Following the release of R 3, I was having several yum error messages relating to R when yum updating my system. After yum removing R and its dependencies I started again from scratch. However, I cannot get R-devel or R-core-devel installed and cannot get around this issue. Here are my error messages following yum install R-core-devel R-devel
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package R-core-devel.x86_64 0:3.1.0-5.el6 will be installed
--> Processing Dependency: xz-devel for package: R-core-devel-3.1.0-5.el6.x86_64
--> Processing Dependency: libicu-devel for package: R-core-devel-3.1.0-5.el6.x86_64
---> Package R-devel.x86_64 0:3.1.0-5.el6 will be installed
--> Processing Dependency: R-java-devel = 3.1.0-5.el6 for package: R-devel-3.1.0-5.el6.x86_64
--> Running transaction check
---> Package R-core-devel.x86_64 0:3.1.0-5.el6 will be installed
--> Processing Dependency: libicu-devel for package: R-core-devel-3.1.0-5.el6.x86_64
---> Package R-java-devel.x86_64 0:3.0.2-1.el6 will be updated
---> Package R-java-devel.x86_64 0:3.1.0-5.el6 will be an update
---> Package xz-devel.x86_64 0:4.999.9-0.3.beta.20091007git.el6 will be installed
--> Finished Dependency Resolution
Error: Package: R-core-devel-3.1.0-5.el6.x86_64 (epel)
Requires: libicu-devel
You could try using --skip-broken to work around the problem
** Found 2 pre-existing rpmdb problem(s), 'yum check' output follows:
R-java-3.0.2-1.el6.x86_64 has missing requires of R-core = ('0', '3.0.2', '1.el6')
R-java-devel-3.0.2-1.el6.x86_64 has missing requires of R-core-devel = ('0', '3.0.2', '1.el6')
What does this mean and how can I resolve the issue
I had the same problem. The following answer worked for me:
Problems installing R on Linux CentOS 6.2
Specifically, I did this:
$ sudo yum install texinfo-tex
$ rpm -Uvh http://dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm
$ sudo yum install tcl
$ sudo yum clean all
$ sudo yum install R
Related
I am trying to install R on RHEL 7 but i get the following error.
Error: Package: R-core-devel-3.2.3-4.el7.x86_64 (epel)
Requires: blas-devel >= 3.0
Error: Package: R-core-devel-3.2.3-4.el7.x86_64 (epel)
Requires: lapack-devel
Error: Package: R-core-devel-3.2.3-4.el7.x86_64 (epel)
Requires: texinfo-tex
I installed epel-release-7-8.noarch. I also tried to group install Development tools as below.
yum group install "Development tools"
Tried to enable repos
yum-config-manager --enable epel
I tried several suggestions posted in internet. but nothing seems to work or solve my issue. Can somebody help me install R? It should be a simple three steps process but now it became a nightmare for me to complete it. Please find below system details.
Red Hat Enterprise Linux Server release 7.1 (Maipo)
Many thanks!
You should just install couple of dependencies.
$ sudo dnf -y install blas-devel lapack-devel texinfo-tex
centos 6.5 yum php 5.5.35 I run yum install php-xml
Get the error messageļ¼
Loaded plugins: fastestmirror, security
Loading mirror speeds from cached hostfile
* base: mirrors.nwsuaf.edu.cn
* epel: mirrors.opencas.cn
* extras: mirrors.pubyun.com
* remi-safe: mirror.awanti.com
* updates: mirrors.pubyun.com
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package php-xml.x86_64 0:5.3.3-46.el6_7.1 will be installed
--> Processing Dependency: php-common(x86-64) = 5.3.3-46.el6_7.1 for package: php-xml-5.3.3-46.el6_7.1.x86_64
--> Finished Dependency Resolution
Error: Package: php-xml-5.3.3-46.el6_7.1.x86_64 (updates)
Requires: php-common(x86-64) = 5.3.3-46.el6_7.1
Installed: php-common-5.5.35-1.el6.remi.x86_64 (#remi-php55)
php-common(x86-64) = 5.5.35-1.el6.remi
Available: php-common-5.3.3-40.el6_6.x86_64 (base)
php-common(x86-64) = 5.3.3-40.el6_6
Available: php-common-5.3.3-46.el6_6.x86_64 (updates)
php-common(x86-64) = 5.3.3-46.el6_6
Available: php-common-5.3.3-46.el6_7.1.x86_64 (updates)
php-common(x86-64) = 5.3.3-46.el6_7.1
You could try using --skip-broken to work around the problem
** Found 2 pre-existing rpmdb problem(s), 'yum check' output follows:
php5-xmlreader-5.5.14-38.1.x86_64 has missing requires of php5 = ('0', '5.5.14', None)
php5-xmlreader-5.5.14-38.1.x86_64 has missing requires of php5-dom = ('0', '5.5.14', None)
I am searching for a long time on net. But no use. Please help or try to give some ideas how to achieve this
PHP 5.5.35 is installed from "remi-php55" which is not enabled by default, so you need to enable it to get correct version of php-xml.
