R devel - Nov 2016 - Missing objects using dump.frames for post-mortem debugging of crashed batch jobs. Bug or gap in documentation?

Martin, thanks for the good news and sorry for wasting your (and others
time) by not doing my homework and query bugzilla first (lesson learned!
).

I have tested the new implementation from R-devel and observe a semantic
difference when playing with the parameters:

  # Test script 1
  g <- "global"
  f <- function(p) {
    l <- "local"
    dump.frames()
  }
  f("parameter")

results in
  # > debugger()
  # Message:  object 'server' not foundAvailable environments had calls:
  # 1: source("~/.active-rstudio-document", echo = TRUE)
  # 2: withVisible(eval(ei, envir))
  # 3: eval(ei, envir)
  # 4: eval(expr, envir, enclos)
  # 5: .active-rstudio-document#9: f("parameter")
  # 
  # Enter an environment number, or 0 to exit  
  # Selection: 5
  # Browsing in the environment with call:
  #   .active-rstudio-document#9: f("parameter")
  # Called from: debugger.look(ind)
  # Browse[1]> g
  # [1] "global"
  # Browse[1]> 

while dumping to a file

  # Test script 2
  g <- "global"
  f <- function(p) {
    l <- "local"
    dump.frames(to.file = TRUE, include.GlobalEnv = TRUE)
  }
  f("parameter")

results in
  # > load("last.dump.rda")
  # > debugger()
  # Message:  object 'server' not foundAvailable environments had calls:
  # 1: .GlobalEnv
  # 2: source("~/.active-rstudio-document", echo = TRUE)
  # 3: withVisible(eval(ei, envir))
  # 4: eval(ei, envir)
  # 5: eval(expr, envir, enclos)
  # 6: .active-rstudio-document#11: f("parameter")
  # 
  # Enter an environment number, or 0 to exit  
  # Selection: 6
  # Browsing in the environment with call:
  #   .active-rstudio-document#11: f("parameter")
  # Called from: debugger.look(ind)
  # Browse[1]> g
  # Error: object 'g' not found
  # Browse[1]> 

The semantic difference is that the global variable "g" is visible
within the function "f" in the first version, but not in the second
version.

If I dump to a file and load and debug it then the search path through
the
frames is not the same during run time vs. debug time.

An implementation with the same semantics could be achieved
by applying this workaround currently:

  dump.frames()
  save.image(file = "last.dump.rda")

Does it possibly make sense to unify the semantics?

THX!


