add vagrantfile and ansible provisining

Add CI/CD

.gitlab-ci.yml

+stages:
+  - build
+  - deploy
+
+Gen-VM:
+  tags:
+    - "virtualbox"
+    - "ansible"
+    - "vagrant"
+  stage: build
+  scripts:
+    - Vagrant up
+    - Vagrant halt windows10R4
+
+Deploy-VM:
+  tags:
+    - "virtualbox"
+    - "ansible"
+    - "vagrant"
+  stage: deploy
+  when: on_success
+  scripts:
+    - vboxmanager unregistervm --delete win10R4
+    - vboxmanager modifyvm windows10R4 --name win10R4 

Vagrantfile

+Vagrant.configure("2") do |config|
+  config.vm.box = "GAEV/win10"
+	config.vm.boot_timeout = 600
+
+	# Configure Vagrant to use WinRM instead of SSH
+  config.vm.communicator = "winrm"
+ 
+  # Configure WinRM Connectivity
+	config.winrm.basic_auth_only = true
+  config.winrm.username = "vagrant"
+  config.winrm.password = "vagrant"
+
+	config.vm.provider "virtualbox" do |vb|
+     # Display the VirtualBox GUI when booting the machine
+     vb.gui = false
+		 vb.name = "windows10R4"
+		 vb.customize ["modifyvm", :id, "--memory", 4096]
+     vb.customize ["modifyvm", :id, "--cpus", 4]
+     vb.customize ["modifyvm", :id, "--vram", 128]
+     vb.customize ["modifyvm", :id, "--graphicscontroller","vboxsvga"]
+     vb.customize ["modifyvm", :id, "--clipboard", "bidirectional"]
+     vb.customize ["setextradata", "global", "GUI/SuppressMessages", "all" ]
+  end
+	
+	config.vm.provision "ansible" do |ansible|
+    ansible.playbook = "ansible_provisioning/playbook.yml"
+		ansible.inventory_path = "ansible_provisioning/group_vars/inventory.yml"
+		ansible.verbose = "-vv"
+		ansible.limit= "windows"
+  end
+end
+

ansible_provisioning/files/configure-msys2.sh

+#!/bin/sh
+
+## execute using bash C:\Rtools\usr\bin\bash.exe
+
+# Add repository
+sed -i.bak -e "s/^#\[msys\]/\[msys\]/" -e "s/^#Include/Include/" /etc/pacman.conf
+echo -e "Server = http://repo.msys2.org/mingw/\$arch/" >> /etc/pacman.d/mirrorlist.msys
+echo -e "Server = http://repo.msys2.org/mingw/x86_64/" >> /etc/pacman.d/mirrorlist.mingw64
+
+# Update server gpg key
+curl -O http://repo.msys2.org/msys/x86_64/msys2-keyring-r21.b39fb11-1-any.pkg.tar.xz
+curl -O http://repo.msys2.org/msys/x86_64/msys2-keyring-r21.b39fb11-1-any.pkg.tar.xz.sig
+pacman-key --verify msys2-keyring-r21.b39fb11-1-any.pkg.tar.xz.sig
+pacman -U msys2-keyring-r21.b39fb11-1-any.pkg.tar.xz --noconfirm
+pacman --noconfirm -U --config <(echo) msys2-keyring-r21.b39fb11-1-any.pkg.tar.xz
+
+# Update msys2 (just one time to keep Rtools dependences versions)
+pacman -Syuu --noconfirm
+
+#pacman -S openssh cygrunsrv mingw-w64-x86_64-editrights --noconfirm

ansible_provisioning/files/install-gitlab-runner.ps1

+# Install R Tools 4.0
+Write-Output "Installing GitLab Runners"
+
+Write-Output "Downloading Gitlab Runners Last Version"
+## download last relase name
+$url = "https://gitlab-runner-downloads.s3.amazonaws.com/latest/binaries/gitlab-runner-windows-amd64.exe"
+$output = 'C:\GitLab-Runner\gitlab-runner.exe'
+$wcR = New-Object System.Net.WebClient
+
+Write-Output "Downloading $url"
+#Download the exe
+$wcR.DownloadFile($url, $output)
+Write-Output "Download completed $url"
+
+# Add GitLab to PATH
+$oldpath = (Get-ItemProperty -Path 'Registry::HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\Session Manager\Environment' -Name PATH).path
+$newPath = "$oldpath;C:\GitLab-Runner\\"
+Set-ItemProperty -Path 'Registry::HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\Session Manager\Environment' -Name PATH -Value $newPath
+

