Script starting...
Mon Jul  3 18:42:07 CEST 2023: Waiting for port '22123' to open...
++ date
+ echo 'TIMING - Starting main script at: Mon Jul  3 18:42:07 CEST 2023'
TIMING - Starting main script at: Mon Jul  3 18:42:07 CEST 2023
+ module load tools/Apptainer/1.1.9-GCCcore-12.2.0
+ local __lmod_my_status
+ local __lmod_sh_dbg
+ '[' -z '' ']'
+ case "$-" in
+ __lmod_sh_dbg=x
+ '[' -n x ']'
+ set +x
Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for Lmod's output
Shell debugging restarted
+ return 0
+ RSTUDIO_SERVER_IMAGE=/home/<username>/testing/apptainer/build/4.2.0-RStudio_Server_2022.02.2.485-SIF.sif
+ echo ''

+ echo 'The Following SIF Image Is Selected:'
The Following SIF Image Is Selected:
+ echo /home/<username>/testing/apptainer/build/4.2.0-RStudio_Server_2022.02.2.485-SIF.sif
/home/<username>/testing/apptainer/build/4.2.0-RStudio_Server_2022.02.2.485-SIF.sif
+ echo ''

+ echo ''

+ echo 'Creating Config file'
Creating Config file
+ echo ''

+ cat
+ echo ''

+ echo 'Config file created...'
Config file created...
+ echo ''

+ echo ''

+ echo 'Creating Session Config file'
Creating Session Config file
+ echo ''

+ cat
+ echo ''

+ echo 'Session Config file created'
Session Config file created
+ echo ''

