RStudio

Web: https://posit.co/ (GitHub, IDE trouble-shooting, Latest builds, Posit signed builds)

Module rstudio/2024.04.2+764 now works with R 4.4.1 (from its standard location).

CSD3 modules

We first check its availability,

module avail rstudio

and we get

------------------------------------------------- /usr/local/Cluster-Config/modulefiles --------------------------------------------------
rstudio/0.99/rstudio-0.99    rstudio/1.3.1093             rstudio-server/2023.06.0-421
rstudio/1.1.383              rstudio-server/2021.09.0-351 rstudio-server/2023.09.1-494

and

----------------------------- /usr/local/software/spack/spack-modules/icelake-20211027/linux-centos8-icelake -----------------------------
rstudio/1.4.1717/gcc/intel-oneapi-mkl/dlvykrma

------------------------------------------------- /usr/local/Cluster-Config/modulefiles --------------------------------------------------
rstudio-server/2021.09.0-351  rstudio-server/2023.09.1-494  rstudio/1.1.383
rstudio-server/2023.06.0-421  rstudio/0.99/rstudio-0.99     rstudio/1.3.1093

on cclake and icelake, respectively. The two desktop modules do not work on icelake, and on cclake we could use

module load rstudio/1.1.383
rstudio

This module actually works quite well with ceuadmin/R/latest, to be able to render WebGL as required by R/plotly. Nevertheless, the module fails the following test,

suppressMessages(library(dplyr))
INF <- "/rds/project/jmmh2/rds-jmmh2-projects/olink_proteomics/scallop/INF"
d <- read.csv(file.path(INF,"work","INF1.merge.cis.vs.trans"),as.is=TRUE) %>%
     mutate(log10p=-log10p)
r <- qtl3dplotly(d,zmax=300)
r

in that it crashes on the last call trying to display r.

Moreover, rstudio/1.3.1093 cannot be loaded and a fix is available as ceuadmin/rstudio/1.3.1093 which is also able to work with ceuadmin/R/latest but not WebGL.

Module 2023.09.2-508/ is added which works with ceuadmin/R/4.4.0-icelake. We have module avail ceuadmin/rstudio

-------------------------------------------------- /usr/local/Cluster-Config/modulefiles --------------------------------------------------
ceuadmin/rstudio/1.3.1093              ceuadmin/rstudio/2023.09.2-508         ceuadmin/rstudio/2023.09.2-508-icelake

Module 2023.09.2-508-icelake/ works with ceuadmin/R/4.4.0-icelake which is a significant update from rstudio/1.1.383.

Module ceuadmin/rstudio/2024.04.0-735-icelake is now available, which can work with R/4.3.3 on CSD3.

Module ceuadmin/rstudio/2023.12.1+402 is now available, which can work with R/4.2.2 on CSD3.

Module ceuadmin/rstudio/2023.03.0+386 is now available; there is no need to load gcc/6 and ceuadmin/R/4.2.2. There is also rstudio-default.

module ceuadmin/rstudio/2022.12.0+353 is now available. Since there are issues with libstdc++.so¹, it loads gcc/6 and ceuadmin/R/4.2.2.

We now use a modified call. The original command is available as rstudio-default, with which we see error,

[102106:0323/213152.555182:ERROR:bus.cc(398)] Failed to connect to the bus: Could not parse server address: Unknown address type (examples of valid types are "tcp" and on UNIX "unix")

module load rstudio/1.3.1093 fails with error messages and a way forward is as follows,

# of primary importance
export QT_QPA_PLATFORM=xcb
export QT_PLUGIN_PATH=/usr/lib64/qt5/plugins
# effective by default
export QTDIR=/usr/lib64/qt-3.3
export QTINC=/usr/lib64/qt-3.3/include
export QTLIB=/usr/lib64/qt-3.3/lib
export QT_GRAPHICSSYSTEM_CHECKED=1
# gcc/6 is necessary here, since it is used to build R
# We also take advantage of R's TeX-awareness
module load gcc/6 texlive
rstudio --no-sandbox

A fix is provided which is available from module load ceuadmin/rstudio/1.3.1093.

