Install LaTeX (TeXLive)

If you plan to install LaTeX, you should do so before compiling R since the latter will look for it during compilation.

$ wget http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz
$ tar -xvf install-tl-unx.tar.gz
$ cd install-tl-20190119/
$ ./install-tl

Depending on your preferences, you might want to make the directory /usr/local/texlive owned by your user account instead of root to simplify the maintenance of TeXLive. Note that downloading a full TeXLive installation can take quite a while.

To add LaTeX to the system-wide PATH, I added the following line to /etc/profile:

PATH="/usr/local/texlive/2018/bin/x86_64-linux:$PATH"

This will make the LaTeX executables findable by R and other programs on the host (you might have to logout and log back in for the change to take effect).

Compile R from source

I have found that compiling R from source (on the host) aids considerably in achieving a working R session on each guest, because whereas compiled R lives entirely inside the /opt/R/ directory, the R installated from the Debian repos gets parts of it installed all over the filesystem (/usr/lib/R/, /usr/local/lib/R/, among other places) which makes it unworkable to setup KVM filesystem passthrough.

For removing an existing R installed by the apt package manager, see the appendix. But please don’t remove your existing R installation before reading through the installation instructions below carefully.

Download and extract the R source tarball (at the time I compiled R, version 3.5.1 was available).

chepec@yourhost:~/Downloads
$ wget https://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz
$ tar -xzvf R-3.5.1.tar.gz
$ cd R-3.5.1

Depending on which R packages you plan to install, you might need to install certain dependencies before compiling R. How to figure out which dependencies you need may not be entirely straight-forward. You should at least have a look at the capabilities() of your current R installation (before removing it):

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua
       TRUE        TRUE        TRUE        TRUE       FALSE       FALSE
   http/ftp     sockets      libxml        fifo      cledit       iconv
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE
        NLS     profmem       cairo         ICU long.double     libcurl
       TRUE        TRUE        TRUE       FALSE        TRUE        TRUE

Some of these capabilities/dependencies appear to be packaged together with apt’s R installation, so when we remove it, we also uninstall the dependencies. Anyway, I found that, on my particular system, tcltk was missing and had to be installed prior to compiling R for a whole bunch of R packages to work later. So we need to install the tcl and tk development packages:

chepec@yourhost:~
$ sudo apt install tcl8.6-dev tk8.6-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
  libxft-dev libxss-dev x11proto-scrnsaver-dev
Suggested packages:
  tcl8.6-doc tk8.6-doc
The following NEW packages will be installed:
  libxft-dev libxss-dev tcl8.6-dev tk8.6-dev x11proto-scrnsaver-dev
0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded.

Now let’s build R from the source tarball we downloaded (note the build flags, and adapt to your needs).

chepec@yourhost:~/Downloads/R-3.5.1
$ ./configure --prefix=/opt/R/$(cat VERSION) --enable-R-shlib --with-blas --with-lapack --with-tcltk

This should produce lots of output, ending with a block looking like this:

R is now configured for x86_64-pc-linux-gnu

  Source directory:          .
  Installation directory:    /opt/R/3.5.1

  C compiler:                gcc  -g -O2
  Fortran 77 compiler:       f95  -g -O2

  Default C++ compiler:      g++   -g -O2
  C++98 compiler:            g++ -std=gnu++98 -g -O2
  C++11 compiler:            g++ -std=gnu++11 -g -O2
  C++14 compiler:            g++ -std=gnu++14 -g -O2
  C++17 compiler:
  Fortran 90/95 compiler:    gfortran -g -O2
  Obj-C compiler:

  Interfaces supported:      X11, tcltk
  External libraries:        readline, BLAS(generic), LAPACK(generic), curl
  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo, ICU
  Options enabled:           shared R library, R profiling

  Capabilities skipped:
  Options not enabled:       shared BLAS, memory profiling

  Recommended packages:      yes

To figure out if anything was amiss during the compilation, you really should spend some time scrolling through config.log in the compilation directory. It might save you a bunch of time later.

Now if you’re happy with the build, let’s make and install.

