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

3 messages · Wang, Zhe, Hervé Pagès

Original
Wang, Zhe
# 
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
Hervé Pagès
# 
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:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
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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 at spectre:~/Rsubread$ git log ef5e4c21d -n 1
   commit ef5e4c21d5a6d633aec0b2922dd9f230fed23463
   Author: Yang Liao <dbpzdbpz at 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: