update offer to installation instructions for ubuntu

[GalAvineri]

Hello :)
I've been working on installing wholebrain on freshly installed ubuntu 18.04 and I wanted to offer an improvement to the instructions on your website.

1. installing opencv could be done more easily by using ROpenCVLite (as has been mentioned already in the gitter)
2. There are some additional libraries I found required for the installation process.
   They could be installed as follows:
   sudo apt-get install ibv8-dev libxml2-dev libglu1-mesa-dev freeglut3-dev mesa-common-dev
   install.packages("XML", repos = "http://www.omegahat.net/R")
3. I had issues trying to installing other R packages before devtools, therefore I suggest installing it first.

Maybe these changes could help other users in the installation process.

I've written my entire installation process, which worked for me on a freshly installed ubuntu 18.04:

On terminal:
sudo apt update && sudo apt upgrade
sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev
sudo apt-get -y install r-base
sudo apt-get install fftw3 fftw3-dev pkg-config
sudo apt-get install cmake git libgtk2.0-dev pkg-config libavcodec-dev libavformat-dev libswscale-dev
sudo apt-get install libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libjasper-dev libdc1394-22-dev
sudo apt-get install libv8-dev libxml2-dev libglu1-mesa-dev freeglut3-dev mesa-common-dev
R (opens R)

In R:
install.packages("devtools")
install.packages("ROpenCVLite")
library(ROpenCVLite)
install.packages("rstan", dependencies = TRUE)
install.packages("XML", repos = "http://www.omegahat.net/R")
devtools::install_github("tractatus/wholebrain") (choose to not update any dependencies)

[dprotter]

This worked for me, although I had to go back and uninstall the opencv i compiled the first time I tried to install ( a sketchy seek-and-destroy mission, haha), followed by re-installing ROpenCVLite.

also, I needed to open R with sudo privileges to get the install to work.

[GalAvineri]

At which part exactly did it require you to use sudo? Because I wasn't required at all when I did this.

…

On Sat, Aug 29, 2020, 00:56 dprotter ***@***.***> wrote: This worked for me, although I had to go back and uninstall the opencv i compiled the first time I tried to install ( a sketchy seek-and-destroy mission, haha), followed by re-installing ROpenCVLite. also, I needed to open R with sudo privileges to get the install to work. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#34 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFUF4HHXIUI3ELZD3YZ66OTSDARYXANCNFSM4QE44WWA> .

[dprotter]

the R package manager didnt have access to certain directories by default and asked if I wanted to use a different filepath for the install. I cancelled out, restarted R with sudo, and then it ran fine with the default paths. seemed more robust in the long term, but I'm also only a month in to using linux as my main work computer, so perhaps it was unnecessary.

[matiasandina]

Just to add to this, I have struggled with different installs and I ended up compiling a sort of manual. https://matiasandina.github.io/wholebrain_install/ My original idea was for it to be updated by the community. This is the repo github.com/matiasandina/wholebrain_install

[ucaszhu]

Hello :) I've been working on installing wholebrain on freshly installed ubuntu 18.04 and I wanted to offer an improvement to the instructions on your website.

1. installing opencv could be done more easily by using ROpenCVLite (as has been mentioned already in the gitter)
2. There are some additional libraries I found required for the installation process.
   They could be installed as follows:
   sudo apt-get install ibv8-dev libxml2-dev libglu1-mesa-dev freeglut3-dev mesa-common-dev
   install.packages("XML", repos = "http://www.omegahat.net/R")
3. I had issues trying to installing other R packages before devtools, therefore I suggest installing it first.

Maybe these changes could help other users in the installation process.

I've written my entire installation process, which worked for me on a freshly installed ubuntu 18.04:

On terminal: sudo apt update && sudo apt upgrade sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev sudo apt-get -y install r-base sudo apt-get install fftw3 fftw3-dev pkg-config sudo apt-get install cmake git libgtk2.0-dev pkg-config libavcodec-dev libavformat-dev libswscale-dev sudo apt-get install libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libjasper-dev libdc1394-22-dev sudo apt-get install libv8-dev libxml2-dev libglu1-mesa-dev freeglut3-dev mesa-common-dev R (opens R)

In R: install.packages("devtools") install.packages("ROpenCVLite") library(ROpenCVLite) install.packages("rstan", dependencies = TRUE) install.packages("XML", repos = "http://www.omegahat.net/R") devtools::install_github("tractatus/wholebrain") (choose to not update any dependencies)

你的教程太棒了，我安装了几天，总是遇到各种问题，曾经一度想放弃了，但是按照这个步骤来，我的终于安装成功了，很开心。

[gaofan83]

@GalAvineri I tried to install on my ubuntu 20.04 using a slightly different protocol (R 4.2.1 already installed).

On terminal:
sudo apt update && sudo apt upgrade
sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev
#sudo apt-get -y install r-base
sudo apt-get install fftw3 fftw3-dev pkg-config
sudo apt-get install cmake git libgtk2.0-dev pkg-config libavcodec-dev libavformat-dev libswscale-dev
sudo add-apt-repository 'deb http://security.ubuntu.com/ubuntu xenial-security main'
sudo apt update
sudo apt install libjasper1 libjasper-dev
sudo apt-get install libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libdc1394-22-dev
sudo apt-get install libv8-dev libxml2-dev libglu1-mesa-dev freeglut3-dev mesa-common-dev
R (opens R)

In R:
install.packages("devtools")
install.packages("XML")
install.packages("ROpenCVLite")
library(ROpenCVLite)
install.packages("rstan", dependencies = TRUE)
library(XML)
library(ROpenCVLite)
devtools::install_github("tractatus/wholebrain") #(choose to not update any dependencies)

Everything was fine. However, when I restarted R to load wholebrain package, I saw the following. Anyone knows what to Select here?

library(wholebrain)
Loading required package: Rcpp
Loading required package: png
Loading required package: MASS
Loading required package: grImport
Loading required package: grid
Loading required package: XML
Loading required package: sp
Loading required package: rgl
Selection: