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Old 11-16-2015, 07:07 PM   #1
moonst
LQ Newbie
 
Registered: Nov 2015
Posts: 15

Rep: Reputation: Disabled
Install R on RHEL6

Hello all,
I am unable to install R on RHEL6.6 machine. This is what I have so far-

-sh-4.1$ sudo yum install R
....
---> Package libgpg-error.i686 0:1.7-4.el6 will be installed
--> Finished Dependency Resolution
Error: Package: libX11-1.5.0-4.el6.i686 (rhel-6Server-x86_64-updates)
Requires: libX11-common = 1.5.0-4.el6
Installed: libX11-common-1.6.0-2.2.el6.noarch (@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6)
libX11-common = 1.6.0-2.2.el6
Available: libX11-common-1.3-2.el6.noarch (rhel-6Server-x86_64-base_os)
libX11-common = 1.3-2.el6
Available: libX11-common-1.5.0-4.el6.noarch (rhel-6Server-x86_64-updates)
libX11-common = 1.5.0-4.el6
You could try using --skip-broken to work around the problem
You could try running: rpm -Va --nofiles --nodigest

When I search for libX11-common I find this;

-sh-4.1$ sudo rpm -q libX11-common
libX11-common-1.6.0-2.2.el6.noarch

This link has a lot of useful info that helped me with other dependencies.

https://brucebcampbell.wordpress.com...r-on-rhel-6-6/

wget http://download.fedoraproject.org/pu...6-8.noarch.rpm
yum localinstall epel-release-6-8.noarch.rpm
wget http://mirror.centos.org/centos/6/os...el6.x86_64.rpm
wget http://mirror.centos.org/centos/6/os...el6.x86_64.rpm
wget http://mirror.centos.org/centos/6/os...el6.x86_64.rpm
wget http://mirror.centos.org/centos/6/os...6_2.x86_64.rpm
sudo yum localinstall *.rpm
yum install R

Any suggestions on how to proceed?

-sh-4.1$ uname -a
Linux protein.x.com 2.6.32-504.el6.x86_64 #1 SMP Tue Sep 16 01:56:35 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux
 
Old 11-17-2015, 10:48 AM   #2
moonst
LQ Newbie
 
Registered: Nov 2015
Posts: 15

Original Poster
Rep: Reputation: Disabled
This seems to be a more generic problem on my linux box where I have a version of library installed but to install a separate package I need another (older/newer) version of the same library. I can understand if the package requires a newer version of a library - but why go backwards and require an older version? Here:

Requires: libX11-common = 1.5.0-4.el6
Installed: libX11-common-1.6.0-2.2.el6.noarch
 
Old 11-17-2015, 12:41 PM   #3
moonst
LQ Newbie
 
Registered: Nov 2015
Posts: 15

Original Poster
Rep: Reputation: Disabled
Ok so this link talks about updating libraries.

https://www.centos.org/forums/viewtopic.php?t=4339

But looks like yum can "upgrade" - not sure about downgrading. This attempt failed with this error in my case

-sh-4.1$ sudo yum --disablerepo \* update libX11-1.5.0-4.el6.i686.rpm
Loaded plugins: downloadonly, product-id, rhnplugin, security
This system is not registered with RHN Classic or RHN Satellite.
You can use rhn_register to register.
RHN Satellite or RHN Classic support will be disabled.
Setting up Update Process
Examining libX11-1.5.0-4.el6.i686.rpm: libX11-1.5.0-4.el6.i686
libX11-1.5.0-4.el6.i686.rpm: does not update installed package.
No Packages marked for Update
 
Old 11-17-2015, 03:14 PM   #4
moonst
LQ Newbie
 
Registered: Nov 2015
Posts: 15

Original Poster
Rep: Reputation: Disabled
Since R wants libX11-common-1.5 but I seem to have libX11-common-1.6 installed, I tried to remove libX11-common-1.6 with yum and it looks like a 363Mb set of libraries. Since I was unsure of what headaches this would create, I did not go ahead with the removal. Looks like a large number of other programs depend on this. Any suggestions on how to proceed?


