x86_64
rpm -e --justdb --nodeps cpio-2.11-25.el7_4.x86_64
rpm -e --justdb --nodeps cpp-4.8.5-16.el7.x86_64
rpm -e --justdb --nodeps cronie-1.4.11-17.el7.x86_64
rpm -e --justdb --nodeps cronie-anacron-1.4.11-17.el7.x86_64
rpm -e --justdb --nodeps cryptsetup-libs-1.7.4-3.el7.x86_64
rpm -e --justdb --nodeps cups-libs-1.6.3-29.el7.x86_64
rpm -e --justdb --nodeps curl-7.29.0-42.el7.x86_64
rpm -e --justdb --nodeps cyrus-imapd-utils-2.4.17-13.el7.x86_64
rpm -e --justdb --nodeps cyrus-sasl-2.1.26-21.el7.x86_64
rpm -e --justdb --nodeps cyrus-sasl-devel-2.1.26-21.el7.x86_64
rpm -e --justdb --nodeps cyrus-sasl-lib-2.1.26-21.el7.x86_64
rpm -e --justdb --nodeps device-mapper-1.02.140-8.el7.x86_64
rpm -e --justdb --nodeps device-mapper-libs-1.02.140-8.el7.x86_64
rpm -e --justdb --nodeps dhclient-4.2.5-58.el7.centos.x86_64
rpm -e --justdb --nodeps dhcp-common-4.2.5-58.el7.centos.x86_64
rpm -e --justdb --nodeps dhcp-libs-4.2.5-58.el7.centos.x86_64
rpm -e --justdb --nodeps dmidecode-3.0-5.el7.x86_64
rpm -e --justdb --nodeps dracut-033-502.el7.x86_64
rpm -e --justdb --nodeps dracut-network-033-502.el7.x86_64
rpm -e --justdb --nodeps e2fsprogs-1.42.9-10.el7.x86_64
rpm -e --justdb --nodeps e2fsprogs-libs-1.42.9-10.el7.x86_64
rpm -e --justdb --nodeps elfutils-libelf-0.168-8.el7.x86_64
rpm -e --justdb --nodeps elfutils-libelf-devel-0.168-8.el7.x86_64
rpm -e --justdb --nodeps elfutils-libs-0.168-8.el7.x86_64
rpm -e --justdb --nodeps ethtool-4.8-1.el7.x86_64
rpm -e --justdb --nodeps fipscheck-1.4.1-6.el7.x86_64
rpm -e --justdb --nodeps fipscheck-lib-1.4.1-6.el7.x86_64
rpm -e --justdb --nodeps fontconfig-2.10.95-11.el7.x86_64
rpm -e --justdb --nodeps freetype-2.4.11-15.el7.x86_64
rpm -e --justdb --nodeps freetype-devel-2.4.11-15.el7.x86_64
rpm -e --justdb --nodeps gcc-4.8.5-16.el7.x86_64
rpm -e --justdb --nodeps gdk-pixbuf2-2.36.5-1.el7.x86_64
rpm -e --justdb --nodeps gettext-0.19.8.1-2.el7.x86_64
rpm -e --justdb --nodeps gettext-common-devel-0.19.8.1-2.el7.noarch
rpm -e --justdb --nodeps gettext-libs-0.19.8.1-2.el7.x86_64
rpm -e --justdb --nodeps ghostscript-9.07-28.el7_4.2.x86_64
rpm -e --justdb --nodeps git-1.8.3.1-12.el7_4.x86_64
rpm -e --justdb --nodeps glib2-2.50.3-3.el7.x86_64
rpm -e --justdb --nodeps glibc-2.17-196.el7.x86_64
rpm -e --justdb --nodeps glibc-common-2.17-196.el7.x86_64
rpm -e --justdb --nodeps glibc-devel-2.17-196.el7.x86_64
rpm -e --justdb --nodeps glibc-headers-2.17-196.el7.x86_64
rpm -e --justdb --nodeps gmp-6.0.0-15.el7.x86_64
rpm -e --justdb --nodeps gobject-introspection-1.50.0-1.el7.x86_64
rpm -e --justdb --nodeps grep-2.20-3.el7.x86_64
rpm -e --justdb --nodeps grubby-8.28-23.el7.x86_64
