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When i use
sudo apt install <package> --install-suggests
this will install ALL of suggested packages. But i dont want to install all of them. I want to exclude some suggested packages, and not install them
Example:
sudo apt install vlc
it suggest 4 packages, and install 35 packages.
sudo apt install vlc --install-suggests
will install 219 packages!
I think, that --install-suggests takes action not only to installation of furst vlc package, but to all of the dependencies, so dependencies has they oun 'suggestions', and so on...
I expected, that --install-suggests not will be applied to install dependencies, recomenations and suggests, but only to
a far from ideal solution of this problem:
I installed 'vls' by sudo apt install vlc(35 packages at all),
then i do sudo apt remove vlc(removed 1 package 'vlc'),
and after that i used command sudo apt install vlc --install-suggests(it installed 'vlc' and 3 suggested packages).
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I have R 2.12.1 installed in my ubuntu, and I'd like upgrade to lastest version 2.15, how can achieve that ? Thanks
Since R is already installed, you should be able to upgrade it with this method. First of all, you may want to have the packages you installed in the previous version in the new one,so it is convenient to check this post. Then, follow the instructions from here
Open the sources.list file:
sudo nano /etc/apt/sources.list
Add a line with the source from where the packages will be retrieved. For example:
deb https://cloud.r-project.org/bin/linux/ubuntu/ version/
Replace https://cloud.r-project.org with whatever mirror you would like to use, and replace
version/ with whatever version of Ubuntu you are using (eg, trusty/, xenial/, and so on). If you're getting a "Malformed line error", check to see if you have a space between /ubuntu/ and version/.
Fetch the secure APT key:
gpg --keyserver keyserver.ubuntu.com --recv-key E298A3A825C0D65DFD57CBB651716619E084DAB9
or
gpg --hkp://keyserver keyserver.ubuntu.com:80 --recv-key E298A3A825C0D65DFD57CBB651716619E084DAB9
Add it to keyring:
gpg -a --export E084DAB9 | sudo apt-key add -
Update your sources and upgrade your installation:
sudo apt-get update && sudo apt-get upgrade
Install the new version
sudo apt-get install r-base-dev
Recover your old packages following the solution that best suits to you (see this). For instance, to recover all the packages (not only those from CRAN) the idea is:
-- copy the packages from R-oldversion/library to R-newversion/library, (do not overwrite a package if it already exists in the new version!).
-- Run the R command update.packages(checkBuilt=TRUE, ask=FALSE).
I'm a newbie to Linux and try to install the latest R version on my Raspberry.
My Raspberry runs on Wheezy 7.8.
I followed instructions on CRAN, so I
added
deb http://cran.rstudio.com/bin/linux/debian wheezy-cran3/
to /etc/apt/sources.list
ran apt-get update which was successful and gave me only a "signature error" for the public key as pointed out on the CRAN-site
ran apt-get install r-base
But the result of the last command is
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-base : Depends: r-base-core (>= 3.1.2-1~wheezycran3.0) but it is not going to be installed
Depends: r-recommended (= 3.1.2-1~wheezycran3.0) but it is not going to be installed
Recommends: r-base-html but it is not going to be installed
Recommends: r-doc-html but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
I tried to install R-2.15 before and then run the above commands. R-2.15 could be installed successfuly, but I'd need R-3* really.
I did browse the web, but couldn't find any useful hints for my specific problem, so I appreciate any support you could give me.
Thanks!
If it is of any use:
apt-cache policy r-base gives
r-base:
Installed: (none)
Candidate: 3.1.2-1~wheezycran3.0
Version table:
3.1.2-1~wheezycran3.0 0
500 http://cran.rstudio.com/bin/linux/debian/ wheezy-cran3/ Packages
3.1.0-1~wheezycran3.0 0
500 http://cran.rstudio.com/bin/linux/debian/ wheezy-cran3/ Packages
2.15.1-4 0
500 http://mirrordirector.raspbian.org/raspbian/ wheezy/main armhf Packages
apt-cache policy r-base-core gives
r-base-core:
Installed: (none)
Candidate: 2.15.1-4
Version table:
2.15.1-4 0
500 http://mirrordirector.raspbian.org/raspbian/ wheezy/main armhf Packages
uname -a gives
Linux raspberrypi 3.18.5+ #744 PREEMPT Fri Jan 30 18:19:07 GMT 2015 armv6l GNU/Linux
I had the same situation and decided to install that from the source code instead of install R from the repository(apt-get command).