$ make
$ sudo make install

That’s it. Now either put the opt/R/<version-number>/bin/ directory into the system PATH, or symlink the two R executables into somewhere already on the system PATH. I prefer the latter approach, so:

$ sudo ln -s /opt/R/3.5.1/bin/R /usr/bin/R
$ sudo ln -s /opt/R/3.5.1/bin/Rscript /usr/bin/Rscript

When we create our first VM we will create the same symlinks on there. And don’t forget that these symlinks should be changed once you have upgraded to a newer R version.

NOTE: at this point, it’s perhaps worth underscoring that going forward, everything R-related should be kept inside this /opt/R/ tree. That includes config files (by default placed in /opt/R/3.5.1/lib/R/etc/) as well as installed system and user packages. Anything you place outside this tree will not be visible on the VM which would defeat the purpose of this whole project.

Install KVM and the virtual machine OS

Install the VM hypervisor (KVM/libvirt):

$ sudo apt install qemu-kvm libvirt-bin virtinst bridge-utils cpu-checker

Verify the KVM installation by running kvm-ok. Also check that the libvirtd service is running: systemctl status libvirtd.service. If it’s not, start it: sudo systemctl start libvirtd.service.

For networking, I decided to setup the server’s physical network interface card (NIC) as a bridge adapter. This way, each VM will act as its own NIC visavi the router, and I can simply let the router assign IP addresses as usual (and it allows me to use my router’s DHCP server to set a static IP address for each VM). This was simpler to setup than iptables redirects on the host or other alternatives (there are many ways to setup networking for VMs). And if you want SSH access to the VM, just setup port forwarding of the SSH port on the router, as per usual.

To set up your NIC as a bridge adapter, first make sure the bridge-utils package is installed on the host. We will edit /etc/network/interfaces, so make sure to take a backup copy of it first: sudo cp /etc/network/interfaces /etc/network/interfaces.backup. For good measure, you might want to backup /etc/resolv.conf as well.

This is how my /etc/network/interfaces looked before any changes:

# The loopback network interface
auto lo
iface lo inet loopback

# The primary network interface
auto eth1
iface eth1 inet dhcp

and this is the same file now configured for bridging:

# The loopback network interface
auto lo
iface lo inet loopback

# The physical network interface
auto eth1
iface eth1 inet manual

auto br0
iface br0 inet dhcp
bridge_ports eth1
bridge_stp off
bridge_fd 0
bridge maxwait 0

This sets up the new br0 interface, and effectively makes eth1 just a physical transport layer to it. Bridging means the VM will be exposed to whatever the bridged NIC is connected to, in our case to our LAN and the router. As such it will get an IP address from the router’s DHCP server just like any other networked device on the LAN.

Note that by default, KVM creates its own bridge at 192.168.122.1. This device acts as a virtual router for your VMs. (We will not use this virtual router for anything in this project).

With the edits in place, restart the networking service (but be warned: if your connection to the host is over SSH, at this point you will lose the connection! I found it useful to apply these networking changes while physically connected to the host).

$ sudo systemctl restart networking.service

With KVM installed and with the host’s network configured, we are now ready to install our first virtual machine. The installation is done over VNC.

All virtual machine files and other related files will be stored under /var/lib/libvirt/. The default path of saved ISO images is /var/lib/libvirt/boot/.

We will go ahead and download the latest netinst Ubuntu Server 16.04 64-bit image, and save it in /var/lib/libvirt/boot/. Installing is fairly straight-forward once you figure out the virt-install command parameters (lots of guides online, see the Bibliography). I used the following command with success:

$ sudo virt-install --virt-type=kvm --name <guestname> --ram 4096 --vcpus=2 \
  --os-variant=ubuntu16.04 --hvm \
  --cdrom=/var/lib/libvirt/boot/ubuntu-16.04.3-amd64-netinst.iso \
  --network=bridge=br0,model=virtio --graphics vnc \
  --disk path=/var/lib/libvirt/images/<guestname>.qcow2,size=20,bus=virtio,format=qcow2

Here we allocate a maximum of 4 GB RAM, 2 CPU cores and 20 GB disk space to the new virtual machine. KVM is pretty smart and won’t use up those resources until usage demands it, so most of the time the load on the host from this VM will be much less than this. As for the disk space, 20 GB should be plenty. In fact, if you don’t plan to keep your work files on the VM itself, even half that would be plenty). Anyway, it’s fairly easy to expand a qcow2 disk at a later date, but slightly complicated to shrink one.

