duplicate rpm after migration

[samary]

Hi,

I managed to migrate some servers from 13.1 (spma) to 14.2 (yum). I have a strange package behavior : There are a lot of duplicate rpms via rpm -qa

eg.

atk-devel-1.28.0-2.el6.x86_64
atk-devel-1.30.0-1.el6.x86_64

attr-2.4.44-4.el6.x86_64
attr-2.4.44-7.el6.x86_64

bind-libs-9.8.2-0.17.rc1.el6_4.4.x86_64
bind-libs-9.8.2-0.23.rc1.el6_5.1.x86_64

....

Yum should upgrade the existing rpms and not only install the latest available, isn't it ? Does someone have the same issue ?

Thanks

[stdweird]

did the yum run finish properly. i've seen this behaviour while yum was still running. anything in (any of) the logfile(s)?

[samary]

Hi, yum finished properly, if I look in /var/log/yum.log, I see it claims to update the package :

Updated: atk-1.30.0-1.el6.x86_64
Updated: attr-2.4.44-7.el6.x86_64
Updated: 32:bind-libs-9.8.2-0.23.rc1.el6_5.1.x86_64

But anyway, I see both version in rpm -qa and yum list installed

Really strange behavior.

[stdweird]

can you run yum check? and what happens if you run spma again (with --debug 5 --verbose). and what yum version was there this before spma ran?

[stdweird]

@samary (and thanks for helping to chase bugs ;)

[samary]

Hi,

@stdweird : You're welcome ;-)

So here is the two yum version installed (the second-one is the previous version) :

yum.noarch                             3.2.29-17.el6_1.1         installed      
yum.noarch                             3.2.29-17.el6             @anaconda-ScientificLinux-201107271550.x86_64

Here is the yum check output :

