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

Lars Velten |@r@@ve|ten @end|ng |rom emb|@de
Wed Feb 20 09:20:40 CET 2019

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,


> 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 <http://tibco.com/>
> On Tue, Feb 19, 2019 at 11:59 AM Jeff Newmiller <jdnewmil using dcn.davis.ca.us <mailto: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 <mailto: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]]
> >
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