Web: (GitHub, IDE trouble-shooting, Latest builds, Posit signed builds)

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


----------------------------- /usr/local/software/spack/spack-modules/icelake-20211027/linux-centos8-icelake -----------------------------

------------------------------------------------- /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

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,

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

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.

10/5/2024 Update

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
9/5/2024 Update

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

2/5/2024 Update

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

4/3/2024 Update

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

22/3/2023 Update

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.

31/12/2022 Update

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/] Failed to connect to the bus: Could not parse server address: Unknown address type (examples of valid types are "tcp" and on UNIX "unix")
27/11/2022 Update

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
# 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.

26/3/2022 Update

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.


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": "",
  "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- | tar xfz -
./configure --prefix=${HPC_WORK}
make install

icu 70.1

module load gcc/6
wget -qO- | tar xfz -
cd icu/source
./configure --prefix=${HPC_WORK}
gmake install

The –enable-static option is also available.

electron 19.1.3


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- | tar xfz -
cd libuv-v1.43.0/
./configure --prefix=$HPC_WORK
make install


wget -qO- | tar xvfz -
cd yaml-cpp-yaml-cpp-0.7.0/
mkdir build
cd build
make install

Note that brotli, icu, libuv, yaml-cpp are now ceuadmin modules while nghttp2 is available from and chromium from

An attempt with qt is as follows,


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
cd rstudio
mkdir build
cd build
      -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 ..
  1. libstdc++

    A version which satisfies this can be furnished as follows,

    module load gcc-4.9.4-gcc-4.8.5-3sdjf2c
    strings  /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/gcc-4.9.4-3sdjf2ct5necl5qb26ymnu5ptekysdye/lib64/ | \
    grep GLIBCXX_3.4.20

    Information can be see from

    Fedora packages are available from and, e.g.,

    rpm2cpio libstdc++-11.3.1-2.fc34.x86_64.rpm | cpio -idnum
    strings /lib64/ | grep GLIBCXX

  2. qt/5


    The following are side notes on installation of Qt5 according to, though no longer necessary for reasons above.

    git clone git://
    cd qt5
    git checkout 5.15
    perl init-repository
    export LLVM_INSTALL_DIR=${HPC_WORK}/llvm
    cd -
    mkdir qt_build
    cd qt_build
    ../qt5/configure -prefix /usr/local/Cluster-Apps/ceuadmin/qt/5.15.13 -developer-build -opensource -no-sql-mysql -sqlite \
                     -nomake examples -nomake tests -Wno-unused-function -Wno-pragmas -Wno-unused-result -Wno-attributes

    The Makefile thus generated records the information at its header.

    /rds/project/jmmh2/rds-jmmh2-public_databases/software/qt_build_5.15.13/qtbase/bin/qmake -o Makefile /rds/project/jmmh2/rds-jmmh2-public_databases/software/qt5/ -- -opensource -prefix /usr/local/Cluster-Apps/ceuadmin/qt/5.15.13 -developer-build -opensource -nomake examples -nomake tests -Wno-unused-function -Wno-pragmas -Wno-unused-result -Wno-attributes

    With error qglobal_p.h: No such file or directory (5.15.7), according to we get around with

    ln -sf /rds/project/jmmh2/rds-jmmh2-projects/olink_proteomics/scallop/qt5/qtbase/include/QtCore/5.15.7/QtCore/private /rds/user/jhz22/hpc-work/include/QtCore

    The installation directory is visible/specified in qtbase/bin/qt.conf, namely,


    It requires ninja, module load ninja;ninja --versions gives 1.10.0 while source py27/bin/activate;pip install ninja uses 1.11.1.

    It also calls NSPR, which is installed as follows,

    wget -qO- | \
    tar xfz -
    cd nspr-4.35/nspr
    configure --prefix=${HPC_WORK}
              --with-mozilla \
              --with-pthreads \
              $([ $(uname -m) = x86_64 ] && echo --enable-64bit) &&

  3. openssl

    This is with respect to a version under Debian though the Fedora distribution should be used,

    wget -qO- | tar xfz -
    cd rstudio-1.4.1106

    However it requires, which in turn requires specific installation to get away with No version informaiton for, with openssl.ld, according to, as follows

    OPENSSL_1.0.0 {


    wget -qO- | tar xfz -
    cd openssl-1.0.0s
    ./config --prefix=${HPC_WORK} shared -Wl,--version-script=${HPC_WORK}/openssl-1.0.0s/openssl.ld
    make install

    We can proceed after setting export QT_PLUGIN_PATH=/usr/lib64/qt5/plugins as above. It is certainly more desirable to do this only once, as follows,

    echo "export QT_PLUGIN_PATH=/usr/lib64/qt5/plugins" >> ~/.bashrc

    and invoke with source ~/.bashrc from current session or automatically from the next onwards.