yum check
Loaded plugins: priorities, product-id, refresh-packagekit, security,
              : subscription-manager, versionlock
Updating Red Hat repositories.
DeviceKit-power-014-3.el6.x86_64 is a duplicate with DeviceKit-power-014-1.el6.x86_64
1:NetworkManager-0.8.1-15.el6.x86_64 is a duplicate with 1:NetworkManager-0.8.1-9.el6_1.3.x86_64
1:NetworkManager-glib-0.8.1-15.el6.x86_64 is a duplicate with 1:NetworkManager-glib-0.8.1-9.el6_1.3.x86_64
atk-1.30.0-1.el6.x86_64 is a duplicate with atk-1.28.0-2.el6.x86_64
atk-devel-1.30.0-1.el6.x86_64 is a duplicate with atk-devel-1.28.0-2.el6.x86_64
attr-2.4.44-7.el6.x86_64 is a duplicate with attr-2.4.44-4.el6.x86_64
32:bind-libs-9.8.2-0.23.rc1.el6_5.1.x86_64 is a duplicate with 32:bind-libs-9.8.2-0.17.rc1.el6_4.4.x86_64
32:bind-utils-9.8.2-0.23.rc1.el6_5.1.x86_64 is a duplicate with 32:bind-utils-9.8.2-0.17.rc1.el6_4.4.x86_64
ca-certificates-2013.1.95-65.1.el6_5.noarch is a duplicate with ca-certificates-2010.63-3.el6_1.5.noarch
1:control-center-2.28.1-39.el6.x86_64 is a duplicate with 1:control-center-2.28.1-25.el6.x86_64
1:control-center-filesystem-2.28.1-39.el6.x86_64 is a duplicate with 1:control-center-filesystem-2.28.1-25.el6.x86_64
coreutils-8.4-31.el6.x86_64 is a duplicate with coreutils-8.4-13.el6.x86_64
coreutils-libs-8.4-31.el6.x86_64 is a duplicate with coreutils-libs-8.4-13.el6.x86_64
cryptsetup-luks-1.2.0-3.el6_1.2.x86_64 is a duplicate with cryptsetup-luks-1.2.0-3.el6.x86_64
cryptsetup-luks-libs-1.2.0-3.el6_1.2.x86_64 is a duplicate with cryptsetup-luks-libs-1.2.0-3.el6.x86_64
1:dmidecode-2.11-2.el6_1.x86_64 is a duplicate with 1:dmidecode-2.10-1.30.1.el6.x86_64
dracut-004-336.el6.noarch is a duplicate with dracut-004-53.el6.noarch
dracut-kernel-004-336.el6.noarch is a duplicate with dracut-kernel-004-53.el6.noarch
evolution-data-server-2.32.3-18.el6.x86_64 is a duplicate with evolution-data-server-2.28.3-15.el6.x86_64
evolution-data-server-devel-2.32.3-18.el6.x86_64 is a duplicate with evolution-data-server-devel-2.28.3-15.el6.x86_64
evolution-data-server-doc-2.32.3-18.el6.noarch is a duplicate with evolution-data-server-doc-2.28.3-15.el6.noarch
file-5.04-11.el6.x86_64 is a duplicate with file-5.04-6.el6.x86_64
file-libs-5.04-11.el6.x86_64 is a duplicate with file-libs-5.04-6.el6.x86_64
filesystem-2.4.30-3.el6.x86_64 is a duplicate with filesystem-2.4.30-2.1.el6.x86_64
git-1.7.12.4-1.el6.rfx.x86_64 is a duplicate with git-1.7.1-3.el6_4.1.x86_64
glib2-2.26.1-3.el6.x86_64 is a duplicate with glib2-2.22.5-6.el6.x86_64
glib2-devel-2.26.1-3.el6.x86_64 is a duplicate with glib2-devel-2.22.5-6.el6.x86_64
gnome-panel-libs-2.30.2-15.el6.x86_64 is a duplicate with gnome-panel-libs-2.30.2-14.el6.x86_64
gnome-python2-desktop-2.28.0-5.el6.x86_64 is a duplicate with gnome-python2-desktop-2.28.0-4.el6.x86_64
gnome-settings-daemon-2.28.2-30.el6.x86_64 is a duplicate with gnome-settings-daemon-2.28.2-11.el6.x86_64
gnupg2-2.0.14-6.el6_4.x86_64 is a duplicate with gnupg2-2.0.14-4.el6.x86_64
gnutls-2.8.5-13.el6_5.x86_64 is a duplicate with gnutls-2.8.5-10.el6_4.2.x86_64
gnutls-devel-2.8.5-13.el6_5.x86_64 is a duplicate with gnutls-devel-2.8.5-10.el6_4.2.x86_64
gpm-1.20.6-12.el6.x86_64 is a duplicate with gpm-1.20.6-11.el6.x86_64
gpm-libs-1.20.6-12.el6.x86_64 is a duplicate with gpm-libs-1.20.6-11.el6.x86_64
graphviz-2.26.0-7.el6.x86_64 is a duplicate with graphviz-2.26.0-4.el6.x86_64
graphviz-devel-2.26.0-7.el6.x86_64 is a duplicate with graphviz-devel-2.26.0-4.el6.x86_64
graphviz-doc-2.26.0-7.el6.x86_64 is a duplicate with graphviz-doc-2.26.0-4.el6.x86_64
graphviz-gd-2.26.0-7.el6.x86_64 is a duplicate with graphviz-gd-2.26.0-4.el6.x86_64
graphviz-python-2.26.0-7.el6.x86_64 is a duplicate with graphviz-python-2.26.0-4.el6.x86_64
1:grub-0.97-70.el6_1.1.x86_64 is a duplicate with 1:grub-0.97-70.el6.x86_64
gtk2-2.20.1-4.el6.x86_64 is a duplicate with gtk2-2.18.9-10.el6.x86_64
gtk2-devel-2.20.1-4.el6.x86_64 is a duplicate with gtk2-devel-2.18.9-10.el6.x86_64
5:guile-1.8.7-5.el6.x86_64 is a duplicate with 5:guile-1.8.7-4.el6.0.sl6.x86_64
httpd-2.2.15-29.sl6.x86_64 is a duplicate with httpd-2.2.15-28.sl6.x86_64
httpd-tools-2.2.15-29.sl6.x86_64 is a duplicate with httpd-tools-2.2.15-28.sl6.x86_64
infinipath-psm-3.0.1-115.1015_open.2.el6.x86_64 is a duplicate with infinipath-psm-3.0.1-115.1015_open.1.el6.x86_64
1:java-1.6.0-openjdk-1.6.0.0-3.1.13.1.el6_5.x86_64 is a duplicate with 1:java-1.6.0-openjdk-1.6.0.0-1.62.1.11.11.90.el6_4.x86_64
1:java-1.6.0-openjdk-devel-1.6.0.0-3.1.13.1.el6_5.x86_64 is a duplicate with 1:java-1.6.0-openjdk-devel-1.6.0.0-1.62.1.11.11.90.el6_4.x86_64