ansible_provisioning/files/install-miktex.ps1

+# Install miktex for latex support
+Write-Output "Installing MiKTeX"
+
+Write-Output "Downloading installer"
+## download last relase name
+$url = "https://miktex.org/download/win/miktexsetup-x64.zip"
+$output = 'c:\Windows\Temp\miktex.zip'
+$wcR = New-Object System.Net.WebClient
+
+Write-Output "Downloading $url"
+#Download the exe
+$wcR.DownloadFile($url, $output)
+Write-Output "Download completed $url"
+
+Write-Output "unzip"
+Expand-Archive -LiteralPath $output -DestinationPath 'C:\Windows\Temp\' InvoiceUnzipped
+
+Write-Output "Download repository"
+miktexsetup --verbose --local-package-repository=C:\Windows\Temp\miktex --package-set=complete download
+
+Write-Output "Install "
+C:\Windows\Temp\miktex\miktexsetup.exe --quiet --local-package-repository=C:\Windows\Temp\miktex --package-set=basic --shared=yes --common-install='C:\miktex'  install
+
+Write-Output "MiKTeX installed into C:\miktex"
+
+#if ( Test-Path "HKLM:\Software\R-core\Rtools" ) {
+#	$Rtoolsver = (Get-ItemProperty -Path "HKLM:\Software\R-core\Rtools")."Current Version"
+#	Write-Output "Rtools version $Rtoolsver installed"
+#}
+#else {
+#	throw "ERROR: Can't install R $urlRtools"
+#}
+
+# Add miktex to PATH
+#$oldpath = (Get-ItemProperty -Path 'Registry::HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\Session Manager\Environment' -Name PATH).path
+#$newPath = "$oldpath;C:\miktek\bin"
+#Set-ItemProperty -Path 'Registry::HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\Session Manager\Environment' -Name PATH -Value $newPath

ansible_provisioning/files/install-msys2-sshd.sh

+#!/bin/sh
+#
+#  msys2-sshd-setup.sh — configure sshd on MSYS2 and run it as a Windows service
+#
+#  Replaces ssh-host-config <https://github.com/openssh/openssh-portable/blob/master/contrib/cygwin/ssh-host-config>
+#  Adapted from <https://ghc.haskell.org/trac/ghc/wiki/Building/Windows/SSHD> by Sam Hocevar <sam@hocevar.net>
+#  Adapted from <https://gist.github.com/samhocevar/00eec26d9e9988d080ac> by David Macek
+#
+#  Prerequisites:
+#    — a 64-bit installation of MSYS2 itself: https://msys2.org
+#    — some packages: pacman -S openssh cygrunsrv mingw-w64-x86_64-editrights
+#
+#  Gotchas:
+#    — the log file will be /var/log/msys2_sshd.log
+#    — if you get error “sshd: fatal: seteuid XXX : No such device or address”
+#      in the logs, try “passwd -R” (with admin privileges)
+#    — if you get error “chown(/dev/pty1, XXX, YYY) failed: Invalid argument”
+#      in the logs, make sure your account and group names are detectable (see
+#      `id`); issues are often caused by having /etc/{passwd,group} or having
+#      a modified /etc/nsswitch.conf
+#
+#  Changelog:
+#   09 May 2020 — completely remove additional privileged user
+#   16 Apr 2020 — remove additional privileged user
+#               — only touch /etc/{passwd,group} if they exist
+#   27 Jun 2019 — rename service to msys2_sshd to avoid conflicts with Windows OpenSSH
+#               — use mkgroup.exe as suggested in the comments
+#               — fix a problem with CRLF and grep
+#   24 Aug 2015 — run server with -e to redirect logs to /var/log/sshd.log
+#
+
+pacman -Syy
+pacman -S openssh cygrunsrv mingw-w64-x86_64-editrights --noconfirm
+
+set -e
+
+#
+# Configuration
+#
+
+UNPRIV_USER=sshd # DO NOT CHANGE; this username is hardcoded in the openssh code
+UNPRIV_NAME="Privilege separation user for sshd"
+
+EMPTY_DIR=/var/empty
+
+
+#
+# Check installation sanity
+#
+
+if ! /mingw64/bin/editrights -h >/dev/null; then
+    echo "ERROR: Missing 'editrights'. Try: pacman -S mingw-w64-x86_64-editrights."
+    exit 1
+fi
+
+if ! cygrunsrv -v >/dev/null; then
+    echo "ERROR: Missing 'cygrunsrv'. Try: pacman -S cygrunsrv."
+    exit 1
+fi
+
+if ! ssh-keygen -A; then
+    echo "ERROR: Missing 'ssh-keygen'. Try: pacman -S openssh."
+    exit 1
+fi
+
+
+#
+# The unprivileged sshd user (for privilege separation)
+#
+
+add="$(if ! net user "${UNPRIV_USER}" >/dev/null; then echo "//add"; fi)"
+if ! net user "${UNPRIV_USER}" ${add} //fullname:"${UNPRIV_NAME}" \
+              //homedir:"$(cygpath -w ${EMPTY_DIR})" //active:no; then
+    echo "ERROR: Unable to create Windows user ${UNPRIV_USER}"
+    exit 1
+fi
+
+
+#
+# Add or update /etc/passwd entries
+#
+
+if test -f /etc/passwd; then
+    sed -i -e '/^'"${UNPRIV_USER}"':/d' /etc/passwd
+    SED='/^'"${UNPRIV_USER}"':/s?^\(\([^:]*:\)\{5\}\).*?\1'"${EMPTY_DIR}"':/bin/false?p'
+    mkpasswd -l -u "${UNPRIV_USER}" | sed -e 's/^[^:]*+//' | sed -ne "${SED}" \
+             >> /etc/passwd
+    mkgroup.exe -l > /etc/group
+fi
+
+
+#
+# Finally, register service with cygrunsrv and start it
+#
+
+cygrunsrv -R msys2_sshd || true
+cygrunsrv -I msys2_sshd -d "MSYS2 sshd" -p /usr/bin/sshd.exe -a "-D -e" -y tcpip
+
+# The SSH service should start automatically when Windows is rebooted. You can
+# manually restart the service by running `net stop msys2_sshd` + `net start msys2_sshd`
+if ! net start msys2_sshd; then
+    echo "ERROR: Unable to start msys2_sshd service"
+    exit 1
+fi