On Mon, 2016-11-14 at 11:34 +0100, Martin Maechler
wrote:
> >>>>> nospam at altfeld-im de <nospam at
altfeld-im.de>
> >>>>>     on Sun, 13 Nov 2016 13:11:38 +0100 writes:
> 
>     > Dear R friends, to allow post-mortem debugging In my
>     > Rscript based batch jobs I use
> 
>     >    tryCatch( <R expression>, error = function(e) {
>     > dump.frames(to.file = TRUE) })
> 
>     > to write the called frames into a dump file.
> 
>     > This is similar to the method recommended in the "Writing
>     > R extensions" manual in section 4.2 Debugging R code (page
>     > 96):
> 
>     > https://cran.r-project.org/doc/manuals/R-exts.pdf
> 
>     >> options(error = quote({dump.frames(to.file=TRUE); q()}))
> 
> 
> 
>     > When I load the dump later in a new R session to examine
>     > the error I use
> 
>     >     load(file = "last.dump.rda") debugger(last.dump)
> 
>     > My problem is that the global objects in the workspace are
>     > NOT contained in the dump since "dump.frames" does not
>     > save the workspace.
> 
>     > This makes debugging difficult.
> 
> 
> 
>     > For more details see the stackoverflow question + answer
>     > in:
>     >
https://stackoverflow.com/questions/40421552/r-how-make-dump-frames-include-all-variables-for-later-post-mortem-debugging/40431711#40431711
> 
> 
> 
>     > I think the reason of the problem is:
>     > ------------------------------------
> 
>     > If you use dump.files(to.file = FALSE) in an interactive
>     > session debugging works as expected because it creates a
>     > global variable called "last.dump" and the workspace is
>     > still loaded.
> 
>     > In the batch job scenario however the workspace is NOT
>     > saved in the dump and therefore lost if you debug the dump
>     > in a new session.
> 
> 
>     > Options to solve the issue:
>     > --------------------------
> 
>     > 1. Improve the documentation of the R help for
>     > "dump.frames" and the R_exts manual to propose another
>     > code snippet for batch job scenarios:
> 
>     >       dump.frames() save.image(file = "last.dump.rda")
> 
>     > 2. Change the semantics of "dump.frames(to.file = TRUE)"
>     > to include the workspace in the dump.  This would change
>     > the semantics implied by the function name but makes the
>     > semantics consistent for both "to.file" param values.
> 
> There is a third option, already in place for three months now:
> Andreas Kersting did propose it (nicely, as a wish),
> 	https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17116
> and I had added it to the development version of R back then :
> 
> ------------------------------------------------------------------------
> r71102 | maechler | 2016-08-16 17:36:10 +0200 (Tue, 16 Aug 2016) | 1 line
> 
> dump.frames(*, include.GlobalEnv)
> ------------------------------------------------------------------------
> 
> So, if you (or others) want to use this before next spring,
> you should install a version of R-devel
> and you use that, with
> 
>   tryCatch( <R expression>,
>            error = function(e)
> 	           dump.frames(to.file = TRUE, include.GlobalEnv = TRUE))
> 
> Using R-devel is nice and helpful for the R community, as you
> will help finding bugs/problems in the new features (and
> possibly changed features) we've introduced there. 
> 
> 
> Best regards,
> Martin

>>>>> nospam at altfeld-im de <nospam at altfeld-im.de>
>>>>>     on Tue, 15 Nov 2016 01:15:46 +0100 writes:
> Martin, thanks for the good news and sorry for wasting your (and others
> time) by not doing my homework and query bugzilla first (lesson learned!
> ).
> 
> I have tested the new implementation from R-devel and observe a semantic
> difference when playing with the parameters:
> 
>   # Test script 1
>   g <- "global"
>   f <- function(p) {
>     l <- "local"
>     dump.frames()
>   }
>   f("parameter")
> 
> results in
>   # > debugger()
>   # Message:  object 'server' not foundAvailable environments had
calls:
>   # 1: source("~/.active-rstudio-document", echo = TRUE)
>   # 2: withVisible(eval(ei, envir))
>   # 3: eval(ei, envir)
>   # 4: eval(expr, envir, enclos)
>   # 5: .active-rstudio-document#9: f("parameter")
>   # 
>   # Enter an environment number, or 0 to exit  
>   # Selection: 5
>   # Browsing in the environment with call:
>   #   .active-rstudio-document#9: f("parameter")
>   # Called from: debugger.look(ind)
>   # Browse[1]> g
>   # [1] "global"
>   # Browse[1]> 
> 
> while dumping to a file
> 
>   # Test script 2
>   g <- "global"
>   f <- function(p) {
>     l <- "local"
>     dump.frames(to.file = TRUE, include.GlobalEnv = TRUE)
>   }
>   f("parameter")
> 
> results in
>   # > load("last.dump.rda")
>   # > debugger()
>   # Message:  object 'server' not foundAvailable environments had
calls:
>   # 1: .GlobalEnv
>   # 2: source("~/.active-rstudio-document", echo = TRUE)
>   # 3: withVisible(eval(ei, envir))
>   # 4: eval(ei, envir)
>   # 5: eval(expr, envir, enclos)
>   # 6: .active-rstudio-document#11: f("parameter")
>   # 
>   # Enter an environment number, or 0 to exit  
>   # Selection: 6
>   # Browsing in the environment with call:
>   #   .active-rstudio-document#11: f("parameter")
>   # Called from: debugger.look(ind)
>   # Browse[1]> g
>   # Error: object 'g' not found
>   # Browse[1]> 
Your call to f() and the corresponding dump is heavily
obfuscated by all the wrap paper that Rstudio seems to wrap around a
simple function call (or just around using debugger() ?).

All this was to get the correct environments when things are run
in a batch job... and there's no Rstudio gift wrapping in that case.

In my simple use of the above, "g" is clearly available in the
.GlobalEnv
component of last.dump :
> exists("g", last.dump$.GlobalEnv)
[1] TRUE
> get("g", last.dump$.GlobalEnv)
[1] "global"
> 
and that's all what's promised, right?
In such a post mortem debugging, notably from a batch job (!),
you don't want your .GlobalEnv to be *replaced* by the
.GlobalEnv from 'last.dump', do you?

I think in the end, I think you are indirectly asking for new features to be
added to  debugger(), namely that it works more seemlessly with
a last.dump object that has been created via 'include.GlobalEnv = TRUE'.

This wish for a new feature may be a very sensible wish.
I think it's fine if you add it as wish (for a new feature to
debugger()) to the R bugzilla site
( https://bugs.r-project.org/ -- after asking one of R core to
  add you to the list of "registered ones" there, see the
  boldface note in https://www.r-project.org/bugs.html )

Personally, I would only look into this issue if we also get a patch
proposal (see also https://www.r-project.org/bugs.html), because
already now you can easily get to "g" in your example.

Martin
> The semantic difference is that the global variable "g" is
visible
> within the function "f" in the first version, but not in the
second
> version.
> 
> If I dump to a file and load and debug it then the search path through
> the
> frames is not the same during run time vs. debug time.
> 
> An implementation with the same semantics could be achieved
> by applying this workaround currently:
> 
>   dump.frames()
>   save.image(file = "last.dump.rda")
> 
> Does it possibly make sense to unify the semantics?
> 
> THX!
> 
> 
> On Mon, 2016-11-14 at 11:34 +0100, Martin Maechler wrote:
> > >>>>> nospam at altfeld-im de <nospam at
altfeld-im.de>
> > >>>>>     on Sun, 13 Nov 2016 13:11:38 +0100 writes:
> > 
> >     > Dear R friends, to allow post-mortem debugging In my
> >     > Rscript based batch jobs I use
> > 
> >     >    tryCatch( <R expression>, error = function(e) {
> >     > dump.frames(to.file = TRUE) })
> > 
> >     > to write the called frames into a dump file.
> > 
> >     > This is similar to the method recommended in the
"Writing
> >     > R extensions" manual in section 4.2 Debugging R code
(page
> >     > 96):
> > 
> >     > https://cran.r-project.org/doc/manuals/R-exts.pdf
> > 
> >     >> options(error = quote({dump.frames(to.file=TRUE); q()}))
> > 
> > 
> > 
> >     > When I load the dump later in a new R session to examine
> >     > the error I use
> > 
> >     >     load(file = "last.dump.rda")
debugger(last.dump)
> > 
> >     > My problem is that the global objects in the workspace are
> >     > NOT contained in the dump since "dump.frames" does
not
> >     > save the workspace.
> > 
> >     > This makes debugging difficult.
> > 
> > 
> > 
> >     > For more details see the stackoverflow question + answer
> >     > in:
> >     >
https://stackoverflow.com/questions/40421552/r-how-make-dump-frames-include-all-variables-for-later-post-mortem-debugging/40431711#40431711
> > 
> > 
> > 
> >     > I think the reason of the problem is:
> >     > ------------------------------------
> > 
> >     > If you use dump.files(to.file = FALSE) in an interactive
> >     > session debugging works as expected because it creates a
> >     > global variable called "last.dump" and the
workspace is
> >     > still loaded.
> > 
> >     > In the batch job scenario however the workspace is NOT
> >     > saved in the dump and therefore lost if you debug the dump
> >     > in a new session.
> > 
> > 
> >     > Options to solve the issue:
> >     > --------------------------
> > 
> >     > 1. Improve the documentation of the R help for
> >     > "dump.frames" and the R_exts manual to propose
another
> >     > code snippet for batch job scenarios:
> > 
> >     >       dump.frames() save.image(file =
"last.dump.rda")
> > 
> >     > 2. Change the semantics of "dump.frames(to.file =
TRUE)"
> >     > to include the workspace in the dump.  This would change
> >     > the semantics implied by the function name but makes the
> >     > semantics consistent for both "to.file" param
values.
> > 
> > There is a third option, already in place for three months now:
> > Andreas Kersting did propose it (nicely, as a wish),
> > 	https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17116
> > and I had added it to the development version of R back then :
> > 
> >
------------------------------------------------------------------------
> > r71102 | maechler | 2016-08-16 17:36:10 +0200 (Tue, 16 Aug 2016) | 1
line
> > 
> > dump.frames(*, include.GlobalEnv)
> >
------------------------------------------------------------------------
> > 
> > So, if you (or others) want to use this before next spring,
> > you should install a version of R-devel
> > and you use that, with
> > 
> >   tryCatch( <R expression>,
> >            error = function(e)
> > 	           dump.frames(to.file = TRUE, include.GlobalEnv = TRUE))
> > 
> > Using R-devel is nice and helpful for the R community, as you
> > will help finding bugs/problems in the new features (and
> > possibly changed features) we've introduced there. 
> > 
> > 
> > Best regards,
> > Martin

