[R] Save creates huge files, dump doesn't

[William Dunlap]

Also, note that the function
   function(x) x
   <environment: 0x3314db8>
has no free variables so it doesn't matter what environment encloses it.

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Wed, Feb 20, 2019 at 7:47 AM William Dunlap <wdunlap using tibco.com> wrote:

> object using transforms@transforms$PC1.all using f
> function(x) x
> <environment: 0x3314db8>
> Do you know how to 'see' what's in 0x3314db8 ?
>
> ls.str(all=TRUE, environment(object using transforms@transforms$PC1.all using f)
>
> will list the names, types, summaries, etc. of the objects in that
> environment.
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Wed, Feb 20, 2019 at 12:20 AM Lars Velten <lars.velten using embl.de> wrote:
> >
> > Dear Bill, dear all,
> >
> > yes that seems to be it.  The problem orginates from objects of class
> transformMap from package flowCore
> >
> > > object_size(object using transforms@transforms$PC1.all using f)
> > 174 MB
> > > object.size(object using transforms@transforms$PC1.all using f)
> > 1160 bytes
> >
> > object using transforms@transforms$PC1.all using f
> >
> > function(x) x
> > <environment: 0x3314db8>
> >
> > Do you know how to 'see' what's in 0x3314db8 ? Might then drop a line to
> flowCore's developer, this behavior cannot be intended - especially here
> where f literally is just identity :-)
> >
> > Best wishes,
> >
> > Lars
> >
> > On 19. Feb 2019, at 21:30, William Dunlap <wdunlap using tibco.com> wrote:
> >
> > One reason save() makes bigger files than dump() is that save() saves
> environments associated with functions that are saved and those
> environments may contain large datasets that are not really needed.
> >
> > Bill Dunlap
> > TIBCO Software
> > wdunlap tibco.com
> >
> >
> > On Tue, Feb 19, 2019 at 11:59 AM Jeff Newmiller <
> jdnewmil using dcn.davis.ca.us> wrote:
> >>
> >> Make a reproducible example that focuses on the save/load aspect of the
> size problem. You may need to experiment with which variables need to be in
> the save file in order to trigger the behavior. Your example might have to
> involve sending us a link to a large file, but that size may dissuade busy
> experts from tackling it so paring it down by experimentation could be in
> your best interest.
> >>
> >> There is some expected behavior that can lead to larger files than the
> original in-memory data, but offhand I am unaware of any explanation for
> those files then using less space when re-loaded into memory than they
> occupy on disk.
> >>
> >> On February 18, 2019 11:51:11 AM PST, Lars Velten <lars.velten using embl.de>
> wrote:
> >> >Dear list,
> >> >I noticed an extremely odd behavior... I have a rather complex shiny
> >> >app which allows the user to store his/her state which internally
> >> >obviously triggers as call to save as follows
> >> >save(list=c("plots","gates","populations","cg",
> >> >"genelists","colorscores",  "proj", "actds"),file=fname)
> >> >this was all working fine until some time ago (?!?) files created by
> >> >this command became several hundred MBs big... even thought the
> >> >cumulative size of all objects in memory after load() is in the 10s of
> >> >kB.
> >> >Changing to
> >> >dump(list=c("plots","gates","populations","cg",
> >> >"genelists","colorscores",  "proj", "actds"),file=fname)
> >> >solved the problem, output was then only 10s of kB.
> >> >(Why/when) is this behavior intended?
> >> >Best wishes,
> >> >Lars
> >> >
> >> >       [[alternative HTML version deleted]]
> >> >
> >> >______________________________________________
> >> >R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> >https://stat.ethz.ch/mailman/listinfo/r-help
> >> >PLEASE do read the posting guide
> >> >http://www.R-project.org/posting-guide.html
> >> >and provide commented, minimal, self-contained, reproducible code.
> >>
> >> --
> >> Sent from my phone. Please excuse my brevity.
> >>
> >> ______________________________________________
> >> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
>

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