-sh-4.1$ sudo yum remove libX11-common-1.6.0-2.2.el6.noarch
Loaded plugins: downloadonly, product-id, rhnplugin, security
This system is not registered with RHN Classic or RHN Satellite.
You can use rhn_register to register.
RHN Satellite or RHN Classic support will be disabled.
Setting up Remove Process
Resolving Dependencies
--> Running transaction check
---> Package libX11-common.noarch 0:1.6.0-2.2.el6 will be erased
--> Processing Dependency: libX11-common = 1.6.0-2.2.el6 for package:
libX11-1.6.0-2.2.el6.x86_64
--> Running transaction check
---> Package libX11.x86_64 0:1.6.0-2.2.el6 will be erased
--> Processing Dependency: libX11-xcb.so.1()(64bit) for package:
mesa-libGL-9.2-0.5.el6_5.2.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXcomposite-0.4.3-4.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
gd-2.0.35-11.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXaw-1.0.11-2.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
librsvg2-2.26.0-14.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXdamage-1.1.3-4.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
gnuplot-4.2.6-2.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
cairo-1.8.8-3.1.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
1:xorg-x11-xauth-1.0.2-7.1.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
1:xorg-x11-drv-nvidia-libs-352.39-1.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
gdk-pixbuf2-2.24.1-5.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
giflib-4.1.6-3.1.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXfixes-5.0.1-2.1.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXi-1.7.2-2.2.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXmu-1.1.1-2.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
gtk2-2.24.23-6.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
1:emacs-23.1-25.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXpm-3.5.10-2.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
gnuplot-common-4.2.6-2.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
xterm-253-1.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXinerama-1.1.3-2.1.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXft-2.3.1-2.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
1:xorg-x11-drv-nvidia-352.39-1.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libotf-0.9.9-3.1.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
qt3-3.3.8b-30.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
pango-1.28.1-10.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
mesa-libGL-9.2-0.5.el6_5.2.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXrender-0.9.8-2.1.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXt-1.1.4-6.1.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXrandr-1.4.1-2.1.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXcursor-1.1.14-2.1.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXtst-1.2.2-2.1.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXxf86vm-1.1.2-2.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
oprofile-0.9.9-5.el6.x86_64
--> Processing Dependency: libX11.so.6()(64bit) for package:
libXext-1.3.2-2.1.el6.x86_64
