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List: r-devel
Subject: Re: [Rd] Excluding objects from save.image
From: Tim Keitt <tkeitt () utexas ! edu>
Date: 2014-05-22 16:30:36
Message-ID: CANnL8gpXqmcHeRjaLSuE5=XFf8WHnfandLwdPWbU0Xgz-9ChFQ () mail ! gmail ! com
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On Thu, May 22, 2014 at 10:47 AM, Simon Urbanek <simon.urbanek@r-project.org
> wrote:
> On May 22, 2014, at 11:33 AM, Tim Keitt <tkeitt@utexas.edu> wrote:
>
> > On Thu, May 22, 2014 at 9:19 AM, Simon Urbanek <
> simon.urbanek@r-project.org> wrote:
> > Tim,
> >
> > On May 21, 2014, at 9:54 PM, Tim Keitt <tkeitt@utexas.edu> wrote:
> >
> > > When dealing with object holding pointers that are only valid during a
> single session, it would be convenient to exclude them from being saved
> with the session image. (I am assuming that `quit` calls `save.image`
> before quitting or is it internal?) Currently they are saved with the
> pointer converted to NULL. Its a bit surprising for users not realizing the
> object is no longer valid.
> > >
> >
> > than's not surprising - it's actually very useful, because it tells you
> that the object has been restored. Typically, packages using external
> pointers use this to re-inilitialize the object from serialized data or
> other sources if possible.
> >
> > Automatically or with user intervention?
>
>
> Automatically - that is the point :).
>
Have an example? Do you save a promise?
>
>
> > > My thought is to designate a class name (perhaps "no.save") and
> exclude anything that inherits from that.
> >
> > Why would you want to not save it? It exists, so saving it makes it
> possible to decide on the behavior as needed - as opposed to not saving it
> and thus losing the information.
> >
> > That's a valid argument. I don't necessarily disagree, but it does
> depend on the situation and the author's intentions.
> >
> > My question was not about enforcing policy on authors, rather it was
> about whether this would add value for those that would like to use it for
> cases where they deem it a benefit. I see those as separate issues.
> >
> > Incidentally, I suggested many years ago hooks in load to make
> reinitialization possible. Is there some infrastructure for that in R? (And
> actually hooks on save would be quite useful as well eg one could
> substitute an object designed to reinitialize the original object on load.)
> >
>
> Load time is typically not an issue, since you can just do it lazily.
> (Incidentally, doing that eagerly at load time is the hard part since you'd
> have to load the packages necessary in the right order which is not always
> possible to determine from the serialization alone. It's a full can of
> worms, because R doesn't know anything about sharing and dependencies on
> the native side etc.).
>
> However, having a proper save hook for ext ptrs would be very useful. When
> I was asking for it few years ago, Luke mentioned there were issues - maybe
> it's something that could be re-visited.
>
I'd be interested. I can see it might be tricky deciding when to call the
hook.
THK
>
> Cheers,
> Simon
>
>
>
> > Cheers,
> > THK
> >
> >
> > Cheers,
> > Simon
> >
> >
> >
> > > I've hacked a quick implementation below.
> > > I did not issue a warning, but it would be a simple fix.
> > >
> > > Does anyone else see this as useful?
> > >
> > > THK
> > >
> > > --
> > > http://www.keittlab.org/
> > >
> > > .new.save.image = function (file = ".RData", version = NULL, ascii =
> FALSE,
> > > compress = !ascii,
> > > safe = TRUE, omit.no.save = TRUE) # added
> > > "omit.no.save" argument
> > > {
> > > if (!is.character(file) || file == "")
> > > stop("'file' must be non-empty string")
> > > opts <- getOption("save.image.defaults")
> > > if (is.null(opts))
> > > opts <- getOption("save.defaults")
> > > if (missing(safe) && !is.null(opts$safe))
> > > safe <- opts$safe
> > > if (missing(ascii) && !is.null(opts$ascii))
> > > ascii <- opts$ascii
> > > if (missing(compress) && !is.null(opts$compress))
> > > compress <- opts$compress
> > > if (missing(version))
> > > version <- opts$version
> > > if (safe) {
> > > outfile <- paste0(file, "Tmp")
> > > i <- 0
> > > while (file.exists(outfile)) {
> > > i <- i + 1
> > > outfile <- paste0(file, "Tmp", i)
> > > }
> > > }
> > > else outfile <- file
> > > on.exit(file.remove(outfile))
> > >
> > > ### Omit objects inheriting from "no.save" ###
> > >
> > > objns <- ls(envir = .GlobalEnv, all.names = TRUE)
> > >
> > > if ( omit.no.save ) ### make part of options?
> > > objns <- subset(objns, sapply(objns, function(x)
> > > {
> > > ! inherits(get(x, envir = .GlobalEnv), "no.save")
> > > }))
> > >
> > > save(list = objns, file = outfile,
> > > version = version, ascii = ascii, compress = compress,
> > > envir = .GlobalEnv, precheck = FALSE)
> > >
> > > ### End code changes ###
> > >
> > > if (safe)
> > > if (!file.rename(outfile, file)) {
> > > on.exit()
> > > stop(gettextf("image could not be renamed and is left in %s",
> > > outfile), domain = NA)
> > > }
> > > on.exit()
> > > }
> > >
> > > setClass("no.save")
> > > setClass("test.class", slots = c(s1 = "externalptr"))
> > > setIs("test.class", "no.save")
> > > reg.obj = "regular object"
> > > no.save.obj = new("test.class")
> > > .image.file = tempfile()
> > > save.image(.image.file)
> > > rm(reg.obj, no.save.obj)
> > > load(.image.file)
> > > print(ls())
> > > unlink(.image.file)
> > > .new.save.image(.image.file)
> > > rm(reg.obj, no.save.obj)
> > > load(.image.file)
> > > print(ls())
> > > unlink(.image.file)
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-devel
> > >
> >
> >
> >
> >
> > --
> > http://www.keittlab.org/
>
>
--
http://www.keittlab.org/
[[alternative HTML version deleted]]
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