kdebase-workspace-4.3.4-22.el6.x86_64 is a duplicate with kdebase-workspace-4.3.4-19.el6.x86_64
kdebase-workspace-libs-4.3.4-22.el6.x86_64 is a duplicate with kdebase-workspace-libs-4.3.4-19.el6.x86_64
kdebase-workspace-wallpapers-4.3.4-22.el6.noarch is a duplicate with kdebase-workspace-wallpapers-4.3.4-19.el6.noarch
kernel-firmware-2.6.32-431.5.1.el6.noarch is a duplicate with kernel-firmware-2.6.32-358.14.1.el6.noarch
ksysguardd-4.3.4-22.el6.x86_64 is a duplicate with ksysguardd-4.3.4-19.el6.x86_64
libXfont-1.4.5-3.el6_5.x86_64 is a duplicate with libXfont-1.4.5-2.el6.x86_64
libacl-2.2.49-6.el6.x86_64 is a duplicate with libacl-2.2.49-4.el6.x86_64
libattr-2.4.44-7.el6.x86_64 is a duplicate with libattr-2.4.44-4.el6.x86_64
libcgroup-0.37-3.el6.x86_64 is a duplicate with libcgroup-0.37-2.el6.x86_64
libgcrypt-1.4.5-11.el6_4.x86_64 is a duplicate with libgcrypt-1.4.5-5.el6.x86_64
libgcrypt-devel-1.4.5-11.el6_4.x86_64 is a duplicate with libgcrypt-devel-1.4.5-5.el6.x86_64
libibverbs-1.1.7-1.el6.x86_64 is a duplicate with libibverbs-1.1.6-5.el6.x86_64
libibverbs-devel-1.1.7-1.el6.x86_64 is a duplicate with libibverbs-devel-1.1.6-5.el6.x86_64
libjpeg-turbo-1.2.1-3.el6_5.x86_64 is a duplicate with libjpeg-turbo-1.2.1-1.el6.x86_64
librdmacm-1.0.17-1.el6.x86_64 is a duplicate with librdmacm-1.0.17-0.git4b5c1aa.el6.x86_64
librdmacm-devel-1.0.17-1.el6.x86_64 is a duplicate with librdmacm-devel-1.0.17-0.git4b5c1aa.el6.x86_64
librsvg2-2.26.0-6.el6_5.3.x86_64 is a duplicate with librsvg2-2.26.0-5.el6_1.1.x86_64
libsmbclient-3.6.9-167.el6_5.x86_64 is a duplicate with libsmbclient-3.6.9-151.el6.x86_64
libtevent-0.9.18-3.el6.x86_64 is a duplicate with libtevent-0.9.17-1.el6.x86_64
libtiff-3.9.4-10.el6_5.x86_64 is a duplicate with libtiff-3.9.4-9.el6_3.x86_64
lohit-assamese-fonts-2.4.3-5.el6.noarch is a duplicate with lohit-assamese-fonts-2.4.3-4.el6.noarch
lohit-gujarati-fonts-2.4.4-4.el6.noarch is a duplicate with lohit-gujarati-fonts-2.4.4-3.el6.noarch
lohit-tamil-fonts-2.4.5-5.el6.noarch is a duplicate with lohit-tamil-fonts-2.4.5-4.el6.noarch
m17n-lib-1.5.5-2.el6_1.1.x86_64 is a duplicate with m17n-lib-1.5.5-2.el6.x86_64
mailcap-2.1.31-2.el6.noarch is a duplicate with mailcap-2.1.31-1.1.el6.noarch
mdadm-3.2.2-1.el6_1.2.x86_64 is a duplicate with mdadm-3.2.1-1.el6.x86_64
mercurial-2.2.2-1.el6.rfx.x86_64 is a duplicate with mercurial-1.4-3.el6.x86_64
mod_dav_svn-1.7.4-0.1.el6.rfx.x86_64 is a duplicate with mod_dav_svn-1.6.11-9.el6_4.x86_64
mysql-5.1.73-3.el6_5.x86_64 is a duplicate with mysql-5.1.69-1.el6_4.x86_64
mysql-libs-5.1.73-3.el6_5.x86_64 is a duplicate with mysql-libs-5.1.69-1.el6_4.x86_64
mysql-server-5.1.73-3.el6_5.x86_64 is a duplicate with mysql-server-5.1.69-1.el6_4.x86_64
nspr-4.10.2-1.el6_5.x86_64 is a duplicate with nspr-4.9.2-0.el6_3.1.x86_64
nss-3.15.3-3.el6_5.x86_64 is a duplicate with nss-3.14.0.0-12.el6.x86_64
nss-softokn-3.14.3-3.el6_4.x86_64 is a duplicate with nss-softokn-3.12.9-3.el6.x86_64
nss-softokn-freebl-3.14.3-3.el6_4.x86_64 is a duplicate with nss-softokn-freebl-3.12.9-3.el6.x86_64
nss-sysinit-3.15.3-3.el6_5.x86_64 is a duplicate with nss-sysinit-3.14.0.0-12.el6.x86_64
nss-tools-3.15.3-3.el6_5.x86_64 is a duplicate with nss-tools-3.14.0.0-12.el6.x86_64
nss-util-3.15.3-1.el6_5.x86_64 is a duplicate with nss-util-3.14.0.0-2.el6.x86_64
openjpeg-libs-1.3-10.el6_5.x86_64 is a duplicate with openjpeg-libs-1.3-9.el6_3.x86_64
openldap-2.4.23-34.el6_5.1.x86_64 is a duplicate with openldap-2.4.23-26.el6_3.2.x86_64
openmotif-2.3.3-4.el6.x86_64 is a duplicate with openmotif-2.3.3-1.el6.x86_64
openmpi-1.5.4-2.el6.x86_64 is a duplicate with openmpi-1.5.4-1.el6.x86_64
openmpi-psm-1.5.3-3.el6.x86_64 is obsoleted by openmpi-1.5.4-1.el6.x86_64
openmpi-psm-1.5.3-3.el6.x86_64 is obsoleted by openmpi-1.5.4-2.el6.x86_64
openssh-5.3p1-94.el6.x86_64 is a duplicate with openssh-5.3p1-84.1.el6.x86_64
openssh-clients-5.3p1-94.el6.x86_64 is a duplicate with openssh-clients-5.3p1-84.1.el6.x86_64
openssh-server-5.3p1-94.el6.x86_64 is a duplicate with openssh-server-5.3p1-84.1.el6.x86_64
openssl-1.0.1e-16.el6_5.4.x86_64 is a duplicate with openssl-1.0.0-27.el6_4.2.x86_64
oxygen-cursor-themes-4.3.4-22.el6.noarch is a duplicate with oxygen-cursor-themes-4.3.4-19.el6.noarch
p11-kit-trust-0.18.5-2.el6.x86_64 has installed conflicts nss < ('0', '3.14.3', '33'): nss-3.14.0.0-12.el6.x86_64
perl-Git-1.7.12.4-1.el6.rfx.x86_64 is a duplicate with perl-Git-1.7.1-3.el6_4.1.noarch
perl-LC-14.2.1-1.noarch is a duplicate with perl-LC-13.1.0-1.noarch
perl-Net-DNS-0.65-4.el6.x86_64 is a duplicate with perl-Net-DNS-0.65-2.el6.x86_64
perl-Proc-ProcessTable-0.48-1.el6.x86_64 is a duplicate with perl-Proc-ProcessTable-0.44-4.el6.x86_64
pinentry-0.7.6-6.el6.x86_64 is a duplicate with pinentry-0.7.6-5.el6.x86_64
pixman-0.26.2-5.1.el6_5.x86_64 is a duplicate with pixman-0.26.2-5.el6_4.x86_64
pixman-devel-0.26.2-5.1.el6_5.x86_64 is a duplicate with pixman-devel-0.26.2-5.el6_4.x86_64
polkit-0.96-5.el6_4.x86_64 is a duplicate with polkit-0.96-2.el6_0.1.x86_64
polkit-desktop-policy-0.96-5.el6_4.noarch is a duplicate with polkit-desktop-policy-0.96-2.el6_0.1.noarch
polkit-devel-0.96-5.el6_4.x86_64 is a duplicate with polkit-devel-0.96-2.el6_0.1.x86_64
polkit-docs-0.96-5.el6_4.x86_64 is a duplicate with polkit-docs-0.96-2.el6_0.1.x86_64
postgresql-libs-8.4.20-1.el6_5.x86_64 is a duplicate with postgresql-libs-8.4.13-1.el6_3.x86_64
pyparsing-1.5.6-1.el6.noarch is a duplicate with pyparsing-1.5.0-6.el6.noarch
python-2.6.6-51.el6.x86_64 is a duplicate with python-2.6.6-29.el6_2.2.x86_64
python-devel-2.6.6-51.el6.x86_64 has installed conflicts python < ('0', '2.6.6', '51.el6'): python-2.6.6-29.el6_2.2.x86_64
python-devel-2.6.6-51.el6.x86_64 is a duplicate with python-devel-2.6.6-29.el6_2.2.x86_64
python-dmidecode-3.10.12-1.el6_1.1.x86_64 is a duplicate with python-dmidecode-3.10.12-1.el6.x86_64
python-imaging-1.1.6-19.el6.x86_64 is obsoleted by PIL-1.1.7-10.el6.x86_64
python-libs-2.6.6-51.el6.x86_64 is a duplicate with python-libs-2.6.6-29.el6_2.2.x86_64
python-magic-5.04-11.el6.x86_64 is a duplicate with python-magic-5.04-6.el6.x86_64
python-rhsm-0.95.14-1.el6_1.noarch is a duplicate with python-rhsm-0.95.6-1.el6.noarch
python-zope-filesystem-1-5.el6.x86_64 is obsoleted by python-zope-interface-3.7.0-2.el6.x86_64
python-zope-interface-3.7.0-2.el6.x86_64 is a duplicate with python-zope-interface-3.5.2-2.1.el6.x86_64
qt3-3.3.8b-30.el6.x86_64 is a duplicate with qt3-3.3.8b-29.el6.x86_64
rrdtool-1.4.8-1.el6.x86_64 is a duplicate with rrdtool-1.3.8-6.el6.x86_64
rtkit-0.5-2.el6_4.x86_64 is a duplicate with rtkit-0.5-1.el6.x86_64
sabayon-apply-2.29.92-3.el6.x86_64 is a duplicate with sabayon-apply-2.29.92-1.el6.x86_64
samba-common-3.6.9-167.el6_5.x86_64 is a duplicate with samba-common-3.6.9-151.el6.x86_64
samba-winbind-3.6.9-167.el6_5.x86_64 is a duplicate with samba-winbind-3.6.9-151.el6.x86_64
samba-winbind-clients-3.6.9-167.el6_5.x86_64 is a duplicate with samba-winbind-clients-3.6.9-151.el6.x86_64
samba4-libs-4.0.0-60.el6_5.rc4.x86_64 is a duplicate with samba4-libs-4.0.0-55.el6.rc4.x86_64
sed-4.2.1-7.el6.x86_64 is a duplicate with sed-4.2.1-5.el6.x86_64
selinux-policy-3.7.19-231.el6.noarch is a duplicate with selinux-policy-3.7.19-195.el6_4.12.noarch
selinux-policy-targeted-3.7.19-231.el6.noarch is a duplicate with selinux-policy-targeted-3.7.19-195.el6_4.12.noarch
sg3_utils-libs-1.28-4.el6.x86_64 is a duplicate with sg3_utils-libs-1.28-3.el6.x86_64
sl-indexhtml-6-6.5.sl6.1.noarch is a duplicate with sl-indexhtml-6-2.sl6.5.noarch
subscription-manager-0.95.17-1.el6_1.x86_64 is a duplicate with subscription-manager-0.95.11-1.el6.x86_64
subversion-1.7.4-0.1.el6.rfx.x86_64 is a duplicate with subversion-1.6.11-9.el6_4.x86_64
sudo-1.8.6p3-12.el6.x86_64 is a duplicate with sudo-1.7.4p5-12.el6_3.x86_64
system-config-firewall-base-1.2.27-5.el6.noarch is a duplicate with system-config-firewall-base-1.2.27-3.el6_1.3.noarch
tkinter-2.6.6-51.el6.x86_64 is a duplicate with tkinter-2.6.6-29.el6_2.2.x86_64
totem-2.28.6-4.el6.x86_64 is a duplicate with totem-2.28.6-2.el6.x86_64
tzdata-java-2013i-2.el6.noarch is a duplicate with tzdata-java-2013c-2.el6.noarch
udisks-1.0.1-7.el6_5.x86_64 is a duplicate with udisks-1.0.1-2.el6.x86_64
wget-1.12-1.11.el6_5.x86_64 is a duplicate with wget-1.12-1.4.el6.x86_64
which-2.19-6.el6.x86_64 is a duplicate with which-2.19-5.1.el6.x86_64
xdg-utils-1.0.2-17.20091016cvs.el6.noarch is a duplicate with xdg-utils-1.0.2-15.20091016cvs.el6.noarch
xkeyboard-config-1.6-7.el6_1.1.noarch is a duplicate with xkeyboard-config-1.6-7.el6.noarch
xorg-x11-drv-intel-2.21.12-2.el6.x86_64 is a duplicate with xorg-x11-drv-intel-2.20.2-2.el6.x86_64
xorg-x11-drv-wacom-0.16.1-4.el6.x86_64 is a duplicate with xorg-x11-drv-wacom-0.16.1-3.el6.x86_64
xorg-x11-server-Xephyr-1.13.0-23.1.sl6.x86_64 is a duplicate with xorg-x11-server-Xephyr-1.13.0-11.sl6.x86_64
xorg-x11-server-Xorg-1.13.0-23.1.sl6.x86_64 is a duplicate with xorg-x11-server-Xorg-1.13.0-11.sl6.x86_64
xorg-x11-server-common-1.13.0-23.1.sl6.x86_64 is a duplicate with xorg-x11-server-common-1.13.0-11.sl6.x86_64
yum-3.2.29-17.el6_1.1.noarch is a duplicate with yum-3.2.29-17.el6.noarch
yum-rhn-plugin-0.9.1-26.el6_1.1.noarch is a duplicate with yum-rhn-plugin-0.9.1-26.el6.noarch
Error: check all