See the Configuration Wizard
Either:
yum --enablerepo=remi-php55 install php-xml
Or better (to avoid future issues, and get updates)
yum install yum-utils
yum-config-manager --enable remi-php55
yum install php-xml
I am trying to install R with Rstudio on an Amazon AWS AMI. It currently ships R-3.1 and I would like it to have R-3.2. I am currently using 2013.03 release but the new 2015 version also doesn't have the right version.
The yum install R command won't upgrade it.
root#ip-172-31-3-136 tmp]$ sudo yum install R
Loaded plugins: priorities, update-motd, upgrade-helper
amzn-main/latest
| 2.1 kB 00:00
amzn-updates/latest
| 2.3 kB 00:00
704 packages excluded due to repository priority protections
Package R-3.1.1-3.18.amzn1.x86_64 already installed and latest version
Nothing to do
I figured I'd add another rpm repo, so I download the rpm list from the most recent CentOS.
wget http://www.mirrorservice.org/sites/dl.fedoraproject.org/pub/epel/7/x86_64/e/epel-release-7-5.noarch.rpm
sudo yum localinstall epel-release-7-5.noarch.rpm
sudo yum install R
This also doesn't work and gives me a list of errors like:
Error: Package: python26-2.6.9-1.80.amzn1.x86_64 (#amzn-updates)
Requires: libdb-4.7.so()(64bit)
Removing: db4-4.7.25-17.10.amzn1.x86_64 (installed)
libdb-4.7.so()(64bit)
Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
~libdb-4.8.so()(64bit)
Updated By: db4-4.7.25-18.11.amzn1.x86_64 (amzn-main)
libdb-4.7.so()(64bit)
Error: libdb4 conflicts with filesystem-2.4.30-3.8.amzn1.x86_64
Error: Package: rpm-python26-4.11.2-2.64.amzn1.x86_64 (#amzn-updates)
Requires: libdb-4.7.so()(64bit)
Removing: db4-4.7.25-17.10.amzn1.x86_64 (installed)
libdb-4.7.so()(64bit)
Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
~libdb-4.8.so()(64bit)
Updated By: db4-4.7.25-18.11.amzn1.x86_64 (amzn-main)
libdb-4.7.so()(64bit)
Error: Package: httpd-2.2.29-1.5.amzn1.x86_64 (#amzn-main)
Requires: libdb-4.7.so()(64bit)
Removing: db4-4.7.25-17.10.amzn1.x86_64 (installed)
libdb-4.7.so()(64bit)
Obsoleted By: libdb4-4.8.30-13.el7.x86_64 (epel)
~libdb-4.8.so()(64bit)
Updated By: db4-4.7.25-18.11.amzn1.x86_64 (amzn-main)
libdb-4.7.so()(64bit)
I am trying to install R as part of a provisioning script so preferably I would be able to to not have to install from source as this takes a LONG time.
The --enablerepo=epel trick also does not work either.
root#ip-172-31-3-136 tmp]$ sudo yum install R --enablerepo=epel
Loaded plugins: priorities, update-motd, upgrade-helper
amzn-main/latest | 2.1 kB 00:00
amzn-updates/latest | 2.3 kB 00:00
704 packages excluded due to repository priority protections
Package R-3.1.1-3.18.amzn1.x86_64 already installed and latest version
Nothing to do
This all seems very confusing as the following script does work on a CENTOS 7 box when I start it on digital ocean:
[root#servy-server ~]# yum install -y epel-release
[root#servy-server ~]# yum update -y
[root#servy-server ~]# yum install -y R
[root#servy-server ~]# R
The latest Amazon AWS AMI now ships with R version 3.2.
