[R-pkg-devel] new package submission: "check log incomplete, web timeout?"

Uwe Ligges ligges at statistik.tu-dortmund.de
Mon Apr 24 20:56:20 CEST 2017

I ahven't looked at you package, but can you please verify:

1. If you open some (socket) cluster, make sure you close it afterwards!
This is a very frequent source of problems.

2. Do not use more than 2 cores by default.

3. retry whether you pass the winbuilder checks, it could have been a 
random error.  How long does processing your vignettes take?

Uwe Ligges

On 24.04.2017 05:43, Jeremy Volkening wrote:
> Henrik,
>> A completely different alternative, is to have a way to disable
>> parallel processing in your examples / tests / vignettes, e.g. if (np
>> == 1) registerDoSEQ() else registerDoParallel(np).  Personally, I'm
>> not a big fan of that approach because it's an ad-hoc workaround and
>> you're end up not testing all of your package.
> Supporting parallel processing has already caused me untold headaches as
> a not-overly-fluent R user (including over an hour on Friday try to
> figure out why my Windows tests were hanging indefinitely -- had to add
> "Sys.unsetenv("R_TESTS") to the top of my test script which I still
> don't understand). However, I would consider it an important feature of
> the package where actual usage typically involves modeling data from
> thousands of proteins, each of which can be bootstrapped up to 20
> times.  For this reason, I also don't like the idea of "testing around"
> the issue. While I don't use Windows myself, it doesn't make sense to
> claim my package runs on Windows if it is going to randomly freeze up
> for users on that platform.
> I will ask Uwe Ligges to re-check my submission as you suggested. I
> would really like to get this past the pre-check stage so I can start
> dealing with the issues that I'm sure will come up in the human review.
> Regards,
> Jeremy
>> Hope this helps
>> Henrik
>> On Sun, Apr 23, 2017 at 9:17 AM, Jeremy Volkening <jdv at base2bio.com>
>> wrote:
>>> On Sun, Apr 23, 2017 at 10:17:01AM +0200, Alexandre Courtiol wrote:
>>>> Could it be that one your computer you can build vignettes quickly
>>>> thanks
>>>> to some caching of the knitr chunk output but that it takes too much
>>>> time
>>>> building that without the cache...? ... CRAN does not like when
>>>> anything takes more than a few seconds...
>>> Thanks for the reply. The vignettes do take a little time to build,
>>> as the
>>> knitr code is doing some modeling, but I wouldn't have thought it
>>> excessive.
>>> According to the logs from the win-builder service, it took 28s
>>> (about the
>>> same as each of the i386 and x64 tests). Is this too long for the CRAN
>>> submission service? I've already pruned down my example data to just a
>>> couple of samples instead of the thousands normally modeled in a
>>> session.
>>> If this is indeed the issue, do I need to remove the knitr code and just
>>> include static images of the output plots in the vignette? This would
>>> seem
>>> to go against most of the recommendations I have read from various
>>> sources
>>> on best practice.
>>> Regards,
>>> Jeremy
>>>> On 23 April 2017 at 05:08, Jeremy Volkening <jdv at base2bio.com> wrote:
>>>>> Hello,
>>>>> I am trying to submit a package to CRAN for the first time. I have
>>>>> gone
>>>>> through testing on my own machines (Linux, Windows x64, Windows
>>>>> i386), on
>>>>> Travis CI and using win-builder. All tests are now passing on all of
>>>>> these
>>>>> platforms. However, when I try to submit the package to CRAN I get an
>>>>> email
>>>>> that the pre-test has failed, with the following line:
>>>>> Status: NA (check log incomplete, web timeout?)
>>>>> The pre-test link is here: https://win-builder.r-project.
>>>>> org/incoming_pretest/170423_044521_mstherm_047/
>>>>> If I check the '00check.log' file I can see that it ends with the
>>>>> line "*
>>>>> checking re-building of vignette outputs ...", so apparently the
>>>>> test is
>>>>> quitting before it finishes this step. I'm not sure how to proceed,
>>>>> since
>>>>> everything is working for all of my own manual tests (as well as
>>>>> win-builder). See the log for my manual submission of exactly the same
>>>>> package to win-builder, which passes:
>>>>> https://win-builder.r-project.org/4tvH1D2TdMep/
>>>>> Any help would be greatly appreciated. The package itself can be found
>>>>> here:
>>>>> https://github.com/jvolkening/r-mstherm
>>>>> Regards,
>>>>> Jeremy
>>>>> ______________________________________________
>>>>> R-package-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>> --
>>>> Alexandre Courtiol
>>>> http://sites.google.com/site/alexandrecourtiol/home
>>>> *"Science is the belief in the ignorance of experts"*, R. Feynman
>>> --
>>> Nothing so needs reforming as other people's habits.
>>>                 -- Mark Twain, "Pudd'nhead Wilson's Calendar"
>>> ______________________________________________
>>> R-package-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel

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