Here is the output of ncm-ncd --co spma --verbose --debug 5

ncm-ncd --co spma --verbose --debug 5

[INFO] NCM-NCD version 14.2.1 started by root at: Wed Mar 26 16:46:24 2014
[VERB] accessing CCM cache manager..
[VERB] getting locked CCM configuration..
[VERB] checking for ncm-ncd locks...
[DEBUG] no pre dependencies found for spma
[DEBUG] no post dependencies found for spma
[INFO] executing configure on components....

[INFO] running component: spma
---------------------------------------------------------
[VERB] Unlinking outdated repository /etc/yum.repos.d/redhat.repo
[VERB] Opening file /etc/yum.repos.d/quattor_14.2.1.repo
[VERB] Changes to /etc/yum.repos.d/quattor_14.2.1.repo:

[VERB] File /etc/yum.repos.d/quattor_14.2.1.repo was not modified
[VERB] Opening file /etc/yum.repos.d/quattor_14.2.1.pkgs
[VERB] Changes to /etc/yum.repos.d/quattor_14.2.1.pkgs:

[VERB] File /etc/yum.repos.d/quattor_14.2.1.pkgs was not modified
[VERB] Opening file /etc/yum.repos.d/quattor_externals.repo
[VERB] Changes to /etc/yum.repos.d/quattor_externals.repo:

[VERB] File /etc/yum.repos.d/quattor_externals.repo was not modified
[VERB] Opening file /etc/yum.repos.d/quattor_externals.pkgs
[VERB] Changes to /etc/yum.repos.d/quattor_externals.pkgs:

