[Bioc-devel] lazyData

Martin Morgan martin.morgan at roswellpark.org
Fri Jul 29 21:38:35 CEST 2016

On 07/18/2016 10:52 AM, Kasper Daniel Hansen wrote:
> This is a report on my testing with lazyData turned on and off wrt.
> installation time and memory requirements.  It turns out that using
> lazyData dramatically increases memory consumption and time for a
> (admittedly large) annotation package.  Perhaps this is something we should
> think about wrt. annotation and data packages.
> Test example is
>   IlluminaHumanMethylationEPICanno.ilm10b2.hg19
> an annotation package for minfi.  The .tar.gz for the this package is 113
> so its not small.
> I have explored using
>   LazyData: yes/no in DESCRIPTION
>   adding a single line data/datalist file containing the objects in the
> package
> What follows are timings and memory consumption of R CMD build + INSTALL on
> my Mac laptop using an SSD drive.
>   LazyData: yes
>   datalist: no
>   285 seconds
>   3.22 GB (values as high as 3.8GB seen)
>   LazyData: no
>   datalist: no
>   81s
>   1.64 GB
>   LazyData: no
>   datalist: yes
>   19s
>   0.38 GB

Hi Kasper -- I have to admit my ignorance on the miracle of lazy data. 
Can you clarify what one gains from LazyData? I kind of though that with 
LazyData: true the data was only loaded when needed, but that doesn't 
seem consistent with the picture you paint above? Also, what's the 
discussion about global variables?


> (following combination is not mentioned by R-exts, and while it still uses
> tons of memory, it seems to be 1 minute faster; redid measuring once to
> confirm this)
>   LazyData: yes
>   datalist: yes
>   226 s
>   3.26 GB (values as high as 3.9GB seen)
> Make the data LazyLoaded is pretty nice; one thing is it avoids polluting
> the global environment.
> But it seems that it would be worthwhile to consider if some of this could
> be done prior to the package build time.  Perhaps not, but for sure we are
> spending resources on the building and installing of this by the build
> system.
> I started going down this route because my Travis build starting being
> killed due to 3+GB being used. I really don't like turning off LazyLoad
> because of the global environment issue, but the number are kind of extreme
> here.
> Best,
> Kasper
> 	[[alternative HTML version deleted]]
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