X11 nebbiolo2

[jwokaty]

On nebbiolo2:

capabilities()["X11"] X11 FALSE X11() Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : unable to start device X11cairo In addition: Warning message: In X11() : unable to open connection to X11 display '' This causes the following error on the 3.20 report: https://bioconductor.org/checkResults/3.20/bioc-LATEST/adSplit/nebbiolo2-checksrc.html (there could be other packages affected). (edited)

May be resolved by recompiling R. Need to install the new R too.

[hpages]

More likely to be a problem with the Xvfb setup.

For example R/bin/Rscript -e 'png("fig2.png", type="Xlib")' works on nebiolo1, but not on nebbiolo2:

biocbuild@nebbiolo2:~/bbs-3.20-bioc$ R/bin/Rscript -e 'png("fig2.png", type="Xlib")'
Error in .External2(C_X11, paste0("png::", filename), g$width, g$height,  : 
  unable to start device PNG
Calls: png
In addition: Warning message:
In png("fig2.png", type = "Xlib") :
  unable to open connection to X11 display ''
Execution halted

Also service xvfb status reports some anomalies on nebbiolo2:

biocbuild@nebbiolo2:~$ service xvfb status
Warning: The unit file, source configuration file or drop-ins of xvfb.service changed on disk. Run 'systemctl daemon-reload' to reload units.
● xvfb.service - LSB: Loads X Virtual Frame Buffer
     Loaded: loaded (/etc/init.d/xvfb; generated)
     Active: active (exited) since Wed 2024-10-09 11:57:21 EDT; 3 weeks 1 day ago
       Docs: man:systemd-sysv-generator(8)
        CPU: 1min 54.415s

Warning: some journal files were not opened due to insufficient permissions.

compared to nebbiolo1:

biocbuild@nebbiolo1:~$ service xvfb status
● xvfb.service - LSB: Loads X Virtual Frame Buffer
     Loaded: loaded (/etc/init.d/xvfb; generated)
     Active: active (running) since Thu 2024-10-31 06:54:34 EDT; 8h ago
       Docs: man:systemd-sysv-generator(8)
    Process: 501840 ExecStart=/etc/init.d/xvfb start (code=exited, status=0/SUCCESS)
      Tasks: 1 (limit: 153968)
     Memory: 15.7M (peak: 26.2M swap: 6.3M swap peak: 10.4M)
        CPU: 11.239s
     CGroup: /system.slice/xvfb.service
             └─501845 /usr/bin/Xvfb :1 -screen 0 800x600x16

[jwokaty]

Ok, I'll try to set up xvfb again tomorrow when the builds aren't running.

[hpages]

Sounds good. Also it seems that the machine requires a restart. I recommend you do that first.

[jwokaty]

Restarting xvfb seemed to resolve the issue. Everything appeared set up correctly. Now R CMD check doesn't produce a warning for Moonlight2R and capabilities()["X11"] is TRUE.

[hpages]

Great. Don't forget to restart nebbiolo2 when you get a chance. Would be good to check the xvfb service again right after the reboot, just to make sure that the problem we had was not caused by the xvfb service not starting properly in the context of the boot sequence. Thanks!