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@spectre:~/Rsubread$ git log ef5e4c21d -n 1
commit ef5e4c21d5a6d633aec0b2922dd9f230fed23463
Author: Yang Liao <dbpzd...@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
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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