Doug Fir
Reputation: 21204
Install R on redHat CentOs 7. Several errors and dependencies I'm unable to overcome
I'm using redhat centos 7 and am attempting to install R:
sudo yum install R
Returns:
Error: Package: R-java-devel-3.5.1-1.el7.x86_64 (epel)
Requires: java-devel
Available: 1:java-1.7.0-openjdk-devel-1.7.0.171-2.6.13.2.el7.x86_64 (centos-base-prod)
java-devel = 1:1.7.0
Available: 1:java-1.7.0-openjdk-devel-1.7.0.181-2.6.14.5.el7.x86_64 (centos-updates-prod)
java-devel = 1:1.7.0
Available: 1:java-1.7.0-openjdk-devel-1.7.0.181-2.6.14.8.el7_5.x86_64 (centos-updates-prod)
java-devel = 1:1.7.0
Available: 1:java-1.7.0-openjdk-devel-1.7.0.191-2.6.15.4.el7_5.x86_64 (centos-updates-prod)
java-devel = 1:1.7.0
Available: 1:java-1.8.0-openjdk-devel-1.8.0.161-2.b14.el7.i686 (centos-base-prod)
java-devel = 1:1.8.0
Available: 1:java-1.8.0-openjdk-devel-1.8.0.171-7.b10.el7.i686 (centos-updates-prod)
java-devel = 1:1.8.0
Available: 1:java-1.8.0-openjdk-devel-1.8.0.171-8.b10.el7_5.i686 (centos-updates-prod)
java-devel = 1:1.8.0
Available: 1:java-1.8.0-openjdk-devel-1.8.0.181-3.b13.el7_5.i686 (centos-updates-prod)
java-devel = 1:1.8.0
Error: Package: R-java-3.5.1-1.el7.x86_64 (epel)
Requires: java-headless
Available: 1:java-1.7.0-openjdk-headless-1.7.0.171-2.6.13.2.el7.x86_64 (centos-base-prod)
java-headless = 1:1.7.0
Available: 1:java-1.7.0-openjdk-headless-1.7.0.181-2.6.14.5.el7.x86_64 (centos-updates-prod)
java-headless = 1:1.7.0
Available: 1:java-1.7.0-openjdk-headless-1.7.0.181-2.6.14.8.el7_5.x86_64 (centos-updates-prod)
java-headless = 1:1.7.0
Available: 1:java-1.7.0-openjdk-headless-1.7.0.191-2.6.15.4.el7_5.x86_64 (centos-updates-prod)
java-headless = 1:1.7.0
Available: 1:java-1.8.0-openjdk-headless-1.8.0.161-2.b14.el7.i686 (centos-base-prod)
java-headless = 1:1.8.0
Available: 1:java-1.8.0-openjdk-headless-1.8.0.171-7.b10.el7.i686 (centos-updates-prod)
java-headless = 1:1.8.0
Available: 1:java-1.8.0-openjdk-headless-1.8.0.171-8.b10.el7_5.i686 (centos-updates-prod)
java-headless = 1:1.8.0
Available: 1:java-1.8.0-openjdk-headless-1.8.0.181-3.b13.el7_5.i686 (centos-updates-prod)
java-headless = 1:1.8.0
Based on the error message I tried to install java-devel:
sudo yum install java-devel
Which gives:
Package 1:java-1.8.0-openjdk-devel-1.8.0.181-3.b13.el7_5.x86_64 is obsoleted by 2000:gd-jdk8-1.8.0_92-fcs.x86_64 which is already installed
Nothing to do
How can I install java-devel in order to install R?
