I am using Red Hat 6.4 without internet connection. I am trying to install R using CRAN. While I install some dependencies are needed. Some of them are already installed on the server. The issue is when I installed the one of dependency. For example, I need xz version 5.0.3. The server already have xz version 4.9. Is there anyway to update the version of xz? I already tried to install over 4.9 using tar.gz file, but it did not work.
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I am running version 3.6 of R on CentOS (CentOS Linux release 7.9.2009 (Core)). Is there a simple way to upgrade R to the latest version and upgrade all the installed libraries?
EPEL repository on my machine is epel-release-7-13.noarch and by default, it installs version 3.6 of R.
I was referring to the following post -https://stackoverflow.com/questions/1401904/painless-way-to-install-a-new-version-of-r but the package installr is only available for Windows.
There is another post (How to upgrade R in ubuntu?) that describes how to upgrade R on Ubuntu, however some of these commands do not work on CentOS.
I am sure there must be a painless way to upgrade R in CentOS.
I think this post may help you:
How can I install the newest version of R (currently 4.0.0) on CentOS?
At this point, I'm sure you've solved the problem, but perhaps this will help others.
Official centOS instructions are located here:
https://cran.r-project.org/bin/linux/fedora
With centOS, there's not an easy solution, but this may be the best you can find on the topic.
Thought I'd give MRO a spin, to see if it speeds up my usage in general.
I can't find the installed R though. Not as a separate, not as an overwrite.
/usr/local/bin/R contains R version 3.4.0 (2017-04-21) -- "You Stupid Darkness", which is also the one used by RStudio.
/Library/Frameworks/R.framework/Versions/ also only contains 3.4.
The GUI "Microsoft R Open.app" has the description R 3.3.0 GUI 1.68 Mavericks build... but it also returns 3.4.
What am I missing?
You've identified a bug in the installer. Thanks!
Looks like we are not installing the MRO framework files because the package installer is detecting a newer version (CRAN 3.4). We will get this fixed in the next release.
In the meantime, you can work around this by renaming /Library/Frameworks/R.framework/Versions/3.4 to /Library/Frameworks/R.framework/Versions/0.3.4 and reinstalling MRO. Then go ahead and rename it back.
Please note, as a part of the install we update the symlinks to point to our version, so if you would prefer the default R installation to be CRAN 3.4 please do the install in the reverse order or manually update the symlink to Current in the Versions folder.
Apart from doing yum update all, is there any way to update RHEL 7.2 to RHEL 7.2. AM looking for system packages alone to be updated and leave the application level to be in their current version.
I assume by system packages you mean the ones supplied from official RHEL repos, and by application level you mean third-party software installed on top of the RHEL system. If that's the case, then disable the third-party repos for the upgrading process. I.e. something like:
yum --disablerepo=* --enablerepo=rhel-7-server-rpms update
Alternatively, you can exclude specific packages from the upgrade. For that, you can use the versionlock yum plugin (available from the yum-plugin-versionlock package). Use it as follows:
yum versionlock <package>-*
This locks all packages whose names start with <package>- to their current versions.
Yet another method is to use the --exclude option of yum, or--to make it permanent--specify which packages to exclude in the yum.conf file. See How do I exclude kernel or other packages from getting updated in Red Hat Enterprise Linux while updating system via yum? for instructions on how to use those options.
I use Debian sid (amd64), rolling updates as often as weekly. I downloaded recently the desktop version 0.99.902 of RStudio from their offical site and issued (as root, of course):
dpkg -i rstudio-0.99.902-amd64.deb
to no avail:
dpkg: dependency problems prevent configuration of rstudio:
rstudio depends on libgstreamer0.10-0; however:
Package libgstreamer0.10-0 is not installed.
rstudio depends on libgstreamer-plugins-base0.10-0; however:
Package libgstreamer-plugins-base0.10-0 is not installed.
Newer versions (1.0-0) of these 2 packages are installed on the system, but those older ones (0.10-0) are not available anymore on the official Debian repos.
What should be done to have RStudio installed and fully operational under
Debian sid? I have, of course, installed R debs, from official Debian
repositories, without any issues...
Thanks for any help!