--> Processing Dependency: libX11 >= 1.5.99.902 for package:
libXfixes-5.0.1-2.1.el6.x86_64
--> Processing Dependency: libX11 >= 1.5.99.902 for package:
libXinerama-1.1.3-2.1.el6.x86_64
--> Processing Dependency: libX11 >= 1.5.99.902 for package:
libXrender-0.9.8-2.1.el6.x86_64
--> Processing Dependency: libX11 >= 1.5.99.902 for package:
libXt-1.1.4-6.1.el6.x86_64
--> Processing Dependency: libX11 >= 1.5.99.902 for package:
libXcursor-1.1.14-2.1.el6.x86_64
--> Processing Dependency: libX11 >= 1.5.99.902 for package:
libXtst-1.2.2-2.1.el6.x86_64
--> Processing Dependency: libX11 >= 1.5.99.902 for package:
libXi-1.7.2-2.2.el6.x86_64
--> Processing Dependency: libX11 >= 1.5.99.902 for package:
libXext-1.3.2-2.1.el6.x86_64
--> Processing Dependency: libX11 >= 1.5.99.902 for package:
libXrandr-1.4.1-2.1.el6.x86_64
--> Running transaction check
---> Package cairo.x86_64 0:1.8.8-3.1.el6 will be erased
--> Processing Dependency: libcairo.so.2()(64bit) for package:
pycairo-1.8.6-2.1.el6.x86_64
--> Processing Dependency: libcairo.so.2()(64bit) for package:
python-matplotlib-0.99.1.2-1.el6.x86_64
--> Processing Dependency: libcairo.so.2()(64bit) for package:
libgcj-4.4.7-11.el6.x86_64
---> Package emacs.x86_64 1:23.1-25.el6 will be erased
---> Package gd.x86_64 0:2.0.35-11.el6 will be erased
---> Package gdk-pixbuf2.x86_64 0:2.24.1-5.el6 will be erased
--> Processing Dependency: libgdk_pixbuf-2.0.so.0()(64bit) for package:
latencytop-0.5-9.el6.x86_64
--> Processing Dependency: libgdk_pixbuf-2.0.so.0()(64bit) for package:
libfprint-0.1.0-19.pre2.el6.x86_64
---> Package giflib.x86_64 0:4.1.6-3.1.el6 will be erased
---> Package gnuplot.x86_64 0:4.2.6-2.el6 will be erased
---> Package gnuplot-common.x86_64 0:4.2.6-2.el6 will be erased
---> Package gtk2.x86_64 0:2.24.23-6.el6 will be erased
---> Package libXaw.x86_64 0:1.0.11-2.el6 will be erased
---> Package libXcomposite.x86_64 0:0.4.3-4.el6 will be erased
---> Package libXcursor.x86_64 0:1.1.14-2.1.el6 will be erased
---> Package libXdamage.x86_64 0:1.1.3-4.el6 will be erased
---> Package libXext.x86_64 0:1.3.2-2.1.el6 will be erased
--> Processing Dependency: libXext.so.6()(64bit) for package:
libvdpau-0.9-1.el6.x86_64
---> Package libXfixes.x86_64 0:5.0.1-2.1.el6 will be erased
---> Package libXft.x86_64 0:2.3.1-2.el6 will be erased
---> Package libXi.x86_64 0:1.7.2-2.2.el6 will be erased
---> Package libXinerama.x86_64 0:1.1.3-2.1.el6 will be erased
---> Package libXmu.x86_64 0:1.1.1-2.el6 will be erased
---> Package libXpm.x86_64 0:3.5.10-2.el6 will be erased
---> Package libXrandr.x86_64 0:1.4.1-2.1.el6 will be erased
---> Package libXrender.x86_64 0:0.9.8-2.1.el6 will be erased
---> Package libXt.x86_64 0:1.1.4-6.1.el6 will be erased
---> Package libXtst.x86_64 0:1.2.2-2.1.el6 will be erased
---> Package libXxf86vm.x86_64 0:1.1.2-2.el6 will be erased
---> Package libotf.x86_64 0:0.9.9-3.1.el6 will be erased
---> Package librsvg2.x86_64 0:2.26.0-14.el6 will be erased
---> Package mesa-libGL.x86_64 0:9.2-0.5.el6_5.2 will be erased
--> Processing Dependency: libGL.so.1()(64bit) for package:
mesa-libGLU-9.2-0.5.el6_5.2.x86_64
--> Processing Dependency: mesa-libGL for package:
