[Bioc-devel] EXTERNAL: BioC 3.6: timeouts on veracruz1 (OS X)

[Ramon Diaz-Uriarte]

Dear Martin,


On Fri, 13-October-2017, at 12:27:31, Martin Morgan <martin.morgan at roswellpark.org> wrote:
> On 10/12/2017 07:08 AM, Ramon Diaz-Uriarte wrote:
>> Dear All,
>>
>> I have noticed that on the latest build report, a package I maintain,
>> OncoSimulR
>> (http://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/veracruz1-buildsrc.html),
>
> I wonder if it is this issue
>
>    https://github.com/Bioconductor/BiocParallel/issues/67
>
> which would occur if your vignette has parallel code (using 'fork'
> processed via parallel::mclapply or indirectly via
> BiocParallel::MulticoreParam() / doParallel etc.)
>

Yes! I have both explicit calls to mclapply and implicit ones (functions
that call functions that call mclapply) in the vignette.

> If so then the best strategy is to wait for an upstream fix.
>

OK. Thank you.

Best,


R.

> Martin
>
>
>> has status timeout on veracruz1. Package building stalls during
>> creation of the vignette (that is not happening in the malbec1 ---linux---
>> build). I have noticed that this same pattern (timeout with build stopped when
>> creating the vignette in veracruz1 but not in malbec1) seems to affect
>> other packages
>> (http://bioconductor.org/checkResults/devel/bioc-LATEST/index.html#show=timeout).
>>
>> Is there anything we should do? Just looking at the log I do not know how
>> to proceed.
>>
>>
>> Thanks,
>>
>>
>> R.
>>
>>
>>
>> --
>> Ramon Diaz-Uriarte
>> Department of Biochemistry, Lab B-25
>> Facultad de Medicina
>> Universidad Autónoma de Madrid
>> Arzobispo Morcillo, 4
>> 28029 Madrid
>> Spain
>>
>> Phone: +34-91-497-2412
>>
>> Email: rdiaz02 at gmail.com
>>         ramon.diaz at iib.uam.es
>>
>> http://ligarto.org/rdiaz
>>
>> _______________________________________________
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>>
>
>
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--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdiaz02 at gmail.com
       ramon.diaz at iib.uam.es

http://ligarto.org/rdiaz