RStudio 1.0.153, released on July 20th 2017, depends on GStreamer 1.0 instead of GStreamer 0.10. It can be installed on modern Debian/Ubuntu without any additional setup, rendering this question and my answer obsolete.
To be more specific, there are two different DEB packages. One is aimed at Ubuntu 16.04 (or later) and Debian 9 (or later), comes only in 64-bit flavor and depends on newer GStreamer 1.0. Another package supports Ubuntu from 12.04 up to 15.10 and Debian 8 and it comes in both 32-bit and 64-bit flavors. This one still depends on older GStreamer 0.10.
Original answer remains below.
As of mid-2016, RStudio has hard dependency on GStreamer 0.10 and there is no way around it. You have to install libgstreamer0.10-0 and libgstreamer-plugins-base0.10-0 to use RStudio.
These packages can be easily pulled in from Debian Jessie (stable). Just add Jessie repository to your sources.list and use apt-pinning to give it lower priority:
# /etc/apt/sources.list:
deb http://httpredir.debian.org/debian jessie main
# /etc/apt/preferences.d/01_release:
Package: *
Pin: release o=Debian,a=unstable
Pin-Priority: 600
Package: *
Pin: release o=Debian,n=jessie
Pin-Priority: 10
Then issue apt-get update and follow up with apt-get install libgstreamer0.10-0 libgstreamer-plugins-base0.10-0.
If you have happened to put RStudio .deb file into local repository, then use apt-get install rstudio and GStreamer0.10 will be pulled in by dependency resolver. This has additional advantage of marking these libraries as automatically installed - they will be subject to automatic removal once RStudio drop them as dependency.
But will that break my system?
No.
Upstream developers designed GStreamer0.10 and GStreamer1.0 as co-installable and able to run at the same time (source). In fact, both were available in Debian repository since September 2012 up to April 2016.
In this pinning setup, packages from Jessie repository will be pulled in only when Jessie is the only provider of requested package. There is no risk of overwriting any package from unstable with older version from stable.
Why does RStudio depend on obsolete library?
Because GStreamer0.10 is the newest version available in both Debian Jessie and Ubuntu 12.04, two distributions they want to support.
RStudio will eventually have to upgrade their dependency to GStreamer1.0, as it will gradually become the only version available. I guess this change may be introduced in spring 2017. First, support for Ubuntu 12.04 will end in April. Rstudio is likely to bump base system requirement to 14.04 - one that has both GStreamer0.10 and 1.0. Second, Debian Stretch - that will have only GStreamer1.0 available - is expected to be released around that time.
I found Miroslaw's answer to be excellent. But, due to the passage of time you will need one more package: libssl1.0.0, so your setup apt-get will look like
apt-get install libgstreamer0.10-0 libgstreamer-plugins-base0.10-0 libssl1.0.0
Download libgstreamer0.10-0 for your machine from any of the mirrors.
Open terminal in the directory where the file is downloaded.
Install it using the command, sudo dpkg -i file.deb. Example sudo dpkg -i libgstreamer0.10-0_0.10.36-1ubuntu1_amd64.deb.
Now open the directory where rstudio.deb is located and install it in the same way.
Download the libraries
http://ftp.br.debian.org/debian/pool/main/g/gstreamer0.10/libgstreamer0.10-0_0.10.36-1.5_amd64.deb
http://ftp.br.debian.org/debian/pool/main/g/gst-plugins-base0.10/libgstreamer-plugins-base0.10-0_0.10.36-2_amd64.deb
Install them with gdebi or dpkg -i and that is it
How do I install multiple versions of R on a Mac without overwriting the old version? Where are the appropriate places to install them?
The most appropriate place would be in the R.framework directory. I have versions dating back to R 2.7 on this machine. Installing of a new version from the binary installation package will not overwrite earlier versions. This is what dragging the symlink "Current Version" folder gives when I drag-drop it into the current console window:
/Library/Frameworks/R.framework/Versions/Current
It's actually a reference to:
/Library/Frameworks/R.framework/Versions/2.15
(This is where the binary installer from CRAN will put successive versions by default if you just click OK to all the dialog boxes during installation.)