Is there any way to have apt install a package from a specific launchpad repository?
I would like to set up a little test server and install all of the 1000+ r-cran-* packages from the cran2deb4ubuntu launchpad repository. As of last month, all packages in this repository are build for R 3.0.1. So I install a copy of R 3.0.1 and then do:
sudo add-apt-repository marutter/c2d4u
sudo apt-get update
sudo apt-get install r-cran-*
However, this will also install all of the r-cran-* packages form universe which are build for R 2.15, and hence will fail to load. Is there an easy way to install the packages only from c2d4u? Or alternatively, is there a way to blacklist the r-cran- packages in universe from apt?
What I ended up doing is simply install all packages and then remove the ones with an old build. I.e.
sudo add-apt-repository ppa:marutter/c2d4u -y
sudo add-apt-repository ppa:marutter/rrutter -y
sudo apt-get update
sudo apt-get install r-bioc-*
sudo apt-get install r-cran-
And then in R:
which(installed.packages()[,"Built"] < 3.0)
Related
I tried to install R 4.1 on a newly set-up Ubuntu 20.04. After some struggle with the repositories and keys, I chose to install from source.
Visited https://www.r-project.org/ to download latest version of R. Ran ./configure multiple times to note the requirement of various libraries which you may note as follows. I am hoping this will save significant amount of time for anyone intending to build from source. Suggestions welcome for speeding up the process or better solution. However my intention is to share entire set of libraries that I had to install on a naked installation of 20.04 on which the very first package I tried to install was R 4.1 (from source).
Directory where you downloaded the tar.gz (e.g. R-4.1.2.tar.gz in my case)
cd Downloads
Untar
tar -xvzf R-4.1.2.tar.gz
Enter directory
cd R-4.1.2
As root
sudo su
Try validating configuration (encountered many errors throughout and following libraries were installed)
./configure
Installed various libraries:
apt-get install build-essential
apt-get install gfortran
apt-get install fort77
apt-get install libreadline-dev
apt-get install xorg-dev
apt-get install liblzma-dev libblas-dev
apt-get install gcc-multilib
apt-get install libbz2-dev
apt-get install libpcre2-dev
apt-get install libcurl4-openssl-dev
apt install default-jdk
make
make install
The above set worked for me and I am hopeful it may be of help.
The problem:
I'm trying to install the devtools package for R. I'm using Ubuntu 18.04 LTS on WSL, the Windows Subsystem for Linux.
I'm able to install some packages just fine with a simple call to install.packages() from within R on WSL. However, other packages seem to give me trouble.
None of the following methods I've tried seem to work:
* I've tried installing the package with install.packages().
* I've tried installing from source into /usr/local/lib/R/site-library.
* I've tried installing from source into a personal library.
Error message:
I was recieving an error message like that discussed here, but I was unable to fix the problem by editing unpackPkgZip because it didn't exist.
The Question:
How can I install devtools on WSL?
Solution:
I was able to fix the problem by starting over. I uninstalled Ubuntu and then reinstalled it. With a fresh install of Ubuntu 18.04 I followed these instructions. There are other online tutorials which probably work just fine, but I followed this one. You can ignore the bit about installing an rstudio server and the fsl package if you wish.
# Install R on WSL
sudo apt-get update -qq -y
sudo apt-get install -y wget git
OS_DISTRIBUTION=$(lsb_release -cs)
wget -O- http://neuro.debian.net/lists/${OS_DISTRIBUTION}.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
sudo apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
sudo apt-get update
sudo apt-get install libopenblas-base r-base
sudo apt-get update -qq -y
sudo apt-get install -y libgit2-dev
sudo apt-get install -y libcurl4-openssl-dev libssl-dev
sudo apt-get install -y zlib1g-dev libssh2-1-dev libpq-dev libxml2-dev
#sudo apt-get install -y libhdf5 # This didn't work.
Now try installing devtools in R.
# Install devtools
install.packages("devtools", repos = "https://cran.rstudio.com/")
Permission error:
If you encounter a permission error like the following...