ansible_provisioning/files/install-pandoc.ps1

+# Install miktex for latex support
+Write-Output "Installing pandoc"
+
+Write-Output "Downloading installer"
+## download 
+$url = "https://github.com/jgm/pandoc/releases/download/2.10.1/pandoc-2.10.1-windows-x86_64.zip"
+$output = 'c:\Windows\Temp\pandoc.zip'
+$wcR = New-Object System.Net.WebClient
+
+Write-Output "Downloading $url"
+#Download the exe
+$wcR.DownloadFile($url, $output)
+Write-Output "Download completed $url"
+
+$pandocDir = 'C:\pandoc\'
+Write-Output "Install $output into $pandocDir"
+Expand-Archive -LiteralPath $output -DestinationPath $pandocDir InvoiceUnzipped
+
+if (Test-Path 'C:\pandoc\pandoc.exe')
+{
+	Write-Output "pandoc installed"
+}
+else
+{
+	throw "ERROR: Can't install pandoc"
+}
+# Add pandoc to PATH
+$oldpath = (Get-ItemProperty -Path 'Registry::HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\Session Manager\Environment' -Name PATH).path
+$newPath = "$oldpath;C:\pandoc"
+Set-ItemProperty -Path 'Registry::HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\Session Manager\Environment' -Name PATH -Value $newPath