[VERB] File /etc/yum.repos.d/quattor_externals.pkgs was not modified
[VERB] Opening file /etc/yum.repos.d/sl610_x86_64.repo
[VERB] Changes to /etc/yum.repos.d/sl610_x86_64.repo:

[VERB] File /etc/yum.repos.d/sl610_x86_64.repo was not modified
[VERB] Opening file /etc/yum.repos.d/sl610_x86_64.pkgs
[VERB] Changes to /etc/yum.repos.d/sl610_x86_64.pkgs:

[VERB] File /etc/yum.repos.d/sl610_x86_64.pkgs was not modified
[VERB] Opening file /etc/yum.repos.d/sl610_x86_64_errata.repo
[VERB] Changes to /etc/yum.repos.d/sl610_x86_64_errata.repo:

[VERB] File /etc/yum.repos.d/sl610_x86_64_errata.repo was not modified
[VERB] Opening file /etc/yum.repos.d/sl610_x86_64_errata.pkgs
[VERB] Changes to /etc/yum.repos.d/sl610_x86_64_errata.pkgs:

[VERB] File /etc/yum.repos.d/sl610_x86_64_errata.pkgs was not modified
[VERB] Opening file /etc/yum.repos.d/sl610_x86_64_updates.repo
[VERB] Changes to /etc/yum.repos.d/sl610_x86_64_updates.repo:

[VERB] File /etc/yum.repos.d/sl610_x86_64_updates.repo was not modified
[VERB] Opening file /etc/yum.repos.d/sl610_x86_64_updates.pkgs
[VERB] Changes to /etc/yum.repos.d/sl610_x86_64_updates.pkgs:

[VERB] File /etc/yum.repos.d/sl610_x86_64_updates.pkgs was not modified
[VERB] Opening file /etc/yum.repos.d/sl6_addons.repo
[VERB] Changes to /etc/yum.repos.d/sl6_addons.repo:

[VERB] File /etc/yum.repos.d/sl6_addons.repo was not modified
[VERB] Opening file /etc/yum.repos.d/sl6_addons.pkgs
[VERB] Changes to /etc/yum.repos.d/sl6_addons.pkgs:

[VERB] File /etc/yum.repos.d/sl6_addons.pkgs was not modified
[VERB] Opening file /etc/yum.repos.d/sl6_epel.repo
[VERB] Changes to /etc/yum.repos.d/sl6_epel.repo:

[VERB] File /etc/yum.repos.d/sl6_epel.repo was not modified
[VERB] Opening file /etc/yum.repos.d/sl6_epel.pkgs
[VERB] Changes to /etc/yum.repos.d/sl6_epel.pkgs:

[VERB] File /etc/yum.repos.d/sl6_epel.pkgs was not modified
[VERB] Opening file /etc/yum.repos.d/sl6_iihe_x86_64.repo
[VERB] Changes to /etc/yum.repos.d/sl6_iihe_x86_64.repo:

[VERB] File /etc/yum.repos.d/sl6_iihe_x86_64.repo was not modified
[VERB] Opening file /etc/yum.repos.d/sl6_iihe_x86_64.pkgs
[VERB] Changes to /etc/yum.repos.d/sl6_iihe_x86_64.pkgs:

[VERB] File /etc/yum.repos.d/sl6_iihe_x86_64.pkgs was not modified
[VERB] Opening file /etc/yum.conf
[DEBUG] add_or_replace_lines (/etc/yum.conf): re = 'clean_requirements_on_remove'   goodre = 'clean_requirements_on_remove\s*=\s*1' newvalue = '
clean_requirements_on_remove=1' whence = '2'
[DEBUG] add_or_replace_lines (/etc/yum.conf): re = 'obsoletes'  goodre = 'obsoletes\s*=\s*0'    newvalue = '
obsoletes=0'    whence = '2'
[VERB] Changes to /etc/yum.conf:

[VERB] File /etc/yum.conf was not modified
[VERB] Executing command: yum-complete-transaction
[VERB] Command options: stderr=SCALAR(0x171ff78) stdout=SCALAR(0x171ff18)
[VERB] complete previous transactions output: Loaded plugins: priorities, product-id, refresh-packagekit, versionlock
No unfinished transactions left.