[Edit]
Java version:
java -version java version "1.8.0_92" Java(TM) SE Runtime Environment (build 1.8.0_92-b14) Java HotSpot(TM) 64-Bit Server VM (build 25.92-b14, mixed mode)
[Edit]
Have also tried the following:
sudo yum install R-java-devel
Which gives:
Error: Package: R-java-devel-3.5.1-1.el7.x86_64 (epel)
Requires: java-devel
Available: 1:java-1.7.0-openjdk-devel-1.7.0.171-2.6.13.2.el7.x86_64 (centos-base-prod)
java-devel = 1:1.7.0
Available: 1:java-1.7.0-openjdk-devel-1.7.0.181-2.6.14.5.el7.x86_64 (centos-updates-prod)
java-devel = 1:1.7.0
Available: 1:java-1.7.0-openjdk-devel-1.7.0.181-2.6.14.8.el7_5.x86_64 (centos-updates-prod)
java-devel = 1:1.7.0
Available: 1:java-1.7.0-openjdk-devel-1.7.0.191-2.6.15.4.el7_5.x86_64 (centos-updates-prod)
java-devel = 1:1.7.0
Available: 1:java-1.8.0-openjdk-devel-1.8.0.161-2.b14.el7.i686 (centos-base-prod)
java-devel = 1:1.8.0
Available: 1:java-1.8.0-openjdk-devel-1.8.0.171-7.b10.el7.i686 (centos-updates-prod)
java-devel = 1:1.8.0
Available: 1:java-1.8.0-openjdk-devel-1.8.0.171-8.b10.el7_5.i686 (centos-updates-prod)
java-devel = 1:1.8.0
Available: 1:java-1.8.0-openjdk-devel-1.8.0.181-3.b13.el7_5.i686 (centos-updates-prod)
java-devel = 1:1.8.0
Also tried a specific version:
sudo yum install java-1.8.0-openjdk-devel-1.8.0.181-3.b13.el7_5.i686
Which returned: "Package 1:java-1.8.0-openjdk-devel-1.8.0.181-3.b13.el7_5.i686 is obsoleted by 2000:gd-jdk8-1.8.0_92-fcs.x86_64 which is already installed Nothing to do".
How can I overcome these issues? Tag suggestions welcome too.
[Edit]
From comments, here is the output from yum repolist
Loaded plugins: changelog, fastestmirror, priorities, versionlock
Determining fastest mirrors
* epel: mirror.prgmr.com
centos-base-prod 9911/9911
centos-cpm-prod 125/125
centos-epel-prod 15503/15503
centos-extras-prod 402/402
centos-hips-prod 72/72
centos-itsec-prod 82/82
centos-pbis-prod 43/43
centos-puppet3-prod 242/242
centos-serverspec-prod 11/11
centos-updates-prod 1348/1348
centos_itsec_prod 82/82
collectd-enterprise 232/232
epel 12743/12743
gd-prod-centos-v6-64bit-scl 1121/1121
gd-prod-centos-v6-64bit-tms 163/163
gd-prod-centos-v7-64bit-base 9911/9911
gd-prod-centos-v7-64bit-epel 15503/15503
gd-prod-centos-v7-64bit-extras 402/402
gd-prod-centos-v7-64bit-hips 72/72
gd-prod-centos-v7-64bit-pan 83/83
gd-prod-centos-v7-64bit-sensu 2113/2113
gd-prod-centos-v7-64bit-updates 1348/1348
gdsnow 3/3
gutils 11/11
prod_centos_7_noarch_gd-snow 3/3
sensu-enterprise 4560/4560
yumrepos 87/87
repo id repo name status
!centos-base-prod/x86_64 centos-base-prod 9,910+1
!centos-cpm-prod/x86_64 centos-cpm-prod 125
!centos-epel-prod/x86_64 centos-epel-prod 15,503
!centos-extras-prod/x86_64 centos-extras-prod 402
!centos-hips-prod/x86_64 centos-hips-prod 72
!centos-itsec-prod/x86_64 centos-itsec-prod 82
!centos-pbis-prod/x86_64 centos-pbis-prod 43
!centos-puppet3-prod/x86_64 Centos Puppet prod Packages 242
!centos-sclo-rh/x86_64 CentOS-7 - SCLo rh 8,090
!centos-serverspec-prod/x86_64 centos-serverspec-prod 11
!centos-updates-prod/x86_64 centos-updates-prod 1,347+1
!centos_itsec_prod/x86_64 centos_itsec_prod 82
!collectd-enterprise/x86_64 Enterprise Collectd Packages 231+1
!epel/x86_64 Extra Packages for Enterprise Linux 7 - x86_64 12,743
!gd-prod-centos-v6-64bit-scl gd-prod-centos-v6-64bit-scl 1,121
!gd-prod-centos-v6-64bit-tms gd-prod-centos-v6-64bit-tms 163
!gd-prod-centos-v7-64bit-base gd-prod-centos-v7-64bit-base 9,910+1
!gd-prod-centos-v7-64bit-epel gd-prod-centos-v7-64bit-epel 15,503