The above command will simply tell you that installation has started - you will need to connect to the OS installation using VNC to actually proceed with the installation. KVM gives every guest it launches a new VNC instance with its own port (starting with port 5900). So we’ll check the current guest’s VNC port number, and then tunnel in via ssh to proceed with the OS installation:

# find the VNC port number of the VM
$ sudo virsh dumpxml <guestname> | grep vnc
# sample output:
<graphics type='vnc' port='5900' autoport='yes' listen='127.0.0.1'>

Use a VNC client (such as xtightvncviewer) to connect to the port used by the libvirt installer on the server. For security, we will route the connection through an SSH tunnel:

# Create an ssh tunnel from your workstation to the host
$ ssh <username>@yourhost.yourdomain.se -L 5900:localhost:<localport>
# on your workstation, use a local VNC client to connect to the tunnel
$ xtightvncviewer localhost:<localport>

Et voilà! Now proceed with the OS installation as usual. If the VNC connection is dropped during the installation (happens sometimes), reconnect by repeating the last chunk and continue from where you were dropped off.

When the OS installation is done, it’s a good time to setup static DHCP for this VM and port forwarding for the SSH port. Both of these settings are done on your router. (There are some links in the Bibliography to help get you started). You probably also want to setup passwordless SSH access to the VM (since you already have a server, I’m going to assume you know how to do that). Make sure to set the VM’s hostname in both /etc/hostname and /etc/hosts.

With those things in place, we will also setup a new subdomain for accessing this Rstudio server instance from anywhere. If you configured SSH port forwarding earlier, you will also be able to SSH from anywhere. I cannot go into how to do this in detail since it depends on your registrar (Loopia, GoDaddy, Amazon Route 53, etc.). But in summary, go to your registrar, and create a CNAME record that points <name-for-VM>.yourdomain.se to the already existing (sub)domain of your host server (yourhost.yourdomain.se). Once the new DNS settings have propagated across the web, you should be able to reach your new virtual machine using your chosen URL.

While still on the host, make sure that the virtual machine is running:

$ virsh list --all
$ virsh start <guestname>

Share directories on the host to the guests

Shutdown the virtual machine and edit its configuration XML file:

$ virsh shutdown <guestname>
$ virsh edit <guestname>

and add these blocks inside the devices tree:

<filesystem type='mount' accessmode='passthrough'>
   <source dir='/opt/R'/>
   <target dir='R'/>
</filesystem>
<filesystem type='mount' accessmode='passthrough'>
   <source dir='/usr/local/texlive'/>
   <target dir='texlive'/>
</filesystem>
<filesystem type='mount' accessmode='passthrough'>
   <source dir='/usr/share/fonts'/>
   <target dir='fonts'/>
</filesystem>

The string in target dir is just a label, which we will have use for in the fstab (on the guest) to mount these shares. Make the label informative.

Restart the VM.

$ virsh start <guestname>

And with that, let’s move on to mounting the passed-through directories on the VM.

Filesystem passthrough for R, TeXLive and fonts

Log in to the VM. Append the following lines to the file /etc/modules:

loop
virtio
9p
9pnet
9pnet_virtio

then load those modules (make sure to do this step as root):

$ sudo service kmod start

Create the mountpoints for the shares on the guest. The mountpoints for R and TeXLive should not exist on the guest, so simple create those directories (use sudo if necessary):

$ mkdir /opt/R
$ mkdir /usr/local/texlive

The fonts directory probably exists already, so let’s delete it and recreate an empty one:

$ sudo rm -rf /usr/share/fonts
$ sudo mkdir /usr/share/fonts

Now you should be ready to mount the passed-through directories (here we make use the label we set in target dir above):

$ sudo mount R /opt/R -t 9p -o trans=virtio
$ sudo mount texlive /usr/local/texlive -t 9p -o trans=virtio
$ sudo mount fonts /usr/share/fonts -t 9p -o trans=virtio

Now make sure everything works as expected on the guest. You should be able to read from these directories, but not write. If everything works as expected, go ahead and add these shares to /etc/fstab for automatic mounting at boot:

R        /opt/R               9p    trans=virtio   0   0
texlive  /usr/local/texlive   9p    trans=virtio   0   0
fonts    /usr/share/fonts     9p    trans=virtio   0   0

Note: by default, the security profile of KVM will not allow the guest to write to any directories mounted using the passthrough method. And this works just fine for our purposes, since all maintenance of the R, LaTeX and fonts directories should be done on the host machine anyway.

