[Bioc-devel] [External] DSS Bioconductor package

[Nitesh Turaga]

Please note that depending on the “type” of parallel computation you are using, it may not work on Windows. 

You could say something along the lines of (https://stat.ethz.ch/R-manual/R-devel/library/base/html/Platform.html <https://stat.ethz.ch/R-manual/R-devel/library/base/html/Platform.html>) 

	if(.Platform$OS.type == "unix") {
		## <do some parallel computation>	
	} 
	else {
	        ## This will be windows
		## Use serial param or do not use any parallel functions, just use ‘lapply’
		## result should be of the same “type” from both the if and else statements.
	}


Note:  Params listed are supported on all of Unix, Mac and Windows except MulticoreParam which is Unix and Mac only. I do not think “forked” processes are available on windows. Even The mclapply() function (and related mc* functions) works via the fork mechanism on Unix-style operating systems.

(https://bioconductor.org/packages/release/bioc/vignettes/BiocParallel/inst/doc/Introduction_To_BiocParallel.pdf <https://bioconductor.org/packages/release/bioc/vignettes/BiocParallel/inst/doc/Introduction_To_BiocParallel.pdf>).


Nitesh Turaga
Scientist II, Department of Data Science,
Bioconductor Core Team Member
Dana Farber Cancer Institute

> On May 13, 2022, at 11:03 AM, Wu, Hao <hao.wu using emory.edu> wrote:
> 
> Nitesh,
>  
> The compilation error for DSS happened on windows because of the use of parallel computing. However, I have modified my codes to use only a single core on windows. It’s not clear to me why the problem is still there. Could you provide some help on this issue?
>  
> Many thanks,
> Hao
>  
>  
> From: "nturaga.bioc using gmail.com" <nturaga.bioc using gmail.com>
> Date: Friday, March 25, 2022 at 1:58 PM
> To: "Wu, Hao" <hao.wu using emory.edu>, Harry Feng <hxf155 using case.edu>
> Subject: [External] DSS Bioconductor package
>  
> DSS Bioconductor Package Notification
> Nitesh Turaga1
> 
> 1Dana Farber Cancer Institute, Boston, MA, USA
> 
> March 25, 2022
> 
> Package: DSS
> Hi Hao Wu & Hao Feng,
> 
> I am contacting you concerning the DSS package, on the release and devel branch of Bioconductor, for which you are listed as the maintainer.
> 
> The latest build/check report shows that your package is failing on one or more platforms. Please resolve the issues before the next Bioconductor release for your package’s continued inclusion in Bioconductor.
> 
> https://bioconductor.org/checkResults/release/bioc-LATEST/DSS/ https://bioconductor.org/checkResults/devel/bioc-LATEST/DSS/
> 
> Please let me know if you have any questions.
> 
> Regards,
> 
> Nitesh
> 
> Bioconductor Core Team 
> Scientist II 
> Dana Farber Cancer Institute 
> Data Science 
> Boston, MA 
> 


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