Here is the command I run on my Raspberry Pi 2.
I could install and run R(3.1.2) sucessfully.
It might not be complete answer for you because I might already installed the library like gcc you did not have before. If you encounter the other issue, please let me know. I would like to solve it.
Just as a side note on this topic, because sudo make install process took a long time(maybe over a hour. I'm not sure because I feel asleep before I knew it...), I recommend you to do this when you have enough or before going to sleep like me.
wget http://cran.rstudio.com/src/base/R-3/R-3.1.2.tar.gz
mkdir R_HOME
mv R-3.1.2.tar.gz R_HOME/
cd R_HOME/
tar zxvf R-3.1.2.tar.gz
cd R-3.1.2/
sudo apt-get install gfortran libreadline6-dev libx11-dev libxt-dev
./configure
make
sudo make install
R
The cause of your problem is likely that the cran repository provides armel versions of the packages, and not armhf (which is the expected architecture for your RPI). If this is right, then you have two solutions:
The first work-around could be to download the armel version of the packages and then force their installation despite the architecture mismatch. It is supposed to work according to the Debian wiki, although you may experience performance issues:
The CPU in the Raspberry Pi implements the ARMv6 ISA (with VFP2) and
is thus incompatible with the Debian armhf port baseline of ARMv7+VFP3
and ARM hardware-floating-point ports for other distributions, which
all have the same baseline. It is compatible with Debian armel
(armv4t, soft(emulated) FP), but floating-point tasks will be slow
when running the Debian armel port.
To do that, you can try to reinstall the packages by specifying the armel architecture, for example:
apt-get install r-base:armel
If it doesn't work this way, you can otherwise download the packages from http://cran.r-project.org/bin/linux/debian/wheezy-cran3/ and install them manually using a commandline like:
dpkg --install --force-architecture xxxx_armel.deb yyyy_armel.deb zzzz_armel.deb
The other solution would be to compile R from its source.
I solved my initial question by upgrading Wheezy to Jessie. I am not an expert, but Jessie seems to be the current testing version of Debian, while Wheezy is the stable release - see here.
For upgrading, I followed the instructions here, or here, or here. Note: Upgrading takes quite a while and during the process you're required to answer some questions.
A word of caution though: Jessie is still testing and some people recommend not to use it yet, for a discussion see e.g. here.
I did set it up completely from a new completely new image, and it works well.
After having upgraded to Jessie I installed R-3.1.1. using
sudo apt-get install r-base
And I'd like to thank all those who have answered my question and given alternative ways of solving the problem above.
I'm able to install R-3.1.2 into raspbian using answer from teramonagi. I confirm it can install successfully on Raspberry Pi model B/B+.
However, before you can actually use R (install packages and run some R scripts), you have to increase the swap file size for Raspberry Pi due to lack of RAM (This service works very similar to page file in window, it kicks in when RAM usage is high). You can configure it by edit one of the config file by enter command below in LX terminal.
sudo nano /etc/dphys-swapfile
CONF_SWAPSIZE=100 #(change 100 to 512 or 1024, up to you, save the file)
sudo /etc/init.d/dphys-swapfile stop
sudo /etc/init.d/dphys-swapfile start #(restart swap file service with new swap file size)
Take note though, some users argued that increase swap file size can actually ruin your SD card. So apply this change at your own risk. I've been running my Pi with this configuration for my R automation for 1 month now. No issue so far.
Hope this helps.
Edit: If you are using model B/B+, i recommend to configure swap file size first then compile R.
That's what I've done to update my r-base on wheezy:
HOW TO UPDATE r-base 2.15 to 3.x ON DEBIAN WHEEZY
add these lines at the end of "/etc/apt/sources.list"
deb http://cran.revolutionanalytics.com/bin/linux/debian wheezy-cran3/
deb-src http://cran.revolutionanalytics.com/bin/linux/debian wheezy-cran3/
add the missing publich key of cran
gpg --keyserver pgpkeys.mit.edu --recv-key 06F90DE5381BA480
gpg -a --export 06F90DE5381BA480 | sudo apt-key add -
update and upgrade
apt-get update
aptitude -t wheezy-cran3 install r-base r-base-dev
I want to install R on my Red hat cluster which has the version below:
$ cat /etc/redhat-release
Red Hat Enterprise Linux Server release 6.3 (Santiago)
When I went to R's homepage and this is what in their repository:
I am wondering there is only redhat version 4 and 5 there and I don't know which version will best fit my operating system.
Texinfo Problem Goes Here
Since I have asked more than 6 questions today. Stackoverflow doesn't like me to ask more questions. So I will put the following questions into this question, sorry about that.
Hi, I was trying to use Expect to automatically log into a remote server and install R.
When I install R, they came up with all kinds of prompts asking 'The package will take xx MB Is that OK with you'?
The command to install:
su -c 'yum install R R-core R-core-devel R-devel'
You need to type in Yes for a few times to finish the installation.
My question is:
Is there a flag for yum install that you can tell the machine to install everything I want you to install. Don't ask me. So I can install those four packages without any prompt.
If that is hard to install in the 'quiet mode', how to write a while loop in Expect so it will send the Y automatically:
Pseudo Code Not Working!
send -- "sudo su -c yum install ...."
while ("Expect '*Is it OK [Y/N]*'"){
send 'Y\r'
# if (expect 'user$')
{break}
}
Thanks a lot in advance.
This is likely due to there being R RPMs in the Extra Packages for Enterprise Linux (EPEL) repos for RHEL6. You can find out more about EPEL on the Fedora website.
You need to configure yum to use EPEL. The easiest way to do this is to install the epel-release package for your platform, eg
su -c 'rpm -Uvh http://dl.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch.rpm'
or
su -c 'rpm -Uvh http://dl.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm'
for example. The you can use yum to install R, e.g. you will probably want
su -c 'yum install R R-core R-core-devel R-devel'
so that you pull in the packages needed to build other add-on packages as most CRAN package are not in EPEL.
At the moment, the latest version of R in EPEL is 3.0.1, so one patch release point behind the latest version 3.0.2.
It's difficult to tell what is being asked here. This question is ambiguous, vague, incomplete, overly broad, or rhetorical and cannot be reasonably answered in its current form. For help clarifying this question so that it can be reopened, visit the help center.
Closed 9 years ago.
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After having some problems to install new version of R from command line on Ubuntu (straightforward way just updated it to version 2.15.x)
I want to share the way to do this.
This is an old post and I wrote it when it was impossible to install R with simple (it was installing old 2.15 version):
sudo apt-get install r-base-core
Right now you do not need to do all written below and can simply use the abovementioned command. At the time of updating it will give you 3.1 version.
Here is previous post
Uninstall old R
sudo apt-get remove r-base-core
Open sources.list
sudo nano /etc/apt/sources.list
and add deb to it
deb http://cran.rstudio.com/bin/linux/ubuntu precise/
precise is your ubuntu name (may be different)
Add key to sign CRAN packages
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
Add specific PPA to the system
sudo add-apt-repository ppa:marutter/rdev
sudo apt-get update
sudo apt-get upgrade
installing
sudo apt-get install r-base
From R to check version
version
should give you
version.string R version 3.0.0 (2013-04-03)
Hope people will find this helpful
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I have R 2.12.1 installed in my ubuntu, and I'd like upgrade to lastest version 2.15, how can achieve that ? Thanks
Since R is already installed, you should be able to upgrade it with this method. First of all, you may want to have the packages you installed in the previous version in the new one,so it is convenient to check this post. Then, follow the instructions from here
Open the sources.list file:
sudo nano /etc/apt/sources.list
Add a line with the source from where the packages will be retrieved. For example:
deb https://cloud.r-project.org/bin/linux/ubuntu/ version/
Replace https://cloud.r-project.org with whatever mirror you would like to use, and replace
version/ with whatever version of Ubuntu you are using (eg, trusty/, xenial/, and so on). If you're getting a "Malformed line error", check to see if you have a space between /ubuntu/ and version/.
Fetch the secure APT key:
gpg --keyserver keyserver.ubuntu.com --recv-key E298A3A825C0D65DFD57CBB651716619E084DAB9
or
gpg --hkp://keyserver keyserver.ubuntu.com:80 --recv-key E298A3A825C0D65DFD57CBB651716619E084DAB9
Add it to keyring:
gpg -a --export E084DAB9 | sudo apt-key add -
Update your sources and upgrade your installation:
sudo apt-get update && sudo apt-get upgrade
Install the new version
sudo apt-get install r-base-dev
Recover your old packages following the solution that best suits to you (see this). For instance, to recover all the packages (not only those from CRAN) the idea is:
-- copy the packages from R-oldversion/library to R-newversion/library, (do not overwrite a package if it already exists in the new version!).
-- Run the R command update.packages(checkBuilt=TRUE, ask=FALSE).