>> Martin, thanks for the good news and sorry for wasting your (and others
>> time) by not doing my homework and query bugzilla first (lesson
learned!
>> ).
>>
>> I have tested the new implementation from R-devel and observe a
semantic
>> difference when playing with the parameters:
>>
>>   # Test script 1
>>   g <- "global"
>>   f <- function(p) {
>>     l <- "local"
>>     dump.frames()
>>   }
>>   f("parameter")
>>
>> results in
>>   # > debugger()
>>   # Message:  object 'server' not foundAvailable environments
had calls:
>>   # 1: source("~/.active-rstudio-document", echo = TRUE)
>>   # 2: withVisible(eval(ei, envir))
>>   # 3: eval(ei, envir)
>>   # 4: eval(expr, envir, enclos)
>>   # 5: .active-rstudio-document#9: f("parameter")
>>   #
>>   # Enter an environment number, or 0 to exit
>>   # Selection: 5
>>   # Browsing in the environment with call:
>>   #   .active-rstudio-document#9: f("parameter")
>>   # Called from: debugger.look(ind)
>>   # Browse[1]> g
>>   # [1] "global"
>>   # Browse[1]>
>>
>> while dumping to a file
>>
>>   # Test script 2
>>   g <- "global"
>>   f <- function(p) {
>>     l <- "local"
>>     dump.frames(to.file = TRUE, include.GlobalEnv = TRUE)
>>   }
>>   f("parameter")
>>
>> results in
>>   # > load("last.dump.rda")
>>   # > debugger()
>
>>   # Message:  object 'server' not foundAvailable environments
had calls:
>>   # 1: .GlobalEnv
>>   # 2: source("~/.active-rstudio-document", echo = TRUE)
>>   # 3: withVisible(eval(ei, envir))
>>   # 4: eval(ei, envir)
>>   # 5: eval(expr, envir, enclos)
>>   # 6: .active-rstudio-document#11: f("parameter")
>>   #
>>   # Enter an environment number, or 0 to exit
>>   # Selection: 6
>>   # Browsing in the environment with call:
>>   #   .active-rstudio-document#11: f("parameter")
>>   # Called from: debugger.look(ind)
>>   # Browse[1]> g
>>   # Error: object 'g' not found
>>   # Browse[1]>
>
> Your call to f() and the corresponding dump is heavily
> obfuscated by all the wrap paper that Rstudio seems to wrap around a
> simple function call (or just around using debugger() ?).
>
> All this was to get the correct environments when things are run
> in a batch job... and there's no Rstudio gift wrapping in that case.
>
> In my simple use of the above, "g" is clearly available in the
.GlobalEnv
> component of last.dump :
>
>> exists("g", last.dump$.GlobalEnv)
> [1] TRUE
>> get("g", last.dump$.GlobalEnv)
> [1] "global"
>>
>
> and that's all what's promised, right?
> In such a post mortem debugging, notably from a batch job (!),
> you don't want your .GlobalEnv to be *replaced* by the
> .GlobalEnv from 'last.dump', do you?
>
> I think in the end, I think you are indirectly asking for new features to
be
> added to  debugger(), namely that it works more seemlessly with
> a last.dump object that has been created via 'include.GlobalEnv =
TRUE'.
>
> This wish for a new feature may be a very sensible wish.
> I think it's fine if you add it as wish (for a new feature to
> debugger()) to the R bugzilla site
> ( https://bugs.r-project.org/ -- after asking one of R core to
>   add you to the list of "registered ones" there, see the
>   boldface note in https://www.r-project.org/bugs.html )
>
> Personally, I would only look into this issue if we also get a patch
> proposal (see also https://www.r-project.org/bugs.html), because
> already now you can easily get to "g" in your example.
>
> Martin
>
Hi,

