[Bioc-devel] WARNING from Rgl package

[Matteo Tiberti]

Hi again,

I see, doesn't

HTTP 404 Not Found.

Suggest a problem in downloading a file? Also looking a the vignette, the error happens with a function that does download a file.

It's a bit weird that it fails in the same way everywhere for 3.20, but not for 3.21, since the function didn't change in between. I suspect it's still a problem of a file not always being available for download, even though I'm not sure how we could make this more reliable

Best,


________________________________
From: Martin Grigorov <martin.grigorov using gmail.com>
Sent: 09 April 2025 09:52
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 from Rgl package

Hi Matteo,

On Wed, Apr 9, 2025 at 10:25 AM Matteo Tiberti <tiberti using cancer.dk<mailto:tiberti using cancer.dk>> wrote:
Hi Martin,

just to confirm that the new builds are in and the warning gone.

Glad to hear that!


We still have yet another issue with downloading a file, but that is again I guess momentary (also because it's only on one of the builds)

Do you mean https://bioconductor.org/checkResults/3.21/bioc-LATEST/Moonlight2R/lconway-buildsrc.html<https://bioconductor.org/checkResults/3.21/bioc-LATEST/Moonlight2R/lconway-buildsrc.html> ?
The error is not very clear to me. Nothing tells me that a download failed.
The same error happens for all 3.20 builds - https://bioconductor.org/checkResults/3.20/bioc-LATEST/Moonlight2R/kjohnson1-buildsrc.html<https://bioconductor.org/checkResults/3.20/bioc-LATEST/Moonlight2R/kjohnson1-buildsrc.html>
 machine is maintained by the Bioconductor core team.
I maintain the Linux ARM64 machines (kunpeng2 (3.21) and taishan (3.20)).


thank you again and kind regards,


Matteo Tiberti

Danish Cancer Society Research Center
Strandboulevarden 49
DK-2100 Copenhagen
Telephone: +45 35 25 73 07


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________________________________
From: Martin Grigorov <martin.grigorov using gmail.com<mailto:martin.grigorov using gmail.com>>
Sent: 07 April 2025 09:25
To: Matteo Tiberti <tiberti using cancer.dk<mailto:tiberti using cancer.dk>>
Cc: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: [Bioc-devel] WARNING from Rgl package

Hi Matteo,

The problem has been fixed and the next build should be fine!

biocbuild using kunpeng2 ~/git> R CMD INSTALL Moonlight2R
* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘Moonlight2R’ ...
** this is package ‘Moonlight2R’ version ‘1.5.4’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Moonlight2R)

On Fri, Apr 4, 2025 at 3:31 PM Martin Grigorov <mgrigorov using apache.org<mailto:mgrigorov using apache.org>> wrote:
Hi,

On Fri, 4 Apr 2025 at 14:00, Matteo Tiberti via Bioc-devel <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>> wrote:
Dear all,

We are seeing the same warning from the builders for our MoonlightR and Moonlight2R packages, on kungpeng2 only:

* checking whether package ‘Moonlight2R’ can be installed ... WARNING
Found the following significant warnings:
  Warning: 'rgl.init' failed, will use the null device.
  Warning: no DISPLAY variable so Tk is not available
See ‘/home/biocbuild/bbs-3.21-bioc/meat/Moonlight2R.Rcheck/00install.out’ for details.


I’ll investigate this next week.


I assume this should be a problem with the builders, since it's triggered when the Rgl package is loaded there isn't very much we can do about it. Could you please let me know if this is the case, or is there anything we can do to fix it?

I also see Moonlight2R also raises an error in the last build cycle - that is because it couldn't download a file from the internet. I assume this is a temporary problem that would be fixed at the next build.


I guess so too.



Thank you and kind regards

Matteo Tiberti


Danish Cancer Society Research Center
Strandboulevarden 49
DK-2100 Copenhagen
Telephone: +45 35 25 73 07


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