Make R and TeXLive executables accessible

For R and LaTeX to work as expected on the guest, it’s not enough to make the /opt/R and /usr/local/texlive trees available. We should also expose the executables where other programs expect to find them, namely somewhere on the system’s PATH.

Additionally, there are a few crucial TeX utilities that we need to get from the host to the guest.

$ ls -1 /usr/bin/tex*
/usr/bin/texi2any
/usr/bin/texi2dvi
/usr/bin/texi2pdf
/usr/bin/texindex

These are actual files and not links. They are not available on the guest, but need to be for TeXLive to work properly in conjunction with R.

There’s no way to passthrough single files from host to guest, and we definitely do not want to passthrough the entire /usr/bin/ directory. So although inelegant, the best solution appears to be to simply copy these files from host to guest. Note that you will need to redo this if these files should be updated by tlmgr on the host in the future. Assuming you have setup SSH access from host to guest, you can copy them like this:

chepec@yourhost:~
$ scp -p /usr/bin/texi* <guestname>:/home/chepec/Downloads/
$ ssh <guestname>
chepec@<guestname>:~
$ sudo cp -a /home/chepec/Downloads/texi* /usr/bin/
$ sudo chown root:root /usr/bin/texi*

Create symlinks in /usr/bin/ for the R executables:

$ sudo ln -s /opt/R/3.5.1/bin/R /usr/bin/R
$ sudo ln -s /opt/R/3.5.1/bin/Rscript /usr/bin/Rscript

And add the TexLive path to the system PATH. In /etc/profile, append

PATH="/usr/local/texlive/2018/bin/x86_64-linux:$PATH"

Why not add the R/bin directory to PATH as well, you ask? Well, you may well want to do that, especially if you have more than just two executables in there. Both methods (symlinking or editing $PATH) achieve the same result.

NOTE: if you have a network share or similar where you keep your work files, you might want to mount that too on the guest. Since you most definitely want to read and write to this directory from the VM, you might want to use NFS (if it’s inside the LAN) or SSHFS (otherwise) to mount it instead of KVM passthrough. If you do, having your regular user account on the VM have the same username, uid and gid as that on the share will most certainly make your life as an admin easier.

Install Rstudio Server

Browse to https://www.rstudio.com/products/rstudio/download-server/ and follow the instructions to download and install the latest RStudio Server Open Source Edition.

The installation will automatically set up a systemd startup script (or upstart, depending on your system) for Rstudio server. Neat!

By default, RStudio Server listens on port 8787 on all interfaces, 0.0.0.0:8787. At this point, you should be able to verify that RStudio Server is accessible via your browser by entering http://<ip-address-guest>:8787.

Configure Apache reverse proxy and Let’s Encrypt certificates

The Apache web server on our host machine will act as a reverse proxy, and we will also install a free TLS (HTTPS) certificate from Let’s Encrypt for our RStudio Server instance.

Let’s say you named your virtual machine callisto and created a subdomain rstudio.callisto.yourhost.se for it. We would thus create a new Apache virtualhost file /etc/apache2/sites-available/rstudio.callisto.yourhost.se.conf with the following contents:

<VirtualHost *:80>
   ServerAdmin webmaster@yourhost.se
   ServerName rstudio.callisto.yourhost.se

   Redirect permanent / https://rstudio.callisto.yourhost.se/

   ErrorLog ${APACHE_LOG_DIR}/rstudio.callisto.yourhost.se_error.log
   CustomLog ${APACHE_LOG_DIR}/rstudio.callisto.yourhost.se_access.log combined
</VirtualHost>

<VirtualHost *:443>
   ServerAdmin webmaster@yourhost.se
   ServerName rstudio.callisto.yourhost.se

   SSLEngine on
   SSLCertificateKeyFile   /etc/letsencrypt/live/rstudio.callisto.yourhost.se/privkey.pem
   SSLCertificateFile      /etc/letsencrypt/live/rstudio.callisto.yourhost.se/cert.pem
   SSLCertificateChainFile /etc/letsencrypt/live/rstudio.callisto.yourhost.se/chain.pem