rpm -e --justdb --nodeps gsettings-desktop-schemas-3.22.0-1.el7.x86_64
rpm -e --justdb --nodeps gzip-1.5-9.el7.x86_64
rpm -e --justdb --nodeps harfbuzz-1.3.2-1.el7.x86_64
rpm -e --justdb --nodeps hwdata-0.252-8.6.el7.x86_64
rpm -e --justdb --nodeps initscripts-9.49.39-1.el7.x86_64
rpm -e --justdb --nodeps iproute-3.10.0-87.el7.x86_64
rpm -e --justdb --nodeps ipset-libs-6.29-1.el7.x86_64
rpm -e --justdb --nodeps iptables-1.4.21-18.0.1.el7.centos.x86_64
rpm -e --justdb --nodeps iputils-20160308-10.el7.x86_64
rpm -e --justdb --nodeps jansson-2.10-1.el7.x86_64
rpm -e --justdb --nodeps jasper-libs-1.900.1-31.el7.x86_64
rpm -e --justdb --nodeps kbd-legacy-1.15.5-13.el7.noarch
rpm -e --justdb --nodeps kernel-headers-3.10.0-693.2.2.el7.x86_64
rpm -e --justdb --nodeps kernel-tools-libs-3.10.0-693.2.2.el7.x86_64
rpm -e --justdb --nodeps kmod-20-15.el7_4.2.x86_64
rpm -e --justdb --nodeps kmod-libs-20-15.el7_4.2.x86_64
rpm -e --justdb --nodeps kpartx-0.4.9-111.el7.x86_64
rpm -e --justdb --nodeps krb5-devel-1.15.1-8.el7.x86_64
rpm -e --justdb --nodeps krb5-libs-1.15.1-8.el7.x86_64
rpm -e --justdb --nodeps libblkid-2.23.2-43.el7.x86_64
rpm -e --justdb --nodeps libcap-2.22-9.el7.x86_64
rpm -e --justdb --nodeps libcom_err-1.42.9-10.el7.x86_64
rpm -e --justdb --nodeps libcom_err-devel-1.42.9-10.el7.x86_64
rpm -e --justdb --nodeps libcroco-0.6.11-1.el7.x86_64
rpm -e --justdb --nodeps libcurl-7.29.0-42.el7.x86_64
rpm -e --justdb --nodeps libdb-5.3.21-20.el7.x86_64
rpm -e --justdb --nodeps libdb-devel-5.3.21-20.el7.x86_64
rpm -e --justdb --nodeps libdb-utils-5.3.21-20.el7.x86_64
rpm -e --justdb --nodeps libdrm-2.4.74-1.el7.x86_64
rpm -e --justdb --nodeps libdrm-devel-2.4.74-1.el7.x86_64
rpm -e --justdb --nodeps libfontenc-1.1.3-3.el7.x86_64
rpm -e --justdb --nodeps libgcc-4.8.5-16.el7.x86_64
rpm -e --justdb --nodeps libgcrypt-1.5.3-14.el7.x86_64
rpm -e --justdb --nodeps libgnome-keyring-3.12.0-1.el7.x86_64
rpm -e --justdb --nodeps libgomp-4.8.5-16.el7.x86_64
rpm -e --justdb --nodeps libibverbs-13-7.el7.x86_64
rpm -e --justdb --nodeps libICE-1.0.9-9.el7.x86_64
rpm -e --justdb --nodeps libICE-devel-1.0.9-9.el7.x86_64
rpm -e --justdb --nodeps libkadm5-1.15.1-8.el7.x86_64
rpm -e --justdb --nodeps libmount-2.23.2-43.el7.x86_64
rpm -e --justdb --nodeps libnl3-3.2.28-4.el7.x86_64
rpm -e --justdb --nodeps librados2-0.94.5-2.el7.x86_64
rpm -e --justdb --nodeps libselinux-2.5-11.el7.x86_64
rpm -e --justdb --nodeps libselinux-devel-2.5-11.el7.x86_64
rpm -e --justdb --nodeps libselinux-utils-2.5-11.el7.x86_64
rpm -e --justdb --nodeps libsemanage-2.5-8.el7.x86_64
rpm -e --justdb --nodeps libss-1.42.9-10.el7.x86_64