mesa-dri1-drivers-7.11-8.el6.x86_64
---> Package oprofile.x86_64 0:0.9.9-5.el6 will be erased
---> Package pango.x86_64 0:1.28.1-10.el6 will be erased
---> Package qt3.x86_64 0:3.3.8b-30.el6 will be erased
---> Package xorg-x11-drv-nvidia.x86_64 1:352.39-1.el6 will be erased
--> Processing Dependency: xorg-x11-drv-nvidia >= 1:352.39 for package:
cuda-drivers-352.39-0.x86_64
---> Package xorg-x11-drv-nvidia-libs.x86_64 1:352.39-1.el6 will be erased
--> Processing Dependency: libcuda.so.1()(64bit) for package:
1:xorg-x11-drv-nvidia-devel-352.39-1.el6.x86_64
--> Processing Dependency: libnvcuvid.so.1()(64bit) for package:
1:xorg-x11-drv-nvidia-devel-352.39-1.el6.x86_64
--> Processing Dependency: libOpenCL.so.1()(64bit) for package:
1:xorg-x11-drv-nvidia-devel-352.39-1.el6.x86_64
--> Processing Dependency: xorg-x11-drv-nvidia-libs(x86-64) = 1:352.39-1.el6 for
package: 1:xorg-x11-drv-nvidia-devel-352.39-1.el6.x86_64
--> Processing Dependency: xorg-x11-drv-nvidia-libs(x86-64) = 1:352.39-1.el6 for
package: 1:xorg-x11-drv-nvidia-gl-352.39-1.el6.x86_64
---> Package xorg-x11-xauth.x86_64 1:1.0.2-7.1.el6 will be erased
---> Package xterm.x86_64 0:253-1.el6 will be erased
--> Running transaction check
---> Package cuda-drivers.x86_64 0:352.39-0 will be erased
--> Processing Dependency: cuda-driver = 352.39 for package:
gpu-deployment-kit-352.39-0.x86_64
---> Package latencytop.x86_64 0:0.5-9.el6 will be erased
---> Package libfprint.x86_64 0:0.1.0-19.pre2.el6 will be erased
--> Processing Dependency: libfprint.so.0()(64bit) for package:
fprintd-0.1-21.git04fd09cfa.el6.x86_64
---> Package libgcj.x86_64 0:4.4.7-11.el6 will be erased
--> Processing Dependency: libgcj_bc.so.1()(64bit) for package:
gettext-devel-0.17-18.el6.x86_64
---> Package libvdpau.x86_64 0:0.9-1.el6 will be erased
---> Package mesa-dri1-drivers.x86_64 0:7.11-8.el6 will be erased
--> Processing Dependency: mesa-dri1-drivers >= 7.11-6 for package:
mesa-dri-drivers-9.2-0.5.el6_5.2.x86_64
---> Package mesa-libGLU.x86_64 0:9.2-0.5.el6_5.2 will be erased
---> Package pycairo.x86_64 0:1.8.6-2.1.el6 will be erased
---> Package python-matplotlib.x86_64 0:0.99.1.2-1.el6 will be erased
--> Processing Dependency: python-matplotlib for package:
seekwatcher-0.12-5.el6.noarch
---> Package xorg-x11-drv-nvidia-devel.x86_64 1:352.39-1.el6 will be erased
---> Package xorg-x11-drv-nvidia-gl.x86_64 1:352.39-1.el6 will be erased
--> Running transaction check
---> Package fprintd.x86_64 0:0.1-21.git04fd09cfa.el6 will be erased
--> Processing Dependency: fprintd = 0.1-21.git04fd09cfa.el6 for package:
fprintd-pam-0.1-21.git04fd09cfa.el6.x86_64
---> Package gettext-devel.x86_64 0:0.17-18.el6 will be erased
--> Processing Dependency: gettext-devel for package:
intltool-0.41.0-1.1.el6.noarch
---> Package gpu-deployment-kit.x86_64 0:352.39-0 will be erased
---> Package mesa-dri-drivers.x86_64 0:9.2-0.5.el6_5.2 will be erased
---> Package seekwatcher.noarch 0:0.12-5.el6 will be erased
--> Running transaction check
---> Package fprintd-pam.x86_64 0:0.1-21.git04fd09cfa.el6 will be erased
---> Package intltool.noarch 0:0.41.0-1.1.el6 will be erased
--> Finished Dependency Resolution

