Hi Lara, Thanks for trying hard to address this problem. I can reproduce the error by running 'R CMD build ncRNAtools' interactively on nebbiolo1. Yes it seems that the timeout is related to the SSL issue on Ubuntu 20.04. Are you running Ubuntu 20.04 on a Docker image? I've read somewhere recently that some HTTPS/HTTP access issues on Ubuntu 20.04 are not always reproducible on a Docker image.
I see in the 'git log' that yesterday you've reverted back your recent changes and that you are now using HTTPS again together with the following workaround: https://github.com/Ensembl/ensembl-rest/issues/427#issuecomment-702044967 Unfortunately it didn't seem to work (we still see the TIMEOUT on today's report). Thanks for trying this anyway. At this point I don't have a good suggestion, unfortunately. Note that malbec1 (Ubuntu 18.04) is still our primary Linux builder and propagation is still decided on whether or not a package passes BUILD and CHECK there. So the TIMEOUT on nebbiolo1 won't have any practical consequences as far as the next release is concerned. At some point, we really want to make Ubuntu 20.04 our primary Linux target, and get rid of the Ubuntu 18.04 builder. But we won't do this before we have a good solution for the current SSL issue on Ubuntu 20.04. Best, H. On 10/13/20 09:07, Selles Vidal, Lara wrote: > 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 > https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_Renviron.bioc&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=nE6T7FcXLo61NvG8iDhxBeraWyR9mF-daYXZpIwXCkg&s=H9gZj9GQAFFoNmEPlMZCNJSvvxeErCwbVbXJw1bxOxQ&e= > . > > 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.selle...@imperial.ac.uk<mailto:lara.selle...@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 > (https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ncRNAtools_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=nE6T7FcXLo61NvG8iDhxBeraWyR9mF-daYXZpIwXCkg&s=0ntfLi4_hO8Npg0WeCl_20F9KefutInFzvShPjGv6Hs&e= > ). > > 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 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=nE6T7FcXLo61NvG8iDhxBeraWyR9mF-daYXZpIwXCkg&s=_dUDRCIGHEpFPIHLxeFUUn8xWAZE6v4Ku4BIT8VL9kw&e= > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
