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

[Hervé Pagès]

Hi Zhe,

On 2/2/20 18:12, Wang, Zhe wrote:
> Hi Herve,
> 
> I made a few modifications to scruff package trying to reduce computing time for the examples and vignette compilation. But still the development build does not pass on the Windows host due to timeout error. Can you check what went wrong on Windows OS?

What "went wrong" is that for some reason the code in the vignette is 
too slow on Windows. Note that 'R CMD build scruff' takes about 1273 
seconds on malbec2. Given that things tend to run slower on Windows 
compared to Linux (for example, 'R CMD build Rsubread' takes 259 seconds 
on Windows vs 96 seconds only on Linux), it is not unreasonable to 
imagine that 'R CMD build scruff' would take more than 2400 seconds on 
tokay2. Hence the TIMEOUT.

Did you take a look at Rubread's performance regression introduced on 
Jan 7? Did you report it to the Rsubread maintainer? When you choose to 
depend on someone's else package, it means that you are prepared to deal 
with the changes they make to their package. This includes letting them 
know when they introduce problems that affect you.

Cheers,
H.

> 
> Thank you,
> Zhe
> 
> -----Original Message-----
> From: Wang, Zhe
> Sent: Thursday, January 9, 2020 8:16 AM
> To: Pages, Herve <hpages using fredhutch.org>
> Subject: RE: [Bioc-devel] TIMEOUT error in building vignette in package scruff
> 
> Hi Herve,
> 
> Thanks a lot for helping out. I'll take a look at Rsubread's source code and see if there's anything I can do to fix this. If not I guess I'll contact their maintainer for a solution.
> 
> Zhe
> 
> -----Original Message-----
> From: Pages, Herve [mailto:hpages using fredhutch.org]
> Sent: Wednesday, January 8, 2020 7:07 PM
> To: Wang, Zhe <zhe using bu.edu>; bioc-devel using r-project.org
> Subject: Re: [Bioc-devel] TIMEOUT error in building vignette in package scruff
> 
> 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
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpages using fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
> 

-- 
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: hpages using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319