[VERB] Executing command: yum clean expire-cache
[VERB] Command options: stderr=SCALAR(0x1789b80) stdout=SCALAR(0x184f388)
[VERB] clean up caches output: Loaded plugins: priorities, product-id, refresh-packagekit, security,
              : subscription-manager, versionlock
Updating Red Hat repositories.
Cleaning repos: quattor_14.2.1 quattor_externals sl610_x86_64
              : sl610_x86_64_errata sl610_x86_64_updates sl6_addons sl6_epel
              : sl6_iihe_x86_64
8 metadata files removed

[VERB] Executing command: repoquery --show-duplicates --envra nscd-2.12-1.80.el6_3.5.x86_64 dkms-2.2.0.3-2.el6.noarch cuda-documentation-5-5-5.5-22.x86_64 kernel-devel-2.6.32-358.14.1.el6.x86_64 glibc-common-2.12-1.80.el6_3.5.x86_64 cuda-core-libs-5-5-5.5-22.x86_64 ncm-cdp-14.2.1-1.noarch ncm-network-14.2.1-1.noarch cuda-core-5-5-5.5-22.x86_64 ncm-pbsknownhosts-14.2.1-1.noarch ncm-pbsclient-14.2.1-1.noarch ncm-filecopy-14.2.1-1.noarch ncm-ldconf-14.2.1-1.noarch cuda-5-5-5.5-22.x86_64 xorg-x11-drv-nvidia-319.37-2.el6.x86_64 ncm-modprobe-14.2.1-1.noarch cuda-license-5-5-5.5-22.x86_64 ncm-cron-14.2.1-1.noarch xorg-x11-drv-nvidia-libs-319.37-2.el6.x86_64 xorg-x11-drv-nvidia-libs-319.37-2.el6.i686 ncm-autofs-14.2.1-1.noarch ncm-ntpd-14.2.1-1.noarch nvidia-modprobe-319.37-1.el6.x86_64 ncm-authconfig-14.2.1-1.noarch cuda-visual-tools-5-5-5.5-22.x86_64 ncm-symlink-14.2.1-1.noarch libgcc-4.4.5-6.el6.i686 ncm-profile-14.2.1-1.noarch glibc-2.12-1.80.el6_3.5.x86_64 glibc-2.12-1.80.el6_3.5.i686 ncm-chkconfig-14.2.1-1.noarch ncm-named-14.2.1-1.noarch libXau-1.0.6-4.el6.i686 glibc-devel-2.12-1.80.el6_3.5.x86_64 nvidia-kmod-319.37-1.el6.x86_64 ncm-accounts-14.2.1-1.noarch cuda-extra-libs-5-5-5.5-22.x86_64 torque-4.2.7-1.adaptive.el6.x86_64 zlib-1.2.3-29.el6.i686 ncm-altlogrotate-14.2.1-1.noarch glibc-headers-2.12-1.80.el6_3.5.x86_64 libxcb-1.8.1-1.el6.i686 cuda-samples-5-5-5.5-22.x86_64 torque-client-4.2.7-1.adaptive.el6.x86_64 dhcp-common-4.1.1-34.P1.el6.x86_64 nvidia-xconfig-319.37-27.el6.x86_64 nvidia-settings-319.37-30.el6.x86_64 libXext-1.3.1-2.el6.x86_64 libXext-1.3.1-2.el6.i686 xorg-x11-drv-nvidia-devel-319.37-2.el6.x86_64 xorg-x11-drv-nvidia-devel-319.37-2.el6.i686 cuda-headers-5-5-5.5-22.x86_64 cuda-misc-5-5-5.5-22.x86_64 libX11-1.5.0-4.el6.i686 cuda-5.5-22.x86_64 cuda-command-line-tools-5-5-5.5-22.x86_64 ncm-ccm-14.2.1-1.noarch ncm-dirperm-14.2.1-1.noarch kernel-headers-2.6.32-358.14.1.el6.x86_64 ncm-ssh-14.2.1-1.noarch ncm-etcservices-14.2.1-1.noarch
[VERB] Command options: stderr=SCALAR(0x1855190) stdout=SCALAR(0x18bc4e8)
[VERB] determining epochs output: 0:cuda-5.5-22.x86_64
0:cuda-5-5-5.5-22.x86_64
0:cuda-command-line-tools-5-5-5.5-22.x86_64
0:cuda-core-5-5-5.5-22.x86_64
0:cuda-core-libs-5-5-5.5-22.x86_64
0:cuda-documentation-5-5-5.5-22.x86_64
0:cuda-extra-libs-5-5-5.5-22.x86_64
0:cuda-headers-5-5-5.5-22.x86_64
0:cuda-license-5-5-5.5-22.x86_64
0:cuda-misc-5-5-5.5-22.x86_64
0:cuda-samples-5-5-5.5-22.x86_64
0:cuda-visual-tools-5-5-5.5-22.x86_64
12:dhcp-common-4.1.1-34.P1.el6.x86_64
0:dkms-2.2.0.3-2.el6.noarch
0:glibc-2.12-1.80.el6_3.5.i686
0:glibc-2.12-1.80.el6_3.5.x86_64
0:glibc-common-2.12-1.80.el6_3.5.x86_64
0:glibc-devel-2.12-1.80.el6_3.5.x86_64
0:glibc-headers-2.12-1.80.el6_3.5.x86_64
0:kernel-devel-2.6.32-358.14.1.el6.x86_64
0:kernel-headers-2.6.32-358.14.1.el6.x86_64
0:libX11-1.5.0-4.el6.i686
0:libXau-1.0.6-4.el6.i686
0:libXext-1.3.1-2.el6.i686
0:libXext-1.3.1-2.el6.x86_64
0:libgcc-4.4.5-6.el6.i686
0:libxcb-1.8.1-1.el6.i686
0:ncm-accounts-14.2.1-1.noarch
0:ncm-altlogrotate-14.2.1-1.noarch
0:ncm-authconfig-14.2.1-1.noarch
0:ncm-autofs-14.2.1-1.noarch
0:ncm-ccm-14.2.1-1.noarch
0:ncm-cdp-14.2.1-1.noarch
0:ncm-chkconfig-14.2.1-1.noarch
0:ncm-cron-14.2.1-1.noarch
0:ncm-dirperm-14.2.1-1.noarch
0:ncm-etcservices-14.2.1-1.noarch
0:ncm-filecopy-14.2.1-1.noarch
0:ncm-ldconf-14.2.1-1.noarch
0:ncm-modprobe-14.2.1-1.noarch
0:ncm-named-14.2.1-1.noarch
0:ncm-network-14.2.1-1.noarch
0:ncm-ntpd-14.2.1-1.noarch
0:ncm-pbsclient-14.2.1-1.noarch
0:ncm-pbsknownhosts-14.2.1-1.noarch
0:ncm-profile-14.2.1-1.noarch
0:ncm-ssh-14.2.1-1.noarch
0:ncm-symlink-14.2.1-1.noarch
0:nscd-2.12-1.80.el6_3.5.x86_64
1:nvidia-kmod-319.37-1.el6.x86_64
0:nvidia-modprobe-319.37-1.el6.x86_64
0:nvidia-settings-319.37-30.el6.x86_64
0:nvidia-xconfig-319.37-27.el6.x86_64
0:torque-4.2.7-1.adaptive.el6.x86_64
0:torque-client-4.2.7-1.adaptive.el6.x86_64
1:xorg-x11-drv-nvidia-319.37-2.el6.x86_64
1:xorg-x11-drv-nvidia-devel-319.37-2.el6.i686
1:xorg-x11-drv-nvidia-devel-319.37-2.el6.x86_64
1:xorg-x11-drv-nvidia-libs-319.37-2.el6.i686
1:xorg-x11-drv-nvidia-libs-319.37-2.el6.x86_64
0:zlib-1.2.3-29.el6.i686