The 2022.07.2+576 release is packaged and can be loaded with module load ceuadmin/rstudio/2022.07.2+576; rstudio.

module load rstudio/1.3.1093 now functions well, which enables R packages such as `R/heatmaply`.

However, in November 2022 this fails with messages:

qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb.

Aborted

Additional information could also be seen from export QT_DEBUG_PLUGINS=1 and run rstudio again.

The error messages above can be bypassed with²

export QT_PLUGIN_PATH=/usr/lib64/qt5/plugins
module load rstudio/1.3.1093

and also see below³. Another environmental variable is QT_QPA_PLATFORM_PLUGIN_PATH, which should point to the plugins/platforms directory when a particular QT module is loaded.

Building from source (incomplete)

Version 2022.12.0+353 dependencies from rstudio --version-json are as follows,

{
  "node": "16.14.2",
  "v8": "10.2.154.15-electron.0",
  "uv": "1.43.0",
  "zlib": "1.2.11",
  "brotli": "1.0.9",
  "ares": "1.18.1",
  "modules": "106",
  "nghttp2": "1.45.1",
  "napi": "8",
  "llhttp": "6.0.4",
  "openssl": "1.1.1",
  "cldr": "40.0",
  "icu": "70.1",
  "tz": "2021a3",
  "unicode": "14.0",
  "electron": "19.1.3",
  "chrome": "102.0.5005.167",
  "rstudio": "2022.12.0+353"
}

brotli 1.0.9

wget -qO- https://github.com/google/brotli/archive/v1.0.9/brotli-1.0.9.tar.gz | tar xfz -
bootstrap
./configure --prefix=${HPC_WORK}
make
make install

icu 70.1

module load gcc/6
wget -qO- https://github.com/unicode-org/icu/releases/download/release-70-1/icu4c-70_1-src.tgz | tar xfz -
cd icu/source
./configure --prefix=${HPC_WORK}
gmake
gmake install

The –enable-static option is also available.

electron 19.1.3

Web: https://releases.electronjs.org/release/v19.1.3

npm install electron@v19.1.3

Note that a symbolic node_modules will be replaced with a physical node_modules/.

libuv 1.43.0

wget -qO- https://dist.libuv.org/dist/v1.43.0/libuv-v1.43.0.tar.gz | tar xfz -
cd libuv-v1.43.0/
autogen.sh
./configure --prefix=$HPC_WORK
make
make install

yaml-cpp

wget -qO- https://github.com/jbeder/yaml-cpp/archive/refs/tags/yaml-cpp-0.7.0.tar.gz | tar xvfz -
cd yaml-cpp-yaml-cpp-0.7.0/
mkdir build
cd build
make
cmake .. -DCMAKE_INSTALL_PREFIX=$HPC_WORK -DBUILD_SHARED_LIBS=On
make
make install

Note that brotli, icu, libuv, yaml-cpp are now ceuadmin modules while nghttp2 is available from https://src.fedoraproject.org/repo/pkgs/nghttp2/nghttp2-1.45.1.tar.xz/ and chromium from https://chromium.googlesource.com/chromium/src.git/+/refs/tags/102.0.5005.167

An attempt with qt is as follows,

# https://gitlab.freedesktop.org/glvnd/libglvnd/-/tags

module load gcc/6 ceuadmin/gmp/6.2.1 qt-5.9.1-gcc-5.4.0-3qinlch cmake-3.19.7-gcc-5.4-5gbsejo

git clone https://github.com/rstudio/rstudio
cd rstudio
mkdir build
cd build
cmake .. -DRSTUDIO_TARGET=Electron -DRSTUDIO_PACKAGE_BUILD=1 -DCMAKE_INSTALL_PREFIX=$HPC_WORK
cmake -DRSTUDIO_TARGET=Desktop -DRSTUDIO_PACKAGE_BUILD=1 -DCMAKE_INSTALL_PREFIX=$HPC_WORK \
      -DQT_QMAKE_EXECUTABLE=/usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/qt-5.9.1-3qinlchrl6vimsn3suwivchqme5do36l/bin ..