Warning in install.packages("edgeR") :'lib = "/usr/local/lib/R/site-library"' is not writable Would you like to use a personal library instead? (y/n)
...you need to provide the user with write access to the directory where R packages are installed (see here). Try changing the group ownership of this directory:
# Who has ownership of /usr/local/lib/R/site-library/?
ls -l /usr/local/lib/R/
# drwxrwsr-x 1 root staff 512 Jul 18 21:38 site-library
# Change ownership.
sudo chgrp twesleyb /usr/local/lib/R/site-library/
ls -l /usr/local/lib/R/
#drwxrwxr-x 1 root twesleyb 512 Jul 18 21:38 site-library
# In this case I have write access, but in case you need to add it, try:
# $ sudo chmod g+w /usr/local/lib/R/site-library
You should now be able to install.packages("package").
I'm a linux novice, but I think this is an okay thing to do.
Update:
You can also try following duckmayr's instructions.
Simply my Question is How to Install Swoole in Ubuntu 14.04 LTS
I have tried
sudo pecl install swoole
am getting handfull of errors, already posted here
Is there any alternate way to install the same...
Swoole Installation alternate ways
1.Install from source
sudo apt-get install php7-dev
git clone https://github.com/swoole/swoole-src.git
cd swoole-src
phpize
./configure
make && make install
2.Example for static compile
git clone -b PHP-7.2 --depth 1 https://github.com/php/php-src.git
cd php-src/
git clone -b master --depth 1 https://github.com/swoole/swoole-src.git ext/swoole
./buildconf --force
./configure --prefix=/usr/local/php7 --disable-all --enable-cli --disable-cgi --disable-fpm --disable-phpdbg --enable-bcmath --enable-hash --enable-json --enable-mbstring --enable-mbregex --enable-mbregex-backtrack --enable-sockets --enable-pdo --with-sodium --with-password-argon2 --with-sqlite3 --with-pdo-sqlite --with-pcre-regex --with-zlib --with-openssl-dir --enable-swoole-static --enable-openssl --with-swoole
time make -j `cat /proc/cpuinfo | grep processor | wc -l`
sudo make install
Some Linux distributions do not include the PHP-XML extension in their PHP package and will need to be enabled before using PECL. You can install using apt-get install php-xml and you may need to install PHPize to compile Swoole, you can install it using apt-get install php7.*-dev or whatever PHP version you are using.
Then try again with sudo pecl install swoole
For those who installed PHP from ondrej/php PPA (quite common way to install PHP in Ubuntu) it's quite easy now:
sudo apt install php-swoole
Or for specific version:
sudo apt install php7.4-swoole
Tip. This is how you usually install ondrej/php PPA:
sudo apt install software-properties-common
sudo add-apt-repository ppa:ondrej/php
sudo apt-get update
Install swoole for version specific should work for example if you have php 7.3 use
sudo apt install php7.3-swoole
replace the version to your local php env
Hello I am trying to install r-base for Ubuntu 16.04.
I have followed the steps at https://cran.r-project.org/bin/linux/ubuntu/README.html
However I am getting a 'unmet dependencies' error when I run sudo apt-get install r-base
The following packages have unmet dependencies:
r-base : Depends: r-recommended (= 3.4.4-1xenial0) but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
Any ideas for getting around this?
Thanks in advance!
Running the following commands seems to have solved my problem:
sudo apt --fix-broken install
sudo apt-get update
sudo apt-get upgrade
Running the following fixed it for me, but this solution uses r-base-dev not r-base (r-base still didn't work).
sudo apt --fix-broken install
sudo apt autoremove
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install r-base-dev
Make sure to check in the software and properties that if your restricted and universe repositories are enabled. Here's a link with more information.
I started getting this issue because I added the wrong apt-repository for my version of Ubuntu (focal fossa instead of bionic).
Solved by doing sudo vim /etc/apt/sources.list, then deleting any lines containing focal
I am getting this error and i have tried every other solution related to this given on stackoverflow but still not able to install the package.Please suggest a solution.And how can i install any R package using source on linux?
You can try the following:
In shell:
sudo yum install -y epel-release
sudo yum install glibc-common
sudo yum install -y rpm-build make wget tar libxml2-devel
In R:
install.packages('xml2')
Instructions are adapted from https://github.com/opencpu/opencpu-server/tree/master/rpm#readme
Please let me know if it works.