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

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Wed Jan 8 19:30:51 CET 2020

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 


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]]
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=stHSi8EN5PUgMEVus6KdL2z7-DfGzikck8btNROFUx0&s=dSXLn6y8wJtjg6ukcpOpGbSHfXqqsH97r9fuSJkakGo&e=

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

More information about the Bioc-devel mailing list