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]]
Lars
Typically answers regarding shiny are not answered here (I do wish there was a
SIG, however). With that said, are you saying that the object size is increasing
for objects that previously were much smaller? Or, are other things now being
saved into the workspace that were not there previously?
In other words, suppose you have some object called tmp. If you do
object.size(tmp) on your older version and on the newer version are they the
same size? Are the objects of the same class?
-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Lars Velten
Sent: Monday, February 18, 2019 2:51 PM
To: r-help at r-project.org
Subject: [R] Save creates huge files, dump doesn't
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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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 at 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 at 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.
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 at 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 at 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 at 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 at 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. >[[alternative HTML version deleted]]