rpm -e --justdb --nodeps libstdc++-4.8.5-16.el7.x86_64
rpm -e --justdb --nodeps libstdc++-devel-4.8.5-16.el7.x86_64
rpm -e --justdb --nodeps libtasn1-4.10-1.el7.x86_64
rpm -e --justdb --nodeps libuuid-2.23.2-43.el7.x86_64
rpm -e --justdb --nodeps libwebp-0.3.0-7.el7.x86_64
rpm -e --justdb --nodeps libX11-1.6.5-1.el7.x86_64
rpm -e --justdb --nodeps libX11-common-1.6.5-1.el7.noarch
rpm -e --justdb --nodeps libX11-devel-1.6.5-1.el7.x86_64
rpm -e --justdb --nodeps libxcb-1.12-1.el7.x86_64
rpm -e --justdb --nodeps libxcb-devel-1.12-1.el7.x86_64
rpm -e --justdb --nodeps libXcursor-1.1.14-8.el7.x86_64
rpm -e --justdb --nodeps libXfixes-5.0.3-1.el7.x86_64
rpm -e --justdb --nodeps libXfixes-devel-5.0.3-1.el7.x86_64
rpm -e --justdb --nodeps libXi-1.7.9-1.el7.x86_64
rpm -e --justdb --nodeps libXpm-3.5.12-1.el7.x86_64
rpm -e --justdb --nodeps libXrandr-1.5.1-2.el7.x86_64
rpm -e --justdb --nodeps libXrender-0.9.10-1.el7.x86_64
rpm -e --justdb --nodeps libXt-1.1.5-3.el7.x86_64
rpm -e --justdb --nodeps libXxf86vm-1.1.4-1.el7.x86_64
rpm -e --justdb --nodeps libXxf86vm-devel-1.1.4-1.el7.x86_64
rpm -e --justdb --nodeps linux-firmware-20170606-56.gitc990aae.el7.noarch
rpm -e --justdb --nodeps logrotate-3.8.6-14.el7.x86_64
rpm -e --justdb --nodeps lsscsi-0.27-6.el7.x86_64
rpm -e --justdb --nodeps mesa-libEGL-17.0.1-6.20170307.el7.x86_64
rpm -e --justdb --nodeps mesa-libgbm-17.0.1-6.20170307.el7.x86_64
rpm -e --justdb --nodeps mesa-libGL-17.0.1-6.20170307.el7.x86_64
rpm -e --justdb --nodeps mesa-libglapi-17.0.1-6.20170307.el7.x86_64
rpm -e --justdb --nodeps ncurses-base-5.9-14.20130511.el7_4.noarch
rpm -e --justdb --nodeps ncurses-devel-5.9-14.20130511.el7_4.x86_64
rpm -e --justdb --nodeps ncurses-libs-5.9-14.20130511.el7_4.x86_64
rpm -e --justdb --nodeps net-snmp-agent-libs-5.7.2-28.el7.x86_64
rpm -e --justdb --nodeps net-snmp-libs-5.7.2-28.el7.x86_64
rpm -e --justdb --nodeps NetworkManager-1.8.0-9.el7.x86_64
rpm -e --justdb --nodeps NetworkManager-libnm-1.8.0-9.el7.x86_64
rpm -e --justdb --nodeps nss-softokn-3.28.3-8.el7_4.x86_64
rpm -e --justdb --nodeps nss-softokn-freebl-3.28.3-8.el7_4.x86_64
rpm -e --justdb --nodeps nss-util-3.28.4-3.el7.x86_64
rpm -e --justdb --nodeps openldap-2.4.44-5.el7.x86_64
rpm -e --justdb --nodeps openssh-7.4p1-12.el7_4.x86_64
rpm -e --justdb --nodeps openssh-clients-7.4p1-12.el7_4.x86_64
rpm -e --justdb --nodeps openssl-1.0.2k-8.el7.x86_64
rpm -e --justdb --nodeps openssl-devel-1.0.2k-8.el7.x86_64
rpm -e --justdb --nodeps openssl-libs-1.0.2k-8.el7.x86_64
rpm -e --justdb --nodeps p11-kit-0.23.5-3.el7.x86_64
rpm -e --justdb --nodeps p11-kit-trust-0.23.5-3.el7.x86_64