how about changing debugger() to something along the lines:

debugger <- function(dump = last.dump)
{
     # debugger.look <- function(.selection)
     # {
     #     ## allow e.g. '...' to fail
     #     for(.obj in ls(envir=dump[[.selection]], all.names=TRUE))
     #         tryCatch(assign(.obj, get(.obj,envir=dump[[.selection]])),
     #                  error=function(e) {})
     #     cat(gettext("Browsing in the environment with call:\n   "),
     #         calls[.selection], "\n", sep = "")
     #     rm(.obj, .selection)
     #     browser()
     # }
     if (!inherits(dump, "dump.frames")) {
         cat(gettextf("'dump' is not an object of class %s\n",
                      dQuote("dump.frames")))
         return(invisible())
     }
     err.action <- getOption("error")
     on.exit(options(error=err.action))
     if (length(msg <- attr(dump, "error.message")))
         cat(gettext("Message: "), msg)
     n <- length(dump)
     if (!n) {
	cat(gettextf("'dump' is empty\n"))
	return(invisible())
     }
     calls <- names(dump)

     if (calls[1] == ".GlobalEnv") {
         parent.env(dump[[1]]) <- parent.env(.GlobalEnv)
         for (i in seq_along(dump)[-1]) {
             if (identical(parent.env(dump[[i]]), .GlobalEnv)) {
                 parent.env(dump[[i]]) <- dump[[1]]
             }
         }
     }

     repeat {
         cat(gettext("Available environments had calls:\n"))
         cat(paste0(1L:n, ": ", calls), sep = "\n")
         cat(gettext("\nEnter an environment number, or 0 to exit  "))
         repeat {
             ind <- .Call(C_menu, as.character(calls))
             if(ind <= n) break
         }
         if(ind == 0L) return(invisible())
         # debugger.look(ind)
         cat(gettext("Browsing in the environment with call:\n   "),
             calls[ind], "\n", sep = "")
         evalq(browser(), envir = dump[[ind]])
     }
}

So instead of copying all objects of the chosen frame to some new 
environment, i.e. the frame of debugger.look(), we directly inspect the 
dumped one with evalq(browser(), envir = dump[[ind]]). This way we do 
not alter the enclosing environment of the frame.

If the global environment was included in the dump, we change the 
enclosing environment of the dumped .GlobalEnv to search()[2]. For all 
other dumped frames which have the global environment as their enclosing 
one, we change their enclosing environment to the dumped .GlobalEnv.

By doing so we should get an environment tree which is closer to the one 
when dump.frames() was called, with an obvious (potential) difference 
being the search path.