Dependencies Resolved

==================================================================================================== ====
Package Arch Version Repository
Size
==================================================================================================== ====
Removing:
libX11-common noarch 1.6.0-2.2.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 1.6 M
Removing for dependencies:
cairo x86_64 1.8.8-3.1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 779 k
cuda-drivers x86_64 352.39-0 @cuda-7-5-local
0.0
emacs x86_64 1:23.1-25.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 11 M
fprintd x86_64 0.1-21.git04fd09cfa.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6
106 k
fprintd-pam x86_64 0.1-21.git04fd09cfa.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6
17 k
gd x86_64 2.0.35-11.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 536 k
gdk-pixbuf2 x86_64 2.24.1-5.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 2.5 M
gettext-devel x86_64 0.17-18.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 621 k
giflib x86_64 4.1.6-3.1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 80 k
gnuplot x86_64 4.2.6-2.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 1.1 M
gnuplot-common x86_64 4.2.6-2.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 1.3 M
gpu-deployment-kit
x86_64 352.39-0 @cuda-7-5-local
3.8 M
gtk2 x86_64 2.24.23-6.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 12 M
intltool noarch 0.41.0-1.1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 164 k
latencytop x86_64 0.5-9.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 33 k
libX11 x86_64 1.6.0-2.2.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 1.2 M
libXaw x86_64 1.0.11-2.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 468 k
libXcomposite x86_64 0.4.3-4.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 31 k
libXcursor x86_64 1.1.14-2.1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 41 k
libXdamage x86_64 1.1.3-4.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 24 k
libXext x86_64 1.3.2-2.1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 84 k
libXfixes x86_64 5.0.1-2.1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 23 k
libXft x86_64 2.3.1-2.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 116 k
libXi x86_64 1.7.2-2.2.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 64 k
libXinerama x86_64 1.1.3-2.1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 12 k
libXmu x86_64 1.1.1-2.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 154 k
libXpm x86_64 3.5.10-2.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 102 k
libXrandr x86_64 1.4.1-2.1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 40 k
libXrender x86_64 0.9.8-2.1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 39 k
libXt x86_64 1.1.4-6.1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 406 k
libXtst x86_64 1.2.2-2.1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 27 k
libXxf86vm x86_64 1.1.2-2.el6 @rhel-6Server-x86_64-updates
39 k
libfprint x86_64 0.1.0-19.pre2.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6
261 k
libgcj x86_64 4.4.7-11.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 62 M
libotf x86_64 0.9.9-3.1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 184 k
librsvg2 x86_64 2.26.0-14.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 370 k
libvdpau x86_64 0.9-1.el6 installed
60 k
mesa-dri-drivers x86_64 9.2-0.5.el6_5.2 @rhel-6Server-x86_64-updates
23 M
mesa-dri1-drivers x86_64 7.11-8.el6 @rhel-6Server-x86_64-updates
13 M
mesa-libGL x86_64 9.2-0.5.el6_5.2 @rhel-6Server-x86_64-updates
379 k
mesa-libGLU x86_64 9.2-0.5.el6_5.2 @rhel-6Server-x86_64-updates
511 k
oprofile x86_64 0.9.9-5.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 10 M
pango x86_64 1.28.1-10.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 1.0 M
pycairo x86_64 1.8.6-2.1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 414 k
python-matplotlib x86_64 0.99.1.2-1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 13 M
qt3 x86_64 3.3.8b-30.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 11 M
seekwatcher noarch 0.12-5.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 54 k
xorg-x11-drv-nvidia
x86_64 1:352.39-1.el6 @cuda-7-5-local
11 M
xorg-x11-drv-nvidia-devel
x86_64 1:352.39-1.el6 @cuda-7-5-local
579 k
xorg-x11-drv-nvidia-gl
x86_64 1:352.39-1.el6 @cuda-7-5-local
94 M
xorg-x11-drv-nvidia-libs
x86_64 1:352.39-1.el6 @cuda-7-5-local
82 M
xorg-x11-xauth x86_64 1:1.0.2-7.1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 62 k
xterm x86_64 253-1.el6
@anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6 931 k

Transaction Summary
==================================================================================================== ====
Remove 54 Package(s)

Installed size: 363 M
Is this ok [y/N]: n
Exiting on user Command
-sh-4.1$
 
Old 11-17-2015, 03:29 PM   #5
JockVSJock
Senior Member
 
Registered: Jan 2004
Posts: 1,420
Blog Entries: 4

Rep: Reputation: 164Reputation: 164
First, please place your output in code tags, makes it easier to read for everyone trying to troubelshoot.

I looked in the RHEL Download Packages and can't find R, so I though you were being odd. However Googling around, I did see that there is a software package called R.


https://www.r-project.org/

http://www.rpmfind.net/linux/rpm2htm...ch.php?query=R


Looking at the README for RHEL:

https://cran.revolutionanalytics.com/

Quote:
2) Red Hat Enterprise Linux (RHEL)
CentOS
Scientific Linux
Oracle Linux
==================================

The Fedora RPMs for R have been ported to RHEL by the project Extra
Packages for Enterprise Linux (EPEL).

http://fedoraproject.org/wiki/EPEL

These RPMs are also compatible with distributions derived from RHEL.

To use the EPEL repository, it is sufficient to download and install
the appropriate "epel-release" RPM, as described in the EPEL FAQ:

https://fedoraproject.org/wiki/EPEL/..._repository.3F

Then R can be installed as described above in the section on Fedora.

What R rpms do you currently have installed?