I have installed R before on a machine running RedHat EL6.5, but I recently had a problem installing new packages (i.e. install.packages()). Since I couldn't find a solution to this, I tried reinstalling R using:
sudo yum remove R
and
sudo yum install R
But now I get:
....
---> Package R-core-devel.x86_64 0:3.1.0-5.el6 will be installed
--> Processing Dependency: blas-devel >= 3.0 for package: R-core-devel-3.1.0-5.el6.x86_64
--> Processing Dependency: libicu-devel for package: R-core-devel-3.1.0-5.el6.x86_64
--> Processing Dependency: lapack-devel for package: R-core-devel-3.1.0-5.el6.x86_64
---> Package xz-devel.x86_64 0:4.999.9-0.3.beta.20091007git.el6 will be installed
--> Finished Dependency Resolution
Error: Package: R-core-devel-3.1.0-5.el6.x86_64 (epel)
Requires: blas-devel >= 3.0
Error: Package: R-core-devel-3.1.0-5.el6.x86_64 (epel)
Requires: lapack-devel
Error: Package: R-core-devel-3.1.0-5.el6.x86_64 (epel)
Requires: libicu-devel
You could try using --skip-broken to work around the problem
You could try running: rpm -Va --nofiles --nodigest
I already checked, and blas-devel is installed, but the newest version is 0.2.8. Checked using:
yum info openblas-devel.x86_64
Any thoughts as to what is going wrong? Thanks.
Do the following:
vim /etc/yum.repos.d/redhat.repo
Change enabled = 0 in [rhel-6-server-optional-rpms] section of the file to enabled=1
yum install R
DONE!
I think I should give reference to the site of solution:
https://bluehatrecord.wordpress.com/2014/10/13/installing-r-on-red-hat-enterprise-linux-6-5/
I had the same issue. Not sure why these packages are missing from RHEL's repos, but they are in CentOS 6.5, so the follow solution works, if you want to keep things in the package paradigm:
wget http://mirror.centos.org/centos/6/os/x86_64/Packages/lapack-devel-3.2.1-4.el6.x86_64.rpm
wget http://mirror.centos.org/centos/6/os/x86_64/Packages/blas-devel-3.2.1-4.el6.x86_64.rpm
wget http://mirror.centos.org/centos/6/os/x86_64/Packages/texinfo-tex-4.13a-8.el6.x86_64.rpm
wget http://mirror.centos.org/centos/6/os/x86_64/Packages/libicu-devel-4.2.1-9.1.el6_2.x86_64.rpm
sudo yum localinstall *.rpm
cheers
UPDATE: Leon's answer is better -- see below.
The best solution I could come up with was to install from source. This worked and was not too bad. However, now it isn't in my package manager.
i've just setup my server using centos 6.4, and right now i want to install nginx using yum, but i always get error require dependency. but i check on /usr/lib64/ library is not missing.
i really don't understand how to solve this.
this is my nginx.repo
[nginx]
name=nginx repo
baseurl=http://nginx.org/packages/centos/6/$basearch/
gpgcheck=0
enabled=1
this is error from yum install nginx
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package nginx.x86_64 0:1.4.6-1.el6.ngx will be installed
--> Processing Dependency: libssl.so.10(libssl.so.10)(64bit) for package: nginx-1.4.6-1.el6.ngx.x86_64
--> Processing Dependency: libcrypto.so.10(libcrypto.so.10)(64bit) for package: nginx-1.4.6-1.el6.ngx.x86_64
--> Processing Dependency: libcrypto.so.10(OPENSSL_1.0.1_EC)(64bit) for package: nginx-1.4.6-1.el6.ngx.x86_64
--> Finished Dependency Resolution
Error: Package: nginx-1.4.6-1.el6.ngx.x86_64 (nginx)
Requires: libcrypto.so.10(libcrypto.so.10)(64bit)
Error: Package: nginx-1.4.6-1.el6.ngx.x86_64 (nginx)
Requires: libcrypto.so.10(OPENSSL_1.0.1_EC)(64bit)
Error: Package: nginx-1.4.6-1.el6.ngx.x86_64 (nginx)
Requires: libssl.so.10(libssl.so.10)(64bit)
You could try using --skip-broken to work around the problem
You could try running: rpm -Va --nofiles --nodigest