LaTeX

Needs perl so:

aptitude install perl perl-doc

Download latest texlive:

wget "http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz"

tar -xzf install-tl-unx.tar.gz

cd into directory and:

sudo ./install-tl

press I to install

Takes hours...

Test with

PATH=/usr/local/texlive/2020/bin/x86_64-linux:$PATH

and then: pdflatex --version

If all ok make the path permanent with:

vim .bashrc

and add:

PATH=/usr/local/texlive/2020/bin/x86_64-linux:$PATH

MANPATH=/usr/local/texlive/2020/texmf-dist/doc/man

INFOPATH=/usr/local/texlive/2019/texmf-dist/doc/info

Save and exit Vim.

Then so that LaTeX is available to other users on the server:

vim /etc/bash.bashrc

and add the same lines here.

R

sudo apt-get update

sudo R

install.packages(c("ggplot2","tidyverse","knitr","ggthemes","scales","ggmap","plotly","ggfortify","leaflet","leaflet.extras","rgdal","forecast","treemapify","dbscan","survival","googleVis","rmarkdown","flexdashboard","highcharter","devtools","maptools","mapview","treemap","networkD3","visNetwork","DiagrammeR","DT","ggcorrplot", "Hmisc", "anomalize", "fpp2", "h2o", "sweep", "timetk", "xgboost", "prophet","survminer","ggwordcloud", "ggsn", "formattable", "IMD", "car", "maps", "this.path", "triangle", "waterfalls") , repo = 'https://mac.R-project.org')

Correcting errors on install...

also installed rgeos for maptools

prophet required rstan and this required me to first delete the following directory:

/usr/local/lib/R/site-library/00LOCK-rstan

We need to use older versions of some packages:

packageurl<-"https://cran.r-project.org/src/contrib/Archive/nloptr/nloptr_1.2.1.tar.gz" install.packages(packageurl, repos=NULL, type="source")

packageurl<-"https://cran.r-project.org/src/contrib/Archive/pbkrtest/pbkrtest_0.4-7.tar.gz" install.packages(packageurl, repos=NULL, type="source")

packageurl<-"https://cran.r-project.org/src/contrib/Archive/car/car_3.0-2.tar.gz" install.packages(packageurl, repos=NULL, type="source")

for treemapify: packageurl<-"https://cran.r-project.org/src/contrib/Archive/ggfittext/ggfittext_0.6.0.tar.gz" install.packages(packageurl, repos=NULL, type="source")

for mapview:

install.packages("satellite")

install.packages(c("sf", "svglite", "uuid", "webshot"))

packageurl<-"https://cran.r-project.org/src/contrib/Archive/mapview/mapview_2.6.3.tar.gz" install.packages(packageurl, repos=NULL, type="source")

for Hmisc:

install.packages("acepack")

packageurl<-"https://cran.r-project.org/src/contrib/Archive/latticeExtra/latticeExtra_0.6-28.tar.gz" install.packages(packageurl, repos=NULL, type="source")

packageurl<-"https://cran.r-project.org/src/contrib/Archive/Hmisc/Hmisc_4.1-1.tar.gz" install.packages(packageurl, repos=NULL, type="source")

For ggpmisc:

packageurl<-"https://cran.r-project.org/src/contrib/Archive/splus2R/splus2R_1.2-2.tar.gz" install.packages(packageurl, repos=NULL, type="source")

packageurl<-"https://cran.r-project.org/src/contrib/Archive/ggpmisc/ggpmisc_0.3.4.tar.gz" install.packages(packageurl, repos=NULL, type="source")

Addendum Hmmm having trouble with some maps so let's try to upgrade everything instead...

Back out of R and add:

deb http://cloud.r-project.org/bin/linux/debian buster-cran40/

to

/etc/apt/sources.list then

apt update apt install -t buster-cran40 r-base

Then sudo R again:

update.packages(lib.loc="/usr/local/lib/R/site-library", ask = FALSE, checkBuilt = TRUE, Ncpus = 4)

(4 processors in my case - use htop to see.)

then had to add

install.packages("mapproj")

... which was the issue all along... but at least R is now on version 4.

Note Subsequently to update to 4.1 a key is now required: http://cloud.r-project.org/bin/linux/debian/:

apt-key adv --keyserver keyserver.ubuntu.com --recv-key '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7'

Then:

apt update

sudo apt upgrade

The reason for the update was to install IMD. But while we are at it there are a few additional packages I've added since the initial install:

install.packages(c("formattable", "IMD", "car"))

R studio

sudo apt-get install gdebi-core

wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.3.1093-amd64.deb

sudo gdebi rstudio-server-1.3.1093-amd64.deb

sudo adduser rstudio

Since update to R Studio 4.1, an update to R Studio is required:

sudo apt-get install gdebi-core

wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2021.09.2-382-amd64.deb

sudo gdebi rstudio-server-2021.09.2-382-amd64.deb

Python stuff

sudo apt install python3-pip

sudo apt-get install python3-pandas

pip3 install boto3

pip3 install msoffcrypto-tool

Other

sudo apt-get install pandoc

sudo apt-get install xlsx2csv

sudo apt-get install ghostscript

sudo apt-get install poppler-utils

sudo apt-get install p7zip-full

sudo apt-get install mosh

sudo apt-get install ncdu

sudo apt install neofetch

sudo apt install htop

sudo apt install rename

sudo apt install parallel

Setting up git

sudo apt-get install git

su yourname

git config --global user.name "John Doe"

git config --global user.email john.doe@emailprovider.com

ssh-keygen -t rsa -b 4096 -C "john.doe@emailprovider.com"

cat ~/.ssh/id_rsa.pub

add to git settings in web git service.

Overleaf

Full instructions are here: https://github.com/overleaf/toolkit/blob/master/doc/quick-start-guide.md

In brief:

sudo apt-get install docker

sudo apt-get install docker-compose

git clone https://github.com/overleaf/toolkit.git ./overleaf

cd overleaf

bin/init

vim config/overleaf.rc and to enable direct access to Overleaf from your server's IP address change the IP address for SHARELATEX_LISTEN to:

SHARELATEX_LISTEN_IP=0.0.0.0

bin/up and create admin account by visiting http://your-ip-here/launchpad

exit session and gracefully end Overleaf server with Ctrl-C.

Then to run an unattached session:

bin/start

(end with bin/stop)

Chances are a more complete LaTeX installation will be needed, so following https://blog.felixviola.de/overleaf-ce-setup-your-own-latex-server-tutorial/:

bin/shell

wget https://mirror.clientvps.com/CTAN/systems/texlive/tlnet/install-tl-unx.tar.gz

tar -xf install-tl-unx.tar.gz

cd install-tl-*

perl install-tl

Reject using previous config and then press i for full install, which as usual will take a LONG time.

Then exit out of the shell, bin/stop and then bin/start overleaf for good measure.