Code:
yum list R-\*
 
Old 11-17-2015, 04:05 PM   #6
moonst
LQ Newbie
 
Registered: Nov 2015
Posts: 15

Original Poster
Rep: Reputation: Disabled
yum list for R gave many results. But it doesnt look like any of these are actually installed.

Quote:
-sh-4.1$ uname -a
Linux protein.x.com 2.6.32-504.el6.x86_64 #1 SMP Tue Sep 16 01:56:35 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux

-sh-4.1$ sudo yum list R-\* |grep x86
This system is not registered with RHN Classic or RHN Satellite.
You can use rhn_register to register.
RHN Satellite or RHN Classic support will be disabled.
R.x86_64 3.2.2-1.el6 epel
R-RODBC.x86_64 1.3.6-1.el6 epel
R-core.x86_64 3.2.2-1.el6 epel
R-core-devel.x86_64 3.2.2-1.el6 epel
R-devel.x86_64 3.2.2-1.el6 epel
R-java.x86_64 3.2.2-1.el6 epel
R-java-devel.x86_64 3.2.2-1.el6 epel
R-msm.x86_64 1.1.4-1.el6.1 epel
R-mvtnorm.x86_64 1.0.3-1.el6 epel
R-mvtnorm-devel.x86_64 1.0.3-1.el6 epel
R-qtl.x86_64 1.37.11-1.el6 epel

-sh-4.1$ sudo yum install R-core.x86_64
...
--> Finished Dependency Resolution
Error: Multilib version problems found. This often means that the root
cause is something else and multilib version checking is just
pointing out that there is a problem. Eg.:

1. You have an upgrade for audit-libs which is missing some
dependency that another package requires. Yum is trying to
solve this by installing an older version of audit-libs of the
different architecture. If you exclude the bad architecture
yum will tell you what the root cause is (which package
requires what). You can try redoing the upgrade with
--exclude audit-libs.otherarch ... this should give you an error
message showing the root cause of the problem.

2. You have multiple architectures of audit-libs installed, but
yum can only see an upgrade for one of those arcitectures.
If you don't want/need both architectures anymore then you
can remove the one with the missing update and everything
will work.

3. You have duplicate versions of audit-libs installed already.
You can use "yum check" to get yum show these errors.

...you can also use --setopt=protected_multilib=false to remove
this checking, however this is almost never the correct thing to
do as something else is very likely to go wrong (often causing
much more problems).

Protected multilib versions: audit-libs-2.2-2.el6.i686 != audit-libs-2.3.7-5.el6.x86_64
Error: Protected multilib versions: libstdc++-4.4.7-4.el6.i686 != libstdc++-4.4.7-11.el6.x86_64
Error: Protected multilib versions: libgcc-4.4.7-4.el6.i686 != libgcc-4.4.7-11.el6.x86_64
Error: Protected multilib versions: keyutils-libs-1.4-4.el6.i686 != keyutils-libs-1.4-5.el6.x86_64
Error: Protected multilib versions: avahi-libs-0.6.25-12.el6.i686 != avahi-libs-0.6.25-15.el6.x86_64
Error: Protected multilib versions: libcom_err-1.41.12-18.el6.i686 != libcom_err-1.41.12-21.el6.x86_64
Error: Protected multilib versions: gnutls-2.8.5-13.el6_5.i686 != gnutls-2.8.5-14.el6_5.x86_64
Error: Protected multilib versions: 1:cups-libs-1.4.2-50.el6_4.5.i686 != 1:cups-libs-1.4.2-67.el6.x86_64
Error: Protected multilib versions: libtasn1-2.3-3.el6_2.1.i686 != libtasn1-2.3-6.el6_5.x86_64
Error: Protected multilib versions: krb5-libs-1.10.3-15.el6_5.1.i686 != krb5-libs-1.10.3-33.el6.x86_64
Error: Protected multilib versions: libselinux-2.0.94-5.3.el6_4.1.i686 != libselinux-2.0.94-5.8.el6.x86_64
 
Old 11-17-2015, 05:31 PM   #7
chrism01
LQ Guru
 
Registered: Aug 2004
Location: Sydney
Distribution: Rocky 9.2
Posts: 18,359

Rep: Reputation: 2751Reputation: 2751Reputation: 2751Reputation: 2751Reputation: 2751Reputation: 2751Reputation: 2751Reputation: 2751Reputation: 2751Reputation: 2751Reputation: 2751
This
Quote:
This system is not registered with RHN Classic or RHN Satellite.
You can use rhn_register to register.
RHN Satellite or RHN Classic support will be disabled.
implies you have a RHEL system that is NOT registered with RedHat.
To use RHEL properly you have to pay for a subscription which gives you email/phone support AND updates(!).
No registration = no updates...

