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

[Pages, Herve]

On 10/13/20 15:18, Selles Vidal, Lara wrote:
> 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?

Probably.

> Interestingly, my other package on Bioconductor rfaRm had the same issue 
> related to SSL on Ubuntu 20.04.

Yep, I know ;-)

> 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/ 
> 
>  
> ).

Glad it worked. Even though Ubuntu 20.04 is not our primary target, many 
users are probably going to use your package on Ubuntu 20.04 so it's 
worth trying to address this issue.

> 
> This seems to indicate that the same workaround has different effects 
> depending on the URL being accessed possibly?

Apparently. I didn't try Mike Smith's suggested workaround myself so I 
don't know for sure. Based on what you are reporting, we know that it 
works for some of the websites affected by the SSL certificate issue but 
not for all of them. Always good to know even though I have no idea why 
that would be.

> 
> 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.

Thanks for investigating. FWIW, here is what I get on nebbiolo1 (our 
Ubuntu 20.04 builder):

   $ cd ncRNAtools/vignettes

   $ R CMD Stangle ncRNAtools.Rmd
   Output file:  ncRNAtools.R

   $ R

   R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
   Copyright (C) 2020 The R Foundation for Statistical Computing
   Platform: x86_64-pc-linux-gnu (64-bit)

   R is free software and comes with ABSOLUTELY NO WARRANTY.
   You are welcome to redistribute it under certain conditions.
   Type 'license()' or 'licence()' for distribution details.

 Natural language support but running in an English locale

   R is a collaborative project with many contributors.
   Type 'contributors()' for more information and
   'citation()' on how to cite R or R packages in publications.

   Type 'demo()' for some demos, 'help()' for on-line help, or
   'help.start()' for an HTML browser interface to help.
   Type 'q()' to quit R.

   > source("ncRNAtools.R", echo=TRUE)

   > ## setup, 
echo=FALSE
   > knitr::opts_chunk$set(message=FALSE, fig.path='figures/')

   > ## tidy = TRUE, eval = 
FALSE
   > ## if (!requireNamespace("BiocManager", quietly = TRUE))
   > ##  [TRUNCATED]

   > library(GenomicRanges)

   ...

   > ## tidy = 
TRUE--
   > tRNAfragment <- "UGCGAGAGGCACAGGGUUCGAUUCCCUGCAUCUCCA"

   > centroidFoldPrediction <- predictSecondaryStructure(tRNAfragment, 
"centroidFold")
   Secondary structure prediction is running, please wait.
   Secondary structure prediction is running, please wait.
   Secondary structure prediction is running, please wait.
   Secondary structure prediction is running, please wait.
   Secondary structure prediction is running, please wait.
   Secondary structure prediction is running, please wait.
   ...
   etc.. (seems like the while loop in predictSecondaryStructure
   never ends)

Doesn't look like this has anything to do with the code being executed 
inside a knitting context.

Hope this helps.

Cheers,
H.

> 
> Best wishes,
> 
> Lara
> 
> 
> 
>> On 13 Oct 2020, at 22:49, Pages, Herve > > 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 
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>> 

Re: [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 
mailto:hpa...@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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=nE6T7FcXLo61NvG8iDhxBeraWyR9mF-daYXZpIwXCkg=H9gZj9GQAFFoNmEPlMZCNJSvvxeErCwbVbXJw1bxOxQ=
  .

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 
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 

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

[Pages, Herve]

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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=nE6T7FcXLo61NvG8iDhxBeraWyR9mF-daYXZpIwXCkg=H9gZj9GQAFFoNmEPlMZCNJSvvxeErCwbVbXJw1bxOxQ=
>   .
> 
> 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 
> 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_=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=nE6T7FcXLo61NvG8iDhxBeraWyR9mF-daYXZpIwXCkg=0ntfLi4_hO8Npg0WeCl_20F9KefutInFzvShPjGv6Hs=
>  ).
> 
> 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]]
> 
> ___
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> 

-- 
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
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[Bioc-devel] Bioconductor Release Announcement: RELEASE_3_11 branch frozen

[Turaga, Nitesh]

Dear Maintainers,

Following up on my last email, the RELEASE_3_11 branch has now been frozen on 
the Bioconductor git repository. You will no longer be able to make any changes 
on the RELEASE_3_11 branch of your package.

Please keep in mind that we are on schedule for our release as given in 
http://bioconductor.org/developers/release-schedule/.

Best regards,

Nitesh


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[Bioc-devel] Bioconductor Release Announcement: RELEASE_3_11 branch freeze

[Turaga, Nitesh]

Dear Maintainers,

Please keep in mind that we are on schedule for our release as given in 
http://bioconductor.org/developers/release-schedule/.

Today (Oct 13th 2020) at 1:30pm EDT, I will freeze the commits to the 
RELEASE_3_11 branch in Bioconductor. So, commits should be made for any bug 
fixes before that, so this is your last chance to fix the RELEASE_3_11 branch 
of your package (software, data-experiment and workflow).

After 1:30pm today, you will not be able to push to the RELEASE_3_11 branch.

Best regards,

Nitesh Turaga



This email message may contain legally privileged and/or confidential 
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agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
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Re: [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 
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 
(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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Re: [Bioc-devel] Package sitePath check error is bound to an upper dependency package

[Kern, Lori]

Thank you for letting us know.  We appreciate your contributions to the project 
and your continued maintenance of your package.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Chengyang.Ji12 

Sent: Sunday, October 11, 2020 12:30 AM
To: Bioc-devel@r-project.org 
Subject: [Bioc-devel] Package sitePath check error is bound to an upper 
dependency package

Hi,

I�ve noticed the recent build error of my package sitePath on all three 
platforms on the devel branch and was able to figure out what might be causing 
it. Turns out it could  be due to a recent update of the ggtree package. I am 
current trying to contact the author to see if bug can be fixed, if any. Can�t 
do too much on my end now but an alternative will be prepared as a workaround.

I�m aware the check passing deadline is near. Need some time to fix it.

Regards,
Chengyang

Sent from 
Mail
 for Windows 10


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Re: [Bioc-devel] Question for scheduled release

[Kern, Lori]

The officially release will not be until October 28th.  Today,  commmits to 
release/ RELEASE_3_11 (1.4.0) will be frozen and there will be no more commits 
allowed to this branch every.  You can still commit the the master/devel branch 
(1.5.0) .   For version x.y.z ,  if you push to the devel you should still only 
introduce a version bump to the z ... (1.5.1,  1.5.2, ...) ,  The Bioconductor 
core team will handle the version bump to 1.6.0  on the actual release day 
later this month -  Users do not make this version bump.  This is why we always 
recommend pulling down with a git pull upstream​ before making changes locally 
to pick up changes from the core team (like the release version bump)

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Yang,Peng 

Sent: Friday, October 9, 2020 10:11 PM
To: bioc-devel 
Subject: [Bioc-devel] Question for scheduled release

Dear Bioconductor team,

I am the maintainer for DeMixT package (1.5.0 in devel, 1.4.0 in release 
currently). Here I have a question for release schedule.
I notice the scheduled new devel Bioc 3.13 is Oct 13th, does that mean if I 
want to push a new version 1.7.0 on devel, I need to wait for the building of 
Bioc 3.13 (Oct 13th)?
If I push the new version successfully then, the corresponding release version 
1.6.0 will be released automatically on Oct 26th?

Thanks for all the help,
Peng

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