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

[Selles Vidal, Lara]

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 <hpages using fredhutch.org<mailto:hpages using fredhutch.org>> wrote:


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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.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 (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


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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: hpages using fredhutch.org
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