!gd-prod-centos-v7-64bit-extras gd-prod-centos-v7-64bit-extras 402
!gd-prod-centos-v7-64bit-hips gd-prod-centos-v7-64bit-hips 72
!gd-prod-centos-v7-64bit-pan gd-prod-centos-v7-64bit-pan 82+1
!gd-prod-centos-v7-64bit-sensu gd-prod-centos-v7-64bit-sensu 2,113
!gd-prod-centos-v7-64bit-updates gd-prod-centos-v7-64bit-updates 1,347+1
!gdsnow prod_centos_7_noarch_gd-snow 3
!gutils/x86_64 GUtils Packages 11
!prod_centos_7_noarch_gd-snow prod_centos_7_noarch_gd-snow 3
!prod_centos_7_x86_64_saltstack prod_centos_7_x86_64_saltstack 76+26
!sensu-enterprise/x86_64 Enterprise Sensu Packages 4,560
!yumrepos Enterprise Yum Repos Repo 87
repolist: 84,336
[edit]
enabled only epel, base and updates repos per comments yum repolist all:
After that I tried again with sudo yum install R
This produced:
Error: Package: libRmath-devel-3.5.0-1.el7.x86_64 (centos-epel-prod)
Requires: libRmath = 3.5.0-1.el7
Installed: libRmath-3.5.1-1.el7.x86_64 (@epel)
libRmath = 3.5.1-1.el7
Available: libRmath-3.5.0-1.el7.x86_64 (centos-epel-prod)
libRmath = 3.5.0-1.el7
Error: Package: R-java-3.5.0-1.el7.x86_64 (centos-epel-prod)
Requires: R-core = 3.5.0-1.el7
Installed: R-core-3.5.1-1.el7.x86_64 (@epel)
R-core = 3.5.1-1.el7
Available: R-core-3.5.0-1.el7.x86_64 (centos-epel-prod)
R-core = 3.5.0-1.el7
Error: Package: 1:java-1.7.0-openjdk-1.7.0.181-2.6.14.8.el7_5.x86_64 (centos-updates-prod)
Requires: java-1.7.0-openjdk-headless = 1:1.7.0.181-2.6.14.8.el7_5
Available: 1:java-1.7.0-openjdk-headless-1.7.0.171-2.6.13.2.el7.x86_64 (centos-base-prod)
java-1.7.0-openjdk-headless = 1:1.7.0.171-2.6.13.2.el7
Available: 1:java-1.7.0-openjdk-headless-1.7.0.181-2.6.14.5.el7.x86_64 (centos-updates-prod)
java-1.7.0-openjdk-headless = 1:1.7.0.181-2.6.14.5.el7
Available: 1:java-1.7.0-openjdk-headless-1.7.0.181-2.6.14.8.el7_5.x86_64 (centos-updates-prod)
java-1.7.0-openjdk-headless = 1:1.7.0.181-2.6.14.8.el7_5
Installing: 1:java-1.7.0-openjdk-headless-1.7.0.191-2.6.15.4.el7_5.x86_64 (centos-updates-prod)
java-1.7.0-openjdk-headless = 1:1.7.0.191-2.6.15.4.el7_5
Error: Package: R-java-devel-3.5.0-1.el7.x86_64 (centos-epel-prod)
Requires: java-devel
Error: Package: R-core-devel-3.5.0-1.el7.x86_64 (centos-epel-prod)
Requires: R-core = 3.5.0-1.el7
Installed: R-core-3.5.1-1.el7.x86_64 (@epel)
R-core = 3.5.1-1.el7
Available: R-core-3.5.0-1.el7.x86_64 (centos-epel-prod)
R-core = 3.5.0-1.el7
Error: Package: 1:java-1.8.0-openjdk-1.8.0.171-7.b10.el7.x86_64 (centos-updates-prod)
Requires: java-1.8.0-openjdk-headless(x86-64) = 1:1.8.0.171-7.b10.el7
Available: 1:java-1.8.0-openjdk-headless-1.8.0.161-2.b14.el7.x86_64 (centos-base-prod)
java-1.8.0-openjdk-headless(x86-64) = 1:1.8.0.161-2.b14.el7
Available: 1:java-1.8.0-openjdk-headless-1.8.0.171-7.b10.el7.i686 (centos-updates-prod)
~java-1.8.0-openjdk-headless(x86-32) = 1:1.8.0.171-7.b10.el7
Error: Package: 1:java-1.7.0-openjdk-1.7.0.181-2.6.14.5.el7.x86_64 (centos-updates-prod)
Requires: java-1.7.0-openjdk-headless = 1:1.7.0.181-2.6.14.5.el7
Available: 1:java-1.7.0-openjdk-headless-1.7.0.171-2.6.13.2.el7.x86_64 (centos-base-prod)
java-1.7.0-openjdk-headless = 1:1.7.0.171-2.6.13.2.el7
Available: 1:java-1.7.0-openjdk-headless-1.7.0.181-2.6.14.5.el7.x86_64 (centos-updates-prod)
java-1.7.0-openjdk-headless = 1:1.7.0.181-2.6.14.5.el7
Available: 1:java-1.7.0-openjdk-headless-1.7.0.181-2.6.14.8.el7_5.x86_64 (centos-updates-prod)
java-1.7.0-openjdk-headless = 1:1.7.0.181-2.6.14.8.el7_5
Installing: 1:java-1.7.0-openjdk-headless-1.7.0.191-2.6.15.4.el7_5.x86_64 (centos-updates-prod)
java-1.7.0-openjdk-headless = 1:1.7.0.191-2.6.15.4.el7_5
