[Bioc-devel] TIMEOUT error in building vignette in package scruff

[Pages, Herve]

I can confirm that downgrading Rsubread to an older version eliminates 
the slowdown. Here are the timings I get on my laptop (Ubuntu 16.04.6 
LTS) for 'R CMD build scruff' with different versions of Rsubread (all 
these timings use the same R-devel version and the latest master branch 
of scruff):

              Rsubread           |
   commit       date     version | time R CMD build scruff
   ------------------------------+------------------------
   3eb25843  Jan  7 2020   2.1.1 |   49 min 20 sec
   6438d4a9  Dec 17 2019   2.1.1 | > 10 min (*)
   3f716691  Dec 16 2019   2.1.1 | > 10 min (*)
   b3602eb6  Dec 10 2019   2.1.1 | > 10 min (*)
   ef5e4c21  Dec  9 2019   2.1.1 |   45 min 33 sec
   d0b1acfb  Oct 29 2019   2.1.0 |    3 min 47 sec
   ------------------------------+------------------------
             (*) command was interrupted before completion

So the culprit seems to be commit ef5e4c21d:

   hpages using spectre:~/Rsubread$ git log ef5e4c21d -n 1
   commit ef5e4c21d5a6d633aec0b2922dd9f230fed23463
   Author: Yang Liao <dbpzdbpz using gmail.com>
   Date:   Mon Dec 9 13:42:08 2019 +1100

       Updated Ambient-RNA detection algorithm

Hope this helps,
H.


On 1/8/20 10:30, Pages, Herve wrote:
> Hi Zhe,
> 
> The code in the vignette seems to rely a lot on the Rsubread package to
> perform some very computationally intensive operations. Could it be that
> some recent changes to the Rsubread package are somehow related to the
> sudden slowdown of these operations? That's something I suggest you
> investigate.
> 
> Cheers,
> H.
> 
> 
> On 1/8/20 07:50, Wang, Zhe wrote:
>> Hi all,
>>
>> I am the maintainer of package scruff. Recently I encountered a timeout error in creating vignette in the development branch of the package. I tried increasing the number of cores for parallelization from 2 to 3 but it still timed out. I did not make any changes to the R codes in the vignette before this error happened. I tested building the vignette locally and it compiles without error. Does anyone know how I should fix this? Should I comment out some of the command in the vignette to reduce computing time? Should I try increasing the core number a bit more?
>>
>> Thanks,
>> Zhe
>>
>>
>> 	[[alternative HTML version deleted]]
>>
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> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org
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