If you think you can manage without support, you can replace with the equivalent version of Centos ( free RHEL rebuild) - inc updates but not support.
 
Old 11-17-2015, 06:03 PM   #8
JockVSJock
Senior Member
 
Registered: Jan 2004
Posts: 1,420
Blog Entries: 4

Rep: Reputation: 164Reputation: 164
I was going to say that too..run the following command:

Code:
yum repolist
It will list the repositories that your RHEL system is hooked into. It would also get any dependencies that are having issues.

Dependencies are a pain, however being hooked into some sort of repository or having some software to manage the dependencies will really help in the long run.
 
Old 11-17-2015, 06:05 PM   #9
moonst
LQ Newbie
 
Registered: Nov 2015
Posts: 15

Original Poster
Rep: Reputation: Disabled
Here is the output of yum repolist.

Quote:
-sh-4.1$ sudo yum repolist
Loaded plugins: downloadonly, product-id, rhnplugin, security
This system is not registered with RHN Classic or RHN Satellite.
You can use rhn_register to register.
RHN Satellite or RHN Classic support will be disabled.
cuda-7-5-local | 2.5 kB 00:00 ...
elrepo | 2.9 kB 00:00
rhel-6Server-x86_64-base_os | 1.1 kB 00:00
rhel-6Server-x86_64-updates | 951 B 00:00
repo id repo name status
cuda-7-5-local cuda-7-5-local 39
elrepo ELRepo.org Community Enterprise Linux Repository - el6 305
epel Extra Packages for Enterprise Linux 6 - x86_64 11,866
epel-debuginfo Extra Packages for Enterprise Linux 6 - x86_64 - Debug 2,209
epel-source Extra Packages for Enterprise Linux 6 - x86_64 - Source 0
rhel-6Server-x86_64-base_os RHEL 6Server Base Operating System 3,596
rhel-6Server-x86_64-updates Tested RHEL 6Server-x86_64 Updates 5,316
repolist: 23,331
 
Old 11-17-2015, 06:27 PM   #10
moonst
LQ Newbie
 
Registered: Nov 2015
Posts: 15

Original Poster
Rep: Reputation: Disabled
Guys,

Remember when I stopped myself from removing libX11-common-1.6 since it was 363Mb and I was unsure of what misfortune it may bring? Well, I unfortunately got over that hesitation and removed it. Feel like I really shot myself in the foot with this. Any way to backtrack from this?

Quote:
-sh-4.1$ sudo yum remove libX11-common-1.6.0-2.2.el6.noarch
...
---> Package libXi.x86_64 0:1.7.2-2.2.el6 will be erased
---> Package libXinerama.x86_64 0:1.1.3-2.1.el6 will be erased
---> Package libXmu.x86_64 0:1.1.1-2.el6 will be erased
---> Package libXpm.x86_64 0:3.5.10-2.el6 will be erased
---> Package libXrandr.x86_64 0:1.4.1-2.1.el6 will be erased
---> Package libXrender.x86_64 0:0.9.8-2.1.el6 will be erased
---> Package libXt.x86_64 0:1.1.4-6.1.el6 will be erased
---> Package libXtst.x86_64 0:1.2.2-2.1.el6 will be erased
...
after 54 such messages
...
Transaction Summary
==================================================================================================== ====
Remove 54 Package(s)