ansible_provisioning/files/install-r-packages.sh

+#!/bin/bash
+
+echo "Installing system dependencies with pacman"
+
+pacman --noconfirm -S mingw-w64-{i686,x86_64}-fftw \
+  mingw-w64-{i686,x86_64}-gdal \
+  mingw-w64-{i686,x86_64}-geos \
+  mingw-w64-{i686,x86_64}-libxml2 \
+  mingw-w64-{i686,x86_64}-tools-git \
+  mingw-w64-{i686,x86_64}-tools \
+	msys/vim
+
+
+echo "Installing R packages"
+
+echo "dir.create(Sys.getenv('R_LIBS_USER'), recursive=TRUE); \
+  .libPaths( c(Sys.getenv('R_LIBS_USER'), .libPaths()) ) ; \
+  install.packages(c( \
+  'deSolve', \
+  'sp', \
+  'rgeos', \
+  'fields', \
+  'MASS', \
+  'Matrix', \
+  'deldir', \
+  'pracma', \
+  'raster', \
+  'fftwtools', \
+  'mvtnorm', \
+  'rgdal', \
+  'sf', \
+  'splancs', \
+  'knitr', \
+  'rmarkdown', \
+  'testthat', \
+  'Rcpp', \
+  'RcppArmadillo', \
+  'fasterize', \
+  'roxygen2', \
+  'shiny', \
+  'htmltools', \
+  'shinydashboard', \
+  'ggplot2', \
+  'dplyr', \
+  'dbplyr', \
+  'DT', \
+  'magrittr', \
+  'devtools', \
+  'shinyjs', \
+  'stringi', \
+  'stringr', \
+  'jsonlite', \
+  'data.table', \
+  'htmlwidgets', \
+  'RSQLite', \
+  'BiocManager', \
+  'foreach', \
+  'doParallel', \
+  'mvtnorm', \
+  'mapdata', \
+  'proj4', \
+  'gstat', \
+  'automap', \
+  'RCALI', \
+  'rgenoud', \
+  'purrr' \
+  ), \
+  dependencies=TRUE, \
+  repos='https://cran.biotools.fr')" > /c/Windows/Temp/install.R \
+  
+Rscript /c/Windows/Temp/install.R
+
+Rscript -e "BiocManager::install(c('Biostrings', ask=FALSE))"
+Rscript -e "update.packages(ask=FALSE, repos='https://cran.biotools.fr')"
+

ansible_provisioning/files/install-r.ps1

+# Install R 
+Write-Output "Installing R"
+
+Write-Output "Downloading R Last Version"
+## Download R engine for Windows machine
+
+## download last relase name
+$urlR = "https://cran.biotools.fr/bin/windows/base/release.html"
+$outputR = 'c:\Windows\Temp\R-win.exe'
+$wcR = New-Object System.Net.WebClient
+$res = $wcR.DownloadString($urlR)
+
+## get release name in the HTML page
+$pos1 = $res.IndexOf("URL=")
+$pos2 = $res.LastIndexOf('"')
+$Rexe = $res.Substring($pos1+4, $pos2-$pos1-4)
+$urlR = "https://cran.biotools.fr/bin/windows/base/" + $Rexe
+
+Write-Output "Downloading $($urlR)"
+#Download the exe
+$wcR.DownloadFile($urlR, $outputR)
+
+Write-Output "Download completed $Rexe"
+
+$RDir = 'C:\R\'
+Write-Output "Install $outputR into $RDir"
+Start-Process -FilePath $outputR -ArgumentList "/VERYSILENT /DIR=$RDir" -Wait -NoNewWindow
+
+if ( Test-Path "HKLM:\Software\R-core\R" ) {
+	$Rver = (Get-ItemProperty -Path "HKLM:\Software\R-core\R")."Current Version"
+	Write-Output "R version $($Rver) installed"
+}
+else {
+	throw "ERROR: Can't install R $($urlR)"
+}
+
+# Add R to PATH
+$oldpath = (Get-ItemProperty -Path 'Registry::HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\Session Manager\Environment' -Name PATH).path
+$newPath = "$oldpath;C:\R\bin"
+Set-ItemProperty -Path 'Registry::HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\Session Manager\Environment' -Name PATH -Value $newPath

ansible_provisioning/files/install-rtools.ps1

+# Install R Tools 4.0
+Write-Output "Installing Rtools 4.0"
+
+Write-Output "Downloading Rtools Last Version"
+## download last relase name
+$urlRtools = "https://cran.biotools.fr/bin/windows/Rtools/rtools40-x86_64.exe"
+$outputRtools = 'c:\Windows\Temp\Rtools-win.exe'
+$wcR = New-Object System.Net.WebClient
+
+Write-Output "Downloading $urlRtools"
+#Download the exe
+$wcR.DownloadFile($urlRtools, $outputRtools)
+Write-Output "Download completed $urlRtools"
+
+$RtoolsDir = 'C:\Rtools\'
+Write-Output "Install $outputRtools into $RtoolsDir"
+Start-Process -FilePath $outputRtools -ArgumentList "/VERYSILENT /DIR=$RtoolsDir" -Wait -NoNewWindow
+
+if ( Test-Path "HKLM:\Software\R-core\Rtools" ) {
+	$Rtoolsver = (Get-ItemProperty -Path "HKLM:\Software\R-core\Rtools")."Current Version"
+	Write-Output "Rtools version $Rtoolsver installed"
+}
+else {
+	throw "ERROR: Can't install R $urlRtools"
+}
+
+# Add R to PATH
+$oldpath = (Get-ItemProperty -Path 'Registry::HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\Session Manager\Environment' -Name PATH).path
+$newPath = "$oldpath;C:\Rtools\usr\bin"
+Set-ItemProperty -Path 'Registry::HKEY_LOCAL_MACHINE\System\CurrentControlSet\Control\Session Manager\Environment' -Name PATH -Value $newPath
+[System.Environment]::SetEnvironmentVariable('MSYS2_PATH_TYPE', 'inherit', [System.EnvironmentVariableTarget]::Machine)

