[Bioc-devel] WARNING on builders from rgl package

[Matteo Tiberti]

Dear developers,

We have a couple of warnings from the builders from our MoonlightR and Moonlight2R packages, which we haven't had before:

Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See '/home/biocbuild/bbs-3.20-bioc/meat/Moonlight2R.Rcheck/00install.out' for details.

I've seen this on our local servers and it could be related to either missing OpenGL support and/or the fact that it is running on a headless server (not sure why it pops up on nebbiolo2 and not teran2 though). Since rgl.init is run upon package load, I don’t know if we can do anything at code level. A workaround might be to set the system variable RGL_USE_NULL to TRUE prior to building (as implied in the docs<https://rdrr.io/rforge/rgl/man/rgl.useNULL.html>). Any other suggestion?

I’ve also just noticed this other error on top, which seems to be hitting many packages on kungpeng2:

** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/home/biocbuild/R/R-4.4.1/site-library/BiocParallel/libs/BiocParallel.so':
  /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.15' not found (required by /home/biocbuild/R/R-4.4.1/site-library/BiocParallel/libs/BiocParallel.so)
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load

Thank your for your help

Kind regards,

Matteo Tiberti

Danish Cancer Institute
Strandboulevarden 49
DK-2100 Copenhagen
Telephone: +45 35 25 73 07
– a part of the Danish Cancer Society

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