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Things to do after installation of Ubuntu/Lubuntu

This is a documentation of what I do after installing Lubuntu.
After following the steps below, my disk showed 23.21 GiB used.

am currently using Lubuntu. You could also use Ubuntu. to install, you need to go to the download site and also create a bootable usb key that you will use for the installation. That's easy. This document shows you what to do afterwards.

Install xclip

This program will let you copy your public key to the buffer. It is needed when you upload your git key to gihub. It is also lets you paste into the terminal using 

    sudo apt-get install xclip

Install git

    sudo apt-get install git

Set up the Github key. See git hub instructions

https://help.github.com/articles/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/

You might want to save the passcode so you don't have to keep entering it. https://stackoverflow.com/questions/21095054/ssh-key-still-asking-for-password-and-passphrase

ssh-add -k ~/.ssh/id_rsa

Install LaTeX

You will need this in rstudio to create pdf documents

https://help.ubuntu.com/community/LaTeX

sudo apt-get update
sudo apt-get install texlive-full

install pandoc

Pandoc is also used for document conversion.

sudo apt-get install pandoc

Install emacs

If you don't use emacs, skip this step.

sudo apt-get install emacs

install el-get for emacs

https://github.com/dimitri/el-get This is one way to install Lisp packages in emacs. There are other ways, but this works well for me.

Go to https://github.com/dimitri/el-get and the section The Lazy Installer Copy that into the scratch as indicated and run it. Then go to the basic setup and copy that, as indicated, to the .emacs file. If you don't copy to the .emacs file, then the packages you install will not reload after you exit and reenter emacs.

Setup markdown mode to use pandoc

Pandoc can be used to view markdown. Use C-c C-c p to request the preview. The markdown command shown below will be run and call pandoc.

;; pandoc-mode
(add-hook 'markdown-mode-hook 'pandoc-mode)
(setq markdown-command
      "pandoc -f markdown -t html -s --mathjax ")

markdown-mode to emacs

This lets you edit markdown code for pushing to github. If the pandoc command listed above works, you won't need this. Inside emacs use

el-get-install markdown-mode

install node.js

This is needed for the emacs pluging livedown (listed next) to work.

sudo apt-get install nodejs
sudo apt-get install npm
npm install -g livedown

install livedown.

https://github.com/shime/livedown Livedown is a usefull way to view markdown. It requires nodejs and npm. The advantage of livedown over using pandoc is that when you save a md file, livedown will show the results immediately.
Inside emacs, use:

el-get-install livedown

Install Anaconda

https://askubuntu.com/questions/505919/how-to-install-anaconda-on-ubuntu

Don't use sudo. Install anacondo without using sudo.as

CONTREPO=https://repo.continuum.io/archive/
# Stepwise filtering of the html at $CONTREPO
# Get the topmost line that matches our requirements, extract the file name.
ANACONDAURL=$(wget -q -O - $CONTREPO index.html | grep "Anaconda3-" | grep "Linux" | grep "86_64" | head -n 1 | cut -d \" -f 2)
wget -O ~/Downloads/anaconda.sh $CONTREPO$ANACONDAURL
bash ~/Downloads/anaconda.sh

Close your terminal and open a new one to get the .bashrc code to run, or use load.

You will need to update spyder after installation. Use conda This is why you can't use sudo to insall. conda doesn't work with sudo. The note when you first load spyder tells you to use pip and the screen, when spyder loads, tells you not to use pip.
Use conda instead of pip. The code is shown below

https://github.com/spyder-ide/spyder/releases

conda update qt pyqt
conda update spyder

Install Tensorflow

Read this before you install tensorflow.

https://www.tensorflow.org/install/install_linux

conda install tensorflow

Install Some Office Tools

###LibreOffice If you are using Ubuntu, you have this already.

sudo apt-get install libreoffice

Use VIM as your default editor

export VISUAL=vim
export EDITOR="$VISUAL"

Fix errors

https://www.raspberrypi.org/forums/viewtopic.php?t=196070

There is a problem running python from the command line. It might get fixed, but the works for now.

sudo apt-get install at-spi2-core

Install R

rstudio to create pdf documents

https://help.ubuntu.com/community/LaTeX

sudo apt-get update
sudo apt-get install texlive-full
sudo apt-get install libcurl4-openssl-dev 
sudo apt-get install libxml2-dev
sudo apt-get install libssl-dev

install pandoc

Pandoc is also used for document conversion.

sudo apt-get install pandoc

Install emacs

If you don't use emacs, skip this step.

sudo apt-get install emacs

install el-get for emacs

https://github.com/dimitri/el-get This will be the way Lisp packages are installed.