Andreas
>> The semantic difference is that the global variable "g" is
visible
>> within the function "f" in the first version, but not in the
second
>> version.
>>
>> If I dump to a file and load and debug it then the search path through
>> the
>> frames is not the same during run time vs. debug time.
>>
>> An implementation with the same semantics could be achieved
>> by applying this workaround currently:
>>
>>   dump.frames()
>>   save.image(file = "last.dump.rda")
>>
>> Does it possibly make sense to unify the semantics?
>>
>> THX!
>>
>>
>> On Mon, 2016-11-14 at 11:34 +0100, Martin Maechler wrote:
>> > >>>>> nospam at altfeld-im de <nospam at
altfeld-im.de>
>> > >>>>>     on Sun, 13 Nov 2016 13:11:38 +0100
writes:
>> >
>> >     > Dear R friends, to allow post-mortem debugging In my
>> >     > Rscript based batch jobs I use
>> >
>> >     >    tryCatch( <R expression>, error = function(e) {
>> >     > dump.frames(to.file = TRUE) })
>> >
>> >     > to write the called frames into a dump file.
>> >
>> >     > This is similar to the method recommended in the
"Writing
>> >     > R extensions" manual in section 4.2 Debugging R code
(page
>> >     > 96):
>> >
>> >     > https://cran.r-project.org/doc/manuals/R-exts.pdf
>> >
>> >     >> options(error = quote({dump.frames(to.file=TRUE);
q()}))
>> >
>> >
>> >
>> >     > When I load the dump later in a new R session to examine
>> >     > the error I use
>> >
>> >     >     load(file = "last.dump.rda")
debugger(last.dump)
>> >
>> >     > My problem is that the global objects in the workspace
are
>> >     > NOT contained in the dump since "dump.frames"
does not
>> >     > save the workspace.
>> >
>> >     > This makes debugging difficult.
>> >
>> >
>> >
>> >     > For more details see the stackoverflow question + answer
>> >     > in:
>> >     >
https://stackoverflow.com/questions/40421552/r-how-make-dump-frames-include-all-variables-for-later-post-mortem-debugging/40431711#40431711
>> >
>> >
>> >
>> >     > I think the reason of the problem is:
>> >     > ------------------------------------
>> >
>> >     > If you use dump.files(to.file = FALSE) in an interactive
>> >     > session debugging works as expected because it creates a
>> >     > global variable called "last.dump" and the
workspace is
>> >     > still loaded.
>> >
>> >     > In the batch job scenario however the workspace is NOT
>> >     > saved in the dump and therefore lost if you debug the
dump
>> >     > in a new session.
>> >
>> >
>> >     > Options to solve the issue:
>> >     > --------------------------
>> >
>> >     > 1. Improve the documentation of the R help for
>> >     > "dump.frames" and the R_exts manual to propose
another
>> >     > code snippet for batch job scenarios:
>> >
>> >     >       dump.frames() save.image(file =
"last.dump.rda")
>> >
>> >     > 2. Change the semantics of "dump.frames(to.file =
TRUE)"
>> >     > to include the workspace in the dump.  This would change
>> >     > the semantics implied by the function name but makes the
>> >     > semantics consistent for both "to.file" param
values.
>> >
>> > There is a third option, already in place for three months now:
>> > Andreas Kersting did propose it (nicely, as a wish),
>> > 	https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17116
>> > and I had added it to the development version of R back then :
>> >
>> >
------------------------------------------------------------------------
>> > r71102 | maechler | 2016-08-16 17:36:10 +0200 (Tue, 16 Aug 2016) |
1 line
>> >
>> > dump.frames(*, include.GlobalEnv)
>> >
------------------------------------------------------------------------
>> >
>> > So, if you (or others) want to use this before next spring,
>> > you should install a version of R-devel
>> > and you use that, with
>> >
>> >   tryCatch( <R expression>,
>> >            error = function(e)
>> > 	           dump.frames(to.file = TRUE, include.GlobalEnv = TRUE))
>> >
>> > Using R-devel is nice and helpful for the R community, as you
>> > will help finding bugs/problems in the new features (and
>> > possibly changed features) we've introduced there.
>> >
>> >
>> > Best regards,
>> > Martin