rpm -e --justdb --nodeps pango-1.40.4-1.el7.x86_64
rpm -e --justdb --nodeps pciutils-3.5.1-2.el7.x86_64
rpm -e --justdb --nodeps pciutils-libs-3.5.1-2.el7.x86_64
rpm -e --justdb --nodeps pcre-8.32-17.el7.x86_64
rpm -e --justdb --nodeps pcre-devel-8.32-17.el7.x86_64
rpm -e --justdb --nodeps perl-5.16.3-292.el7.x86_64
rpm -e --justdb --nodeps perl-devel-5.16.3-292.el7.x86_64
rpm -e --justdb --nodeps perl-ExtUtils-Install-1.58-292.el7.noarch
rpm -e --justdb --nodeps perl-ExtUtils-ParseXS-3.18-3.el7.noarch
rpm -e --justdb --nodeps perl-Git-1.8.3.1-12.el7_4.noarch
rpm -e --justdb --nodeps perl-libs-5.16.3-292.el7.x86_64
rpm -e --justdb --nodeps perl-macros-5.16.3-292.el7.x86_64
rpm -e --justdb --nodeps perl-Net-SSLeay-1.55-6.el7.x86_64
rpm -e --justdb --nodeps policycoreutils-2.5-17.1.el7.x86_64
rpm -e --justdb --nodeps procps-ng-3.3.10-16.el7.x86_64
rpm -e --justdb --nodeps python-2.7.5-58.el7.x86_64
rpm -e --justdb --nodeps python-libs-2.7.5-58.el7.x86_64
rpm -e --justdb --nodeps python-perf-3.10.0-693.2.2.el7.x86_64
rpm -e --justdb --nodeps readline-6.2-10.el7.x86_64
rpm -e --justdb --nodeps rpm-4.11.3-25.el7.x86_64
rpm -e --justdb --nodeps rpm-build-libs-4.11.3-25.el7.x86_64
rpm -e --justdb --nodeps rpm-devel-4.11.3-25.el7.x86_64
rpm -e --justdb --nodeps rpm-libs-4.11.3-25.el7.x86_64
rpm -e --justdb --nodeps rpm-python-4.11.3-25.el7.x86_64
rpm -e --justdb --nodeps rsync-3.0.9-18.el7.x86_64
rpm -e --justdb --nodeps shared-mime-info-1.8-3.el7.x86_64
rpm -e --justdb --nodeps subversion-libs-1.7.14-11.el7_4.x86_64
rpm -e --justdb --nodeps systemd-219-42.el7_4.1.x86_64
rpm -e --justdb --nodeps systemd-libs-219-42.el7_4.1.x86_64
rpm -e --justdb --nodeps systemd-sysv-219-42.el7_4.1.x86_64
rpm -e --justdb --nodeps systemtap-sdt-devel-3.1-3.el7.x86_64
rpm -e --justdb --nodeps tar-1.26-32.el7.x86_64
rpm -e --justdb --nodeps util-linux-2.23.2-43.el7.x86_64
rpm -e --justdb --nodeps vim-minimal-7.4.160-2.el7.x86_64
rpm -e --justdb --nodeps virt-what-1.13-10.el7.x86_64
rpm -e --justdb --nodeps wpa_supplicant-2.6-5.el7.x86_64
rpm -e --justdb --nodeps xorg-x11-proto-devel-7.7-20.el7.noarch
rpm -e --justdb --nodeps yum-3.4.3-154.el7.centos.noarch
rpm -e --justdb --nodeps yum-plugin-fastestmirror-1.1.31-42.el7.noarch

try yum update

Code (Text):

yum -y update

 

so you did run each of the outputted commands ? i.e.

Code (Text):

rpm -e --justdb --nodeps atk-2.22.0-3.el7.x86_64

who's the web host with ? if it's a cloud based vps provider, are you able to backup data and migrate to another vps with the provider ?

probably be easier to backup data and reinstall unless you have the time to troubleshoot this to resolution