Hi Hervé, Thanks a lot for your reply and clarification. It is reassuring to know that Ubuntu 18.04 is still the primary Linux target!
I am not running Ubuntu 20.04 on a Docker image, but I am running it on a virtual machine (VirtualBox) on RedHat 7. Do you think this could be a similar case as for the Docker image? Interestingly, my other package on Bioconductor rfaRm had the same issue related to SSL on Ubuntu 20.04. I was able to solve it by using the same workaround, and am now getting OK on R CMD install, build and check on nebbiolo1 (http://bioconductor.org/checkResults/devel/bioc-LATEST/rfaRm/ ). This seems to indicate that the same workaround has different effects depending on the URL being accessed possibly? Interestingly, the workaround has at least led to a TIMEOUT in the case of ncRNAtools, and not an ERROR, as was previously the case. The TIMEOUT seems to happen when creating the vignettes. Is it safe to assume then than knitting the vignette under the same environment should also get stuck at some endless/very long step? I will try to see if I can get access to a native Ubuntu 20.04 environment, to try knitting the vignette with different code chunks removed. Maybe we can figure out some additional extra setting to pass to config() for the specific URL that is leading to the TIMEOUT, that will provide a temporary workaround. Best wishes, Lara On 13 Oct 2020, at 22:49, Pages, Herve <hpa...@fredhutch.org<mailto:hpa...@fredhutch.org>> wrote: ******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* 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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
