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

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.

>>>>> 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]> 

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