   <Proxy *>
      Allow from localhost
   </Proxy>

   RewriteEngine on
   RewriteCond %{HTTP:Upgrade} =websocket
   RewriteRule /(.*) ws://192.168.100.110:8787/$1 [P,L]
   RewriteCond %{HTTP:Upgrade} !=websocket
   RewriteRule /(.*) http://192.168.100.110:8787/$1 [P,L]
   ProxyPass / http://192.168.100.110:8787/
   ProxyPassReverse / http://192.168.100.110:8787/
   ProxyRequests Off

   ErrorLog ${APACHE_LOG_DIR}/rstudio.callisto.yourhost.se_error.log
   CustomLog ${APACHE_LOG_DIR}/rstudio.callisto.yourhost.se_access.log combined
</VirtualHost>

You should of course edit domain name, email address and IP address above to fit your setup.

With DNS in place, now is the time to install the Let’s Encrypt certificate. This will be managed by certbot. EFF has excellent instructions on how to install the certbot client. With certbot installed, fetch the certificate (I like to manage the integration with Apache myself, so I use the certonly option):

$ sudo certbot certonly --authenticator standalone \
  --pre-hook "systemctl stop apache2.service" \
  --post-hook "systemctl start apache2.service" \
  --email webmaster@yourhost.se -d rstudio.callisto.yourhost.se

You should really setup a CRON job or a systemd timer for automatic renewals your Let’s Encrypt certificates. Check the Certbot docs and the web for info on how to accomplish that.

With the TLS certificate installed, we are now ready to enable our virtualhost and reload Apache:

$ sudo a2ensite rstudio.callisto.yourhost.se.conf
$ sudo systemctl reload apache2.service

If no errors were thrown, you should new be able to reach your RStudio Server instance running on your VM from your browser using the URL http://<rstudio.callisto.yourhost.se> which should automatically redirect to https.

Create additional VMs (KVM cloning)

Shutdown the VM before cloning.

The cloning operation is straight-forward (should be done as root):

$ virt-clone --original callisto --name ganymede --file /var/lib/libvirt/images/ganymede.qcow2
Allocating 'ganymede.qcow2'                  |  20 GB  00:00:39
Clone 'ganymede' created successfully.

This clones callisto and sets the new VM’s name to ganymede. Note that this naming only affects the VM hypervisor, we still have to login to the new guest and edit the hostname (in /etc/hosts and /etc/hostname).

The bridged networking we setup above means that the new VM will get its own IP address assigned by the router (which you might want to assign statically by the way). We need to create a new subdomain that this instance will be reached on, and once that’s in place we will create a new Apache vhost and download a Let’s Encrypt certificate.

Create /etc/apache2/sites-available/rstudio.ganymede.yourhost.se.conf with the following contents:

<VirtualHost *:80>
   ServerAdmin webmaster@yourhost.se
   ServerName rstudio.ganymede.yourhost.se

   Redirect permanent / https://rstudio.ganymede.yourhost.se/

   ErrorLog ${APACHE_LOG_DIR}/rstudio.ganymede.yourhost.se_error.log
   CustomLog ${APACHE_LOG_DIR}/rstudio.ganymede.yourhost.se_access.log combined
</VirtualHost>

<VirtualHost *:443>
   ServerAdmin webmaster@yourhost.se
   ServerName rstudio.ganymede.yourhost.se

   SSLEngine on
   SSLCertificateKeyFile   /etc/letsencrypt/live/rstudio.ganymede.yourhost.se/privkey.pem
   SSLCertificateFile      /etc/letsencrypt/live/rstudio.ganymede.yourhost.se/cert.pem
   SSLCertificateChainFile /etc/letsencrypt/live/rstudio.ganymede.yourhost.se/chain.pem

   <Proxy *>
      Allow from localhost
   </Proxy>

   RewriteEngine on
   RewriteCond %{HTTP:Upgrade} =websocket
   RewriteRule /(.*) ws://192.168.100.111:8787/$1 [P,L]
   RewriteCond %{HTTP:Upgrade} !=websocket
   RewriteRule /(.*) http://192.168.100.111:8787/$1 [P,L]
   ProxyPass / http://192.168.100.111:8787/
   ProxyPassReverse / http://192.168.100.111:8787/
   ProxyRequests Off

   ErrorLog ${APACHE_LOG_DIR}/rstudio.ganymede.yourhost.se_error.log
   CustomLog ${APACHE_LOG_DIR}/rstudio.ganymede.yourhost.se_access.log combined
</VirtualHost>

Note the different IP address and server name (edit to fit your setup).