ansible_provisioning/group_vars/inventory.yml

+windows:
+  hosts:
+    windows10: 
+      ansible_host: 127.0.0.1
+  vars:
+    ansible_user: vagrant
+    ansible_password: vagrant
+    ansible_port: 55985
+    ansible_connection: winrm
+    ansible_winrm_transport: basic
+    ansible_winrm_server_cert_validation: ignore
+    ansible_winrm_scheme: http
+
+

ansible_provisioning/playbook.yml

+---
+- name: Windows R tools
+  hosts: windows10
+  #remote_user: vagrant
+  #vars:
+  #  ansible_user: vagrant
+  #  ansible_password: vagrant
+  #  ansible_connection: winrm
+  #  ansible_winrm_transport: basic
+  #  ansible_winrm_server_cert_validation: ignore
+  tasks:
+    - name: ping
+      win_ping:
+    - name: Install security updates
+      win_updates:
+        category_names:
+          - SecurityUpdates
+        use_scheduled_task: yes
+    - name: copy R script
+      win_copy:
+        src: ./files/install-r.ps1
+        dest: 'C:\Windows\Temp\'
+        remote_src: no
+    - name: Install R
+      win_command: powershell.exe -File C:\Windows\Temp\install-r.ps1
+    - name: copy Rtools script
+      win_copy:
+        src: ./files/install-rtools.ps1
+        dest: 'C:\Windows\Temp\'
+        remote_src: no
+    - name: Install Rtools4
+      win_command: powershell.exe -File C:\Windows\Temp\install-rtools.ps1
+    - name: copy msys2 config script
+      win_copy:
+        src: ./files/configure-msys2.sh
+        dest: 'C:\Windows\Temp\'
+        remote_src: no
+    - name: Configure MSYS2
+      win_command: C:\Rtools\usr\bin\bash.exe -l C:\Windows\Temp\configure-msys2.sh
+    - name: copy msys2 sshd install script
+      win_copy:
+        src: ./files/install-msys2-sshd.sh
+        dest: 'C:\Windows\Temp\'
+        remote_src: no
+    - name: Install MSYS2 ssh deamon
+      win_command: C:\Rtools\usr\bin\bash.exe -l C:\Windows\Temp\install-msys2-sshd.sh
+    - name: Enable Firewall for sshd
+      win_shell: |
+        netsh advfirewall firewall add rule name="SSHD" dir=in action=allow service=msys2_sshd enable=yes
+        netsh advfirewall firewall add rule name="SSHD" dir=in action=allow program="C:\Rtools\usr\bin\sshd.exe" enable=yes
+        netsh advfirewall firewall add rule name="ssh" dir=in action=allow protocol=TCP localport=22
+    - name: copy R packages script
+      win_copy:
+        src: ./files/install-r-packages.sh
+        dest: 'C:\Windows\Temp\'
+        remote_src: no
+    - name: Install R packages
+      win_command: C:\Rtools\usr\bin\bash.exe -l C:\Windows\Temp\install-r-packages.sh
+    - name: copy GitLab install script
+      win_copy:
+        src: ./files/install-gitlab-runner.ps1
+        dest: 'C:\Windows\Temp\'
+        remote_src: no
+    - name: Install GitLab Runner
+      win_command: powershell.exe -File C:\Windows\Temp\install-gitlab-runner.ps1
+    - name: copy MiKTeX install script
+      win_copy:
+        src: ./files/install-miktex.ps1
+        dest: 'C:\Windows\Temp\'
+        remote_src: no
+    - name: Install MiKTeX
+      win_command: powershell.exe -File C:\Windows\Temp\install-miktex.ps1
+    - name: copy pandoc install script
+      win_copy:
+        src: ./files/install-pandoc.ps1
+        dest: 'C:\Windows\Temp\'
+        remote_src: no
+    - name: Install Pandoc
+      win_command: powershell.exe -File C:\Windows\Temp\install-pandoc.ps1
+
+
+
+
+