[VERB] Opening file /etc/yum/pluginconf.d/versionlock.list
[VERB] Changes to /etc/yum/pluginconf.d/versionlock.list:

[VERB] File /etc/yum/pluginconf.d/versionlock.list was not modified
[VERB] Executing command: yum -y distro-sync
[VERB] Command options: stderr=SCALAR(0x1870e08) stdout=SCALAR(0x1871108)
[VERB] synchronisation with upstream output: Loaded plugins: priorities, product-id, refresh-packagekit, security,
              : subscription-manager, versionlock
Updating Red Hat repositories.
Setting up Distribution Synchronization Process
No Packages marked for Distribution Synchronization

[VERB] Getting output of command: rpm -qa --qf %{NAME}\n%{NAME};%{ARCH}\n
[VERB] Getting output of command: package-cleanup --leaves --all --qf %{NAME};%{ARCH}
[DEBUG] Running transaction: install tetex-latex
transaction solve
transaction run

[VERB] Executing command: yum -y shell
[VERB] Command options: stderr=SCALAR(0x1854800) stdin=install tetex-latex
transaction solve
transaction run
 stdout=SCALAR(0x184f238)
[VERB] running transaction output: Loaded plugins: priorities, product-id, refresh-packagekit, security,
              : subscription-manager, versionlock
Updating Red Hat repositories.
Setting up Yum Shell
> Setting up Install Process
Package texlive-latex-2007-57.el6_2.x86_64 already installed and latest version
> --> Finding unneeded leftover dependencies
Found and removing 0 unneeded dependencies
Success resolving dependencies
> > Leaving Shell

[INFO] configure on component spma executed, 0 errors, 0 warnings

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

[OK]   0 errors, 0 warnings executing configure

Thanks for helping me to debug this.

Cheers

[stdweird]

ok, i have no clue how this happened. @piojo might provide some insight. does package-cleanup --problems show anything? if not, does a package-cleanup --cleandupes resolve the issue?

[samary]

package-cleanup --problems

Loaded plugins: priorities, product-id, refresh-packagekit, versionlock
No Problems Found

package-cleanup --cleandupes : erased old duplicate entries

Thanks a lot, I think it is OK now. Maybe ncm-spma should run this command after installing packages.

Cheers

[piojo-zz]

Thanks for chasing this one. Indeed, it looks like package-cleanup --cleandupes could be run after yum-complete-transaction.

[samary]

I found when I run manually yum-complete-transaction, it ask interactively if I want to remove duplicate packages. Maybe adding the -y switch to this command will do this without prompting and therefore is no need to run package-cleanup --cleandupes anymore.

[samary]

Hi, Since I updated to a more recent version (6x), I don't see this strange behavior anymore. This can be a specific issue related to 6.1. Sorry for the noise