Excluding objects from save.image

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 Its a bit surprising for users not realizing the object is no longer valid.

My thought is to designate a class name (perhaps "no.save") and exclude anything that inherits from that.

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)

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On Thu, May 22, 2014 at 9:19 AM, Simon Urbanek <simon.urbanek at r-project.org> wrote:
Tim,

On May 21, 2014, at 9:54 PM, Tim Keitt <tkeitt at 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?

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.)

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)

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-- 
http://www.keittlab.org/