Error: Package: 1:java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64 (centos-updates-prod)
Requires: java-1.8.0-openjdk-headless(x86-64) = 1:1.8.0.171-8.b10.el7_5
Available: 1:java-1.8.0-openjdk-headless-1.8.0.161-2.b14.el7.x86_64 (centos-base-prod)
java-1.8.0-openjdk-headless(x86-64) = 1:1.8.0.161-2.b14.el7
Available: 1:java-1.8.0-openjdk-headless-1.8.0.171-7.b10.el7.i686 (centos-updates-prod)
~java-1.8.0-openjdk-headless(x86-32) = 1:1.8.0.171-7.b10.el7
Available: 1:java-1.8.0-openjdk-headless-1.8.0.171-8.b10.el7_5.i686 (centos-updates-prod)
~java-1.8.0-openjdk-headless(x86-32) = 1:1.8.0.171-8.b10.el7_5
Error: Package: 1:java-1.7.0-openjdk-1.7.0.171-2.6.13.2.el7.x86_64 (centos-base-prod)
Requires: java-1.7.0-openjdk-headless = 1:1.7.0.171-2.6.13.2.el7
Available: 1:java-1.7.0-openjdk-headless-1.7.0.171-2.6.13.2.el7.x86_64 (centos-base-prod)
java-1.7.0-openjdk-headless = 1:1.7.0.171-2.6.13.2.el7
Available: 1:java-1.7.0-openjdk-headless-1.7.0.181-2.6.14.5.el7.x86_64 (centos-updates-prod)
java-1.7.0-openjdk-headless = 1:1.7.0.181-2.6.14.5.el7
Available: 1:java-1.7.0-openjdk-headless-1.7.0.181-2.6.14.8.el7_5.x86_64 (centos-updates-prod)
java-1.7.0-openjdk-headless = 1:1.7.0.181-2.6.14.8.el7_5
Installing: 1:java-1.7.0-openjdk-headless-1.7.0.191-2.6.15.4.el7_5.x86_64 (centos-updates-prod)
java-1.7.0-openjdk-headless = 1:1.7.0.191-2.6.15.4.el7_5
You could try using --skip-broken to work around the problem
You could try running: rpm -Va --nofiles --nodigest
Upvotes: 1
Views: 1016
Answers (1)
user3788685
Reputation: 3093
So it appears you have conflicting packages installed from possibly 'odd' locations.
1:java-1.8.0-openjdk-devel-1.8.0.181-3.b13.el7_5.i686 is obsoleted by 2000:gd-jdk8-1.8.0_92-fcs.x86_64 is telling us that gd-jdk8 is providing the same thing as java-1.8.0-openjdk-devel but R doesn't like that name and wants a proper java and java-devel package.
First thing you need to do is disable all of these odd repos you have enabled and only use the epel base and updates repos.
If you navigate to; /etc/yum.repos.d/ you should find a folder full of files. open them up and change enabled=1 to enabled=0 which will disable them.
Now you should be able to yum erase gd-jdk8 and remove that along with any deps. Then you should be able to do yum install java-devel which should give you the correct version.
Once you have done that you will need to downgrade you R-core and libRmath packages as it appears from our chat you have some how managed to install newer versions of those that R also wants.
Do; yum downgrade R-core libRmath and say 'yes' to the deps. That should bring you down to the correct version you need.
Lastly do yum install R and with a bit of luck it should install for you!
It looks like a lot of packages my be provided by an internal repo or something, as you had a lot of things prefixed 'gd' which are not actually gd as people might expect! I'd have a word with your operations/IT team to see what's going on.
Lastly remember you disabled all those other repos - well you may wish to re-enable them now BUT... if you ever do a yum update make very sure you know what it's going to do as it might try and replace things with those 'gd' prefixed packages.
Yum did actually tell you what was wrong with the is obsoleted line. But granted digging into the deps requires a little more knowledge especially when your not sure what your looking at, and it's not a 'stock' install of CentOS!
Upvotes: 1
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