Re: [Rd] 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]>
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(
Re: [Rd] Missing objects using dump.frames for post-mortem debugging of crashed batch jobs. Bug or gap in documentation?
> nospam@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@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( , 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 diffi
Re: [Rd] 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@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( , 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)
> --
Re: [Rd] Missing objects using dump.frames for post-mortem debugging of crashed batch jobs. Bug or gap in documentation?
> nospam@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( , 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( ,
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
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R-devel@r-project.org mailing list
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[Rd] 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( ,
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.
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