+ cat
++ pwd
+ singularity -v exec --unsquash --bind=/tmp,/home/<username>/ondemand/data/sys/dashboard/batch_connect/dev/bc_mod_rstudio/output/504faa90-15df-4d89-b45b-8225b7aa8d8c /home/<username>/testing/apptainer/build/4.2.0-RStudio_Server_2022.02.2.485-SIF.sif bash ./genenv.sh
VERBOSE: Unprivileged installation: using user namespace
VERBOSE: Setting HOME=/home/<username>
VERBOSE: Setting PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
INFO:    Converting SIF file to temporary sandbox...
VERBOSE: Set messagelevel to: 4
VERBOSE: Starter initialization
VERBOSE: Check if we are running as setuid
VERBOSE: Spawn stage 1
VERBOSE: Execute stage 1
VERBOSE: stage 1 exited with status 0
VERBOSE: Create user namespace
VERBOSE: Create user namespace
VERBOSE: Spawn master process
VERBOSE: Create mount namespace
VERBOSE: Entering in mount namespace
VERBOSE: Create mount namespace
VERBOSE: Spawn RPC server
VERBOSE: Execute master process
VERBOSE: Serve RPC requests
VERBOSE: Default mount: /proc:/proc
VERBOSE: Default mount: /sys:/sys
VERBOSE: Default mount: /dev:/dev
VERBOSE: Found 'bind path' = /etc/localtime, /etc/localtime
VERBOSE: Found 'bind path' = /etc/hosts, /etc/hosts
VERBOSE: Default mount: /tmp:/tmp
VERBOSE: Default mount: /var/tmp:/var/tmp
VERBOSE: Default mount: /etc/resolv.conf:/etc/resolv.conf
VERBOSE: Checking for template passwd file: /apps/easybuild/core/software/Apptainer/1.1.9-GCCcore-12.2.0/var/apptainer/mnt/session/rootfs/etc/passwd
VERBOSE: Creating passwd content
VERBOSE: Creating template passwd file and appending user data: /apps/easybuild/core/software/Apptainer/1.1.9-GCCcore-12.2.0/var/apptainer/mnt/session/rootfs/etc/passwd
VERBOSE: Default mount: /etc/passwd:/etc/passwd
VERBOSE: Checking for template group file: /apps/easybuild/core/software/Apptainer/1.1.9-GCCcore-12.2.0/var/apptainer/mnt/session/rootfs/etc/group
VERBOSE: Creating group content
VERBOSE: Default mount: /etc/group:/etc/group
VERBOSE: /home/<username>/ondemand/data/sys/dashboard/batch_connect/dev/bc_mod_rstudio/output/504faa90-15df-4d89-b45b-8225b7aa8d8c found within container
VERBOSE: rpc server exited with status 0
VERBOSE: Execute stage 2
VERBOSE: Removing image tempDir /tmp/<username>-tmpdir-3UIDgM/rootfs-2077456302
INFO:    Cleaning up image...
++ cat ./Renviron.path
+ renv_path=/opt/R/4.2.0/lib/R/etc/Renviron
+ mkdir -p /tmp/<username>-tmpdir-3UIDgM/rstudio-server/var/lib
+ mkdir -p /tmp/<username>-tmpdir-3UIDgM/rstudio-server/var/run
+ uuidgen
+ chmod 600 /tmp/<username>-tmpdir-3UIDgM/rstudio-server/secure-cookie-key
+ BPath=/tmp
+ BPath+=,/tmp/<username>-tmpdir-3UIDgM/rstudio-server/var/lib:/var/lib/rstudio-server
+ BPath+=,/tmp/<username>-tmpdir-3UIDgM/rstudio-server/var/run:/var/run/rstudio-server
+ BPath+=,logging.conf:/etc/rstudio/logging.conf
+ BPath+=,rsession.conf:/etc/rstudio/rsession.conf
+ BPath+=,rserver.conf:/etc/rstudio/rserver.conf
+ BPath+=,Renviron.site:/opt/R/4.2.0/lib/R/etc/Renviron
+ BPath+=,sessions:/home/<username>/.local/share/rstudio/sessions
++ date
+ echo 'TIMING - Starting RStudio Server at: Mon Jul  3 18:42:19 CEST 2023'
TIMING - Starting RStudio Server at: Mon Jul  3 18:42:19 CEST 2023
+ '[' -n '' ']'
+ singularity -v exec --unsquash --bind=/tmp,/tmp/<username>-tmpdir-3UIDgM/rstudio-server/var/lib:/var/lib/rstudio-server,/tmp/<username>-tmpdir-3UIDgM/rstudio-server/var/run:/var/run/rstudio-server,logging.conf:/etc/rstudio/logging.conf,rsession.conf:/etc/rstudio/rsession.conf,rserver.conf:/etc/rstudio/rserver.conf,Renviron.site:/opt/R/4.2.0/lib/R/etc/Renviron,sessions:/home/<username>/.local/share/rstudio/sessions /home/<username>/testing/apptainer/build/4.2.0-RStudio_Server_2022.02.2.485-SIF.sif rserver
VERBOSE: Unprivileged installation: using user namespace
VERBOSE: Setting HOME=/home/<username>
VERBOSE: Setting PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
INFO:    Converting SIF file to temporary sandbox...
VERBOSE: Set messagelevel to: 4
VERBOSE: Starter initialization
VERBOSE: Check if we are running as setuid
VERBOSE: Spawn stage 1
VERBOSE: Execute stage 1
VERBOSE: stage 1 exited with status 0
VERBOSE: Create user namespace
VERBOSE: Create user namespace
VERBOSE: Spawn master process
VERBOSE: Create mount namespace
VERBOSE: Entering in mount namespace
VERBOSE: Create mount namespace
VERBOSE: Spawn RPC server
VERBOSE: Execute master process
VERBOSE: Serve RPC requests
VERBOSE: Default mount: /proc:/proc
VERBOSE: Default mount: /sys:/sys
VERBOSE: Default mount: /dev:/dev
VERBOSE: Found 'bind path' = /etc/localtime, /etc/localtime
VERBOSE: Found 'bind path' = /etc/hosts, /etc/hosts
VERBOSE: Default mount: /tmp:/tmp
VERBOSE: Default mount: /var/tmp:/var/tmp
VERBOSE: Default mount: /etc/resolv.conf:/etc/resolv.conf
INFO:    underlay of /etc/rstudio/logging.conf required more than 50 (153) bind mounts
VERBOSE: Checking for template passwd file: /apps/easybuild/core/software/Apptainer/1.1.9-GCCcore-12.2.0/var/apptainer/mnt/session/rootfs/etc/passwd
VERBOSE: Creating passwd content
VERBOSE: Creating template passwd file and appending user data: /apps/easybuild/core/software/Apptainer/1.1.9-GCCcore-12.2.0/var/apptainer/mnt/session/rootfs/etc/passwd
VERBOSE: Default mount: /etc/passwd:/etc/passwd
VERBOSE: Checking for template group file: /apps/easybuild/core/software/Apptainer/1.1.9-GCCcore-12.2.0/var/apptainer/mnt/session/rootfs/etc/group
VERBOSE: Creating group content
VERBOSE: Default mount: /etc/group:/etc/group
VERBOSE: /home/<username>/ondemand/data/sys/dashboard/batch_connect/dev/bc_mod_rstudio/output/504faa90-15df-4d89-b45b-8225b7aa8d8c found within container
VERBOSE: rpc server exited with status 0
VERBOSE: Execute stage 2
Mon Jul  3 18:42:25 CEST 2023: Discovered process listening on port '22123'!
Generating connection YAML file...