Go to https://github.com/dimitri/el-get and the section The Lazy Installer Copy that into the scratch as indicated and run it. Then go to the basic setup and copy that, as indicated, to the .emacs file. If you don't copy to the .emacs file, then the packages you install will not reload after you exit and reenter emacs.

markdown-mode to emacs

This lets you edit markdown code for pushing to github. Inside emacs use

el-get-install markdown-mode

install node.js

This is needed for the emacs pluging livedown (listed next) to work.

sudo apt-get install nodejs
sudo apt-get install npm
npm install -g livedown

install livedown.

https://github.com/shime/livedown This is whay nodejs and npm was installed earlier. Inside emacs, use:

el-get install livedown

Install Anaconda

https://askubuntu.com/questions/505919/how-to-install-anaconda-on-ubuntu

Don't use sudo. Install anacondo without using sudo.as

CONTREPO=https://repo.continuum.io/archive/
# Stepwise filtering of the html at $CONTREPO
# Get the topmost line that matches our requirements, extract the file name.
ANACONDAURL=$(wget -q -O - $CONTREPO index.html | grep "Anaconda3-" | grep "Linux" | grep "86_64" | head -n 1 | cut -d \" -f 2)
wget -O ~/Downloads/anaconda.sh $CONTREPO$ANACONDAURL
bash ~/Downloads/anaconda.sh

Close your terminal and open a new one to get the .bashrc code to run, or use load.

You will need to update spyder after installation. Use conda This is why you can't use sudo to insall. conda doesn't work with sudo. The note when you first load spyder tells you to use pip and the screen, when spyder loads, tells you not to use pip.
Use conda instead of pip.

https://github.com/spyder-ide/spyder/releases

conda update qt pyqt
conda update spyder

Install Tensorflow

Read this before you install tensorflow.

https://www.tensorflow.org/install/install_linux

conda install tensorflow

Install Some Office Tools

###LibreOffice If you are using Ubuntu, you have this already.

sudo apt-get install libreoffice

Use VIM as your default editor

export VISUAL=vim
export EDITOR="$VISUAL"

Fix errors

https://www.raspberrypi.org/forums/viewtopic.php?t=196070

There is a problem running python from the command line. It might get fixed, but the works for now.

sudo apt-get install at-spi2-core

Install R

http://cran.cnr.berkeley.edu/

After you follow the berkeley directions, not that you can do this

sudo apt-get install r-cran-*

It will save you a ton of time.

Install Rstudio

https://www.rstudio.com/products/rstudio/download/#download

install R the Conda Way (recommend not doing this but installing r with apt-get)

https://anaconda.org/r/rstudio https://conda.io/docs/user-guide/tasks/use-r-with-conda.html

Use anaconda:

Make sure you are in an environment first, even if it is the root.

source activate root

conda install r-essentials
conda install rstudio

As soon as you install r and rstudio, you need to start up rstudio and the try to install that package that you love and no one else knows about. This will test to see if your system is set up to install obscure packages with dependencies.

I use the gk package. Packages are installed inside r with

install.packages()

You can also use conda with

conda install r-ggplot2

Many times if a package will not install because of dependencies, you can still use conda to install the package. Here is an example installation. Conda looks for binaries that are available.
There is nothing for r-gk so I have to use

install.packages()

However this produced and error message about gnu-gcc and the package didn't install. This stackoverflow had the answer:

https://stackoverflow.com/questions/46450912/unable-to-execute-x86-64-conda-cos6-linux-gnu-gcc-no-such-file-or-directory

The comment by

https://stackoverflow.com/users/3257826/ray-donnelly is to use:

conda create -n renv r-essentials=1.7.0 gcc_linux-64
source activate renv

There is another user

https://stackoverflow.com/users/1170370/msarahan

who mentioned that activation sets a bunch of important variables so even if you don't have a bunch of environments, it is still a good idea to active.

source activate root

I was able to get rstudio running in the renv above and get the gk package to install. A combination of the two answers would indicate that I only needed to install gcc_linux-64 into the root environment. I avoid using a version number on packages becuase the default would be the latest one. If you are worried about versioning, you can have conda environments with the exact versions of packages you need. But I would suggest that if you are worried about what version of a package is needed to make sure your code works and isn't brocken by some update then use Microsoft R Open. The whole point of MRO is to limit the frequency of updates to ensure that new versions don't break things. I don't like it because I want the latest, but if you are worried about thing breaking, use MRO. Also RevolutionR was bought by MS and their guys are most likely the ones managing it. That is a plus. I recommend having at least one environment where MRO is used.

https://conda.io/docs/user-guide/tasks/use-mro-with-conda.html

Install golang

https://github.com/juhovh/shairplay

sudoapt-get install golang-go

SAS university edition

https://askubuntu.com/questions/367248/how-to-install-virtualbox-from-command-line http://support.sas.com/software/products/university-edition/docs/en/SASUniversityEditionInstallGuideLinux.pdf http://www.oracle.com/technetwork/server-storage/virtualbox/downloads/index.html

apt-get install virtualbox

https://stegard.net/2016/10/virtualbox-secure-boot-ubuntu-fail/

spotify

http://howtoubuntu.org/how-to-install-spotify-in-ubuntu

sudo apt-add-repository -y "deb http://repository.spotify.com stable non-free" &&
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys D2C19886 &&
sudo apt-get update -qq &&
sudo apt-get install spotify-client

Remove old unused packages

Whenever needed, you can get rid if unneeded versions using

sudo apt autoremove

to do