[Bioc-devel] WARNING on builders from rgl package

[Matteo Tiberti]

Hi Martin,

Thank you – we still have the same WARNING on nebbiolo2 as per my message:

* checking whether package ‘MoonlightR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.

The other build ERROR has been solved, as you mention.

Thank you very much again,

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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From: Martin Grigorov <martin.grigorov using gmail.com>
Date: Friday, 25 October 2024 at 13.10
To: Matteo Tiberti <tiberti using cancer.dk>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] WARNING on builders from rgl package
Hi Matteo,

I see your package failed on kunpeng2 (Linux ARM64) - https://bioconductor.org/checkResults/3.20/bioc-LATEST/MoonlightR/kunpeng2-buildsrc.html<https://bioconductor.org/checkResults/3.20/bioc-LATEST/MoonlightR/kunpeng2-buildsrc.html>
This issue has been fixed earlier today. It was reported by Oleksii here on the mailing list.
It should be OK in the next build (tomorrow).
Sorry for the inconvenience!

Martin

On Fri, Oct 25, 2024 at 12:12 PM Matteo Tiberti via Bioc-devel <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>> wrote:
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<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

[An image showing the Danish Cancer Society's name and logo called the bow in red font. Displayed in red]<https://www.cancer.dk/?utm_source=email&utm_medium=medarbejderemail&utm_campaign=medarbejderemail&utm_content=cancerdk>

www.cancer.dk<http://www.cancer.dk><https://www.cancer.dk/international/> | Our privacy policy<https://www.cancer.dk/om-os/privatlivspolitik/>

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