[Bioc-devel] Time-out error on Ubuntu 20.04 build

[Selles Vidal, Lara]

Dear all,

I have been seeing the same problem on all builds of ncRNAtools for a week now. I have run the exact same R CMD build command (R CMD build --keep-empty-dirs --no-resave-data) on an Ubuntu 20.04 environment, using the environment settings described here http://bioconductor.org/checkResults/devel/bioc-LATEST/Renviron.bioc .

After running R CMD build multiple times under such conditions, I have not been able to reproduce the error or even come close to a Timeout. I also have recently tried to make a new version bump to see if that would trigger a new behaviour, but I am still getting the same TIMEOUT.

Since the deadline for submissions to devel branch is coming soon, does anybody have any idea what could be possibly going on, or how I could possibly get more information about what’s causing the error?

Thanks a lot in advance!

Best wishes,

Lara

On 6 Oct 2020, at 19:11, Selles Vidal, Lara <lara.selles12 using imperial.ac.uk<mailto:lara.selles12 using imperial.ac.uk>> wrote:

Dear all,

I have recently pushed some changes to my ncRNAtools package to fix an error caused by a bug in the most recent version of OpenSSL which made requests to https addresses fail with default security settings. The changes have fixed all errors in my local Ubuntu 20.04 environment, and the package is now installing correctly in nebbiolo1. However, I am getting TIMEOUT at the build stage on nebbiolo1. It seems to be stuck at creating the vignette (http://bioconductor.org/checkResults/devel/bioc-LATEST/ncRNAtools/).

I have run successfully multiple times R CMD install, build and check in my local Ubuntu 20.04, and cannot reproduce the error. Does anyone have any idea what I could possibly do to troubleshoot the error? I have seen the TIMEOUT occur in at least two consecutive build reports, so I do not think it is something spurious.

Thanks a lot in advance!

Best wishes,

Lara


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