Installed size: 363 M
Is this ok [y/N]: y
Downloading Packages:
Running rpm_check_debug
Running Transaction Test
Transaction Test Succeeded
Running Transaction
Erasing : intltool-0.41.0-1.1.el6.noarch 1/54
Erasing : seekwatcher-0.12-5.el6.noarch 2/54
Erasing : 1:emacs-23.1-25.el6.x86_64 3/54
Erasing : librsvg2-2.26.0-14.el6.x86_64 4/54
...
Erasing : gdk-pixbuf2-2.24.1-5.el6.x86_64 52/54
Erasing : libX11-1.6.0-2.2.el6.x86_64 53/54
Erasing : libX11-common-1.6.0-2.2.el6.noarch 54/54
Verifying : pycairo-1.8.6-2.1.el6.x86_64 1/54
Verifying : 1:xorg-x11-drv-nvidia-libs-352.39-1.el6.x86_64 2/54
..
Verifying : libX11-common-1.6.0-2.2.el6.noarch 53/54
Verifying : cuda-drivers-352.39-0.x86_64 54/54

Removed:
libX11-common.noarch 0:1.6.0-2.2.el6

Dependency Removed:
cairo.x86_64 0:1.8.8-3.1.el6 cuda-drivers.x86_64 0:352.39-0
..
xorg-x11-drv-nvidia-libs.x86_64 1:352.39-1.el6 xorg-x11-xauth.x86_64 1:1.0.2-7.1.el6
xterm.x86_64 0:253-1.el6

Complete!
 
Old 11-17-2015, 07:02 PM   #11
moonst
LQ Newbie
 
Registered: Nov 2015
Posts: 15

Original Poster
Rep: Reputation: Disabled
On the bright side I typescripted this and know exactly which 54 packages I seem to have erased. I am slowly beginning to install them. Some packages seem to install dependencies that are also on the list. So maybe I wont need to install all 54.
 
Old 11-17-2015, 10:01 PM   #12
moonst
LQ Newbie
 
Registered: Nov 2015
Posts: 15

Original Poster
Rep: Reputation: Disabled
I managed to reinstall most packages that got erased. I now have

Quote:
-sh-4.1$ rpm -q libX11-common
libX11-common-1.5.0-4.el6.noarch
-sh-4.1$ sudo yum install R
..
Error: Protected multilib versions: libxcb-1.8.1-1.el6.i686 != libxcb-1.9.1-2.el6.x86_64
Error: Protected multilib versions: libcom_err-1.41.12-18.el6.i686 != libcom_err-1.41.12-21.el6.x86_64
...

-sh-4.1$ rpm -q libxcb
libxcb-1.9.1-2.el6.x86_64
So libxcb..i686 clashes with libxcb..x86_64. But rpm -q says that I only have libxcb..x86_64. So why the clash?
 
Old 11-17-2015, 10:23 PM   #13
moonst
LQ Newbie
 
Registered: Nov 2015
Posts: 15

Original Poster
Rep: Reputation: Disabled
Whichever way I see, I simply cannot find libxcb.i686 installed.

Quote:
-sh-4.1$ sudo yum list libxcb
Installed Packages
libxcb.x86_64 1.9.1-2.el6 @anaconda-RedHatEnterpriseLinux-201409260744.x86_64/6.6
Available Packages
libxcb.i686 1.8.1-1.el6 rhel-6Server-x86_64-updates

-sh-4.1$ sudo yum install R
..
Error: Protected multilib versions: libxcb-1.8.1-1.el6.i686 != libxcb-1.9.1-2.el6.x86_64
...
 
Old 11-18-2015, 01:47 PM   #14
John VV
LQ Muse
 
Registered: Aug 2005
Location: A2 area Mi.
Posts: 17,624

Rep: Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651Reputation: 2651
in post #3 YOU!!! posted the CAUSE OF THIS PROBLEM
Quote:
This system is not registered with RHN Classic or RHN Satellite.
You can use rhn_register to register.
RHN Satellite or RHN Classic support will be disabled.
then in post #7 "chrism01"
pointed this out to you

FIX THAT!!!!

you MUST buy the required suport contract from redhat to install software!
there are NO!!!! "if's, and's, or but's" on this

buy the REQUIRED support contract
https://www.redhat.com/wapps/store/catalog.html


or
do not use RHEL!!!

plain and SIMPLE!!!!

buy it
https://www.redhat.com/wapps/store/catalog.html

or use one of the FREE alternatives
CentOS 7.1 ( or the older 6.7 )
Scientific Linux 7.1 ( or the older 6.7 )
Last edited by John VV; 11-18-2015 at 01:50 PM.
 
  


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