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

[William Dunlap]

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
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>> 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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