And install the Let’s Encrypt certificate:

$ sudo certbot certonly --authenticator standalone \
  --pre-hook "systemctl stop apache2.service" \
  --post-hook "systemctl start apache2.service" \
  --email webmaster@yourhost.se -d rstudio.ganymede.yourhost.se

Enable the site and reload the web server:

$ sudo a2ensite rstudio.callisto.yourhost.se.conf
$ sudo systemctl reload apache2.service

And that should be it.

Autostart the virtual machines

Virtual machines created with KVM do not autostart by default when the host reboots. But for our application, it might be desirable to have them autostart. To achieve that, issue the following for each VM.

$ virsh autostart <guestname>

You can confirm the new setting by:

$ virsh list --all --autostart
$ virsh list --all --no-autostart

Remove an existing R aptitude installation

Here’s how to completely remove an existing R installation that was installed from the Debian repos. Please be careful to record any configuration you want to move over to your new installation. This will remove everything, including config files.

The installed R version was 3.4.4 (2018-03-15). List all of the installed R packages:

chepec@yourhost:~
$ dpkg -l | grep ^ii | awk '$2 ~ /^r-/ { print $2 }'
r-base
r-base-core
r-base-dev
r-base-html
r-cran-boot
r-cran-class
r-cran-cluster
r-cran-codetools
r-cran-crayon
r-cran-digest
r-cran-evaluate
r-cran-foreign
r-cran-irdisplay
r-cran-jsonlite
r-cran-kernsmooth
r-cran-lattice
r-cran-magrittr
r-cran-mass
r-cran-matrix
r-cran-memoise
r-cran-mgcv
r-cran-nlme
r-cran-nnet
r-cran-pbdzmq
r-cran-r6
r-cran-repr
r-cran-rgl
r-cran-rpart
r-cran-spatial
r-cran-stringi
r-cran-stringr
r-cran-survival
r-cran-uuid
r-doc-html
r-recommended

Uninstall all the R packages identified above in one fell swoop:

chepec@yourhost:~
$ dpkg -l | grep ^ii | awk '$2 ~ /^r-/ { print $2 }' | xargs sudo apt remove --purge -y

Clean up any remaining directories (adapt this to catch all of them):

$ sudo rm -rf /usr/lib/R
$ sudo rm -rf /etc/R

Jupyter, an alternative to RStudio Server?

One drastic solution is to abandon RStudio Server altogether and look for alternatives.

The most obvious being Jupyter notebooks, which should offer a comparable web-based interface in particular with the JupyterLab/JupyterHub module. The advantage is that Jupyter supports not only R but other kernels too. The disadvantage lies mainly in my own unfamiliarity with the JupyterHub setup.

Sharing RStudio Server projects with other users

I like to include a few words on the things I tried that did not pan out, in the hopes my experiences may help someone else save some time, or perhaps spur someone to explore a weak spot in my reasoning.

One of the first things I tried was to use RStudio Server’s project feature with other users. This ultimately failed.

Files and folders inside the RStudio project directory, .Rproj.user/, always end up with no group write permissions, which means the last user of the project effectively takes the project hostage.

This effectively blocks the most obvious route, i.e., to create different user accounts belonging to the same group, and run concurrent RStudio Server sessions in different browsers while logged in as a different user in each one. I found that this works, technically, but only up until you try to actually open a project, which always fails (except by the user that created the project).

One idea is to set the umask value in the system Rprofile to something more permissive, which I tried but I found it had no apparent effect on RStudio Server’s newly created project directories (the setting did seem to affect the R session, except it did not alter the permissions on the *.Rproj file). So, unfortunately, it seems the RStudio project feature is somehow setting its own more restrictive umask independently of the R session, effectively blocking this approach.

In short, I found no way to make RStudio projects work with more than one Linux user. Of course, abandoning the projects feature “solves” this issue, but that’s a trade-off I was not willing to make.

Sidenote: this could possibly, maybe, be solved by using ACL permissions. But that is a whole other can of worms, and I am far from convinced it is a viable approach. Haven’t tried it, though.

TeXLive

• https://www.tug.org/texlive/quickinstall.html
• https://wiki.archlinux.org/index.php/TeX_Live

R compilation from source

• https://rviews.rstudio.com/2018/03/21/multiple-versions-of-r/
• http://docs.rstudio.com/ide/server-pro/r-versions.html#recommended-installation-directories
• https://cran.r-project.org/doc/manuals/R-admin.html
• https://stackoverflow.com/questions/7541101/logic-of-installation-location-of-r-packages-under-linux

KVM setup

• https://linuxnewbieguide.org/how-to-setup-a-kvm-server-the-fast-way/
• https://www.ostechnix.com/setup-headless-virtualization-server-using-kvm-ubuntu/
• https://www.dedoimedo.com/computers/kvm-intro.html
• https://www.cyberciti.biz/faq/installing-kvm-on-ubuntu-16-04-lts-server/
• https://serverfault.com/questions/208693/difference-between-kvm-and-qemu
• http://rabexc.org/posts/how-to-get-started-with-libvirt-on
• http://www.jaredlog.com/?p=1484
• https://www.dedoimedo.com/computers/kvm-clone.html

KVM filesystem passthrough

• https://wiki.qemu.org/Documentation/9psetup
• http://www.linux-kvm.org/page/9p_virtio
• https://troglobit.github.io/2013/07/05/file-system-pass-through-in-kvm-slash-qemu-slash-libvirt/
• https://dustymabe.com/2012/09/11/share-a-folder-between-kvm-host-and-guest/
• https://pascalandreas.wordpress.com/2015/04/24/setting-up-kvm-shared-directory-in-ubuntu-14-04/
• https://serverfault.com/questions/342801/read-write-access-for-passthrough-9p-filesystems-with-libvirt-qemu
• https://askubuntu.com/questions/548208/sharing-folder-with-vm-through-libvirt-9p-permission-denied/567541

Network configuration, bridging, static DHCP, port forwarding

• https://www.linux-kvm.org/page/Networking#Public_Bridge
• https://www.dedoimedo.com/computers/kvm-bridged.html
• https://help.ubuntu.com/community/KVM/Networking
• https://www.cyberciti.biz/faq/debian-ubuntu-linux-kvm-guest-shared-physical-network/
• https://www.howtogeek.com/184310/ask-htg-should-i-be-setting-static-ip-addresses-on-my-router/
• https://wiki.dd-wrt.com/wiki/index.php/Static_DHCP
• https://superuser.com/questions/284051/what-is-port-forwarding-and-what-is-it-used-for
• https://www.lorextechnology.com/self-serve/port-forwarding-a-router/R-sc2900030
• https://help.ubnt.com/hc/en-us/articles/217367937-EdgeRouter-Port-Forwarding

Apache virtual hosts, proxies, etc.

• https://serverfault.com/questions/195611/how-do-i-redirect-subdomains-to-a-different-port-on-the-same-server/195831#195831
• https://serverfault.com/questions/370724/proxypass-apache-over-nonstandard-port-how-can-it-be-that-the-192-168-9999-w
• https://serverfault.com/questions/472482/proxypass-redirect-directory-url-to-non-standard-port
• https://stackoverflow.com/questions/21598787/retaining-protocol-and-port-number-from-reverse-proxy-request

Rstudio server configuration

• How to get your very own RStudio Server and Shiny Server with DigitalOcean, Dean Attali
• Going “Pro” with RStudio Server Open Source, Jeff Stafford, reddit thread

Rstudio server multiple sessions

• Run multiple instances of RStudio in a web browser, StackOverflow
• Multiple R Sessions in RStudio Server Pro, RStudio Support
• Unable to run multiple RStudio Server sessions at the same time, Batch Connect - OSC RStudio Server
• Parallel processes for Rstudio-server, much like Jupyter Notebooks, RStudio Community
• Multiple Rstudio server sessions from one user account, RStudio Support
• Sharing a Project with multiple users
• Troubleshooting Project Sharing in RStudio Server Pro
• Using RStudio projects AND Git with multiple users
• https://discuss.ropensci.org/t/peace-between-git-and-dropbox-with-git-worktree/289

R and Rstudio environment (package management, etc.)

• What are the main limits to R in a production environment?, RStudio Community
• RStudio server professional admin guide (PDF)