Re: [R] how do you know which functions are being debugged?
On Fri, Oct 23, 2009 at 7:06 PM, Duncan Murdoch wrote: > Gabor Grothendieck wrote: >> >> On Fri, Oct 23, 2009 at 2:52 PM, Duncan Murdoch >> wrote: >> >>> >>> On 10/23/2009 2:49 PM, Andrew Yee wrote: >>> Thanks everyone for the responses. As a suggestion, wouldn't it be useful, that when you run isdebugged() without any parameters, it would just report back the functions that are being flagged for debugging? >>> >>> Could you give an example of what the answer would look like? Not all >>> functions have names, not all names are unique, ... >>> >>> >> >> One could use the formal argument list of the function, i.e. the >> output of args, when there is no notion of name since that is always >> available. >> > > It would actually be easier to return a copy of the whole function. But That`s already done when you enter debugging and I find it quite annoying particularly when you have large functions interrupting the flow. I wish there were some way to limit this. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how do you know which functions are being debugged?
Sweet Jesus ... I just read what I wrote earlier ...
On Oct 23, 2009, at 2:57 PM, Steve Lianoglou wrote:
If this is something you just want to use on your own functions that
are set to `debug`, why not just make write a debug wraps the
base::debug and does some keeps track of which functions you're
debugging in some global environment variable (of your creation).
This has to win for one of my most lucid moments.
I feel like I should publicly apologize for letting such an
abomination out of its cage. Hopefully the code I sent explained what
my feeble attempt at "human communication" didn't ... yeesh!
Sorry :-)
-steve
You should probably use something beside "substitute" here, but:
R> .DLIST <- character()
R> debug <- function(fun, text="", condition=NULL) {
.DLIST <<- c(.DLIST, substitute(fun))
base::debug(fun, text=text, condition=condition)
}
R> myfun <- function(something) {
a <- length(something)
b <- sum(something)
b
}
R> debug(myfun)
R> debug(myfun)
R> .DLIST
[[1]]
myfun
R> myfun(1:10)
debugging in: myfun(1:10)
debug: {
a <- length(something)
b <- sum(something)
b
}
Browse[2]> n
debug: a <- length(something)
Browse[2]> n
debug: b <- sum(something)
Browse[2]> n
debug: b
Browse[2]> n
exiting from: myfun(1:10)
[1] 55
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] how do you know which functions are being debugged?
Gabor Grothendieck wrote: On Fri, Oct 23, 2009 at 2:52 PM, Duncan Murdoch wrote: On 10/23/2009 2:49 PM, Andrew Yee wrote: Thanks everyone for the responses. As a suggestion, wouldn't it be useful, that when you run isdebugged() without any parameters, it would just report back the functions that are being flagged for debugging? Could you give an example of what the answer would look like? Not all functions have names, not all names are unique, ... One could use the formal argument list of the function, i.e. the output of args, when there is no notion of name since that is always available. It would actually be easier to return a copy of the whole function. But this wouldn't tell you how to turn off debugging: for example, if an environment captured a copy of a function with the debugging bit set, then you really need to know where it was found, not just what was found. It's tricky to put together examples of this because debug(f) doesn't act like a normal function, but here's an example showing some of the weird behaviour: f <- function(x) x^2 debug(f) g <- f # now both g and f have the debug bit set. Should both be returned by the "showDebugged" function? undebug(f) # that unset both. Now undebug(g) would give a warning. debug(f) # that set both f <- function(x) x^2 # Now g has it set, but f doesn't. In this example, I was doing explicit assignments, but if f had been passed as an argument to a function, an implicit assignment would be made to the local variable holding it, and the same sort of behaviour would result. I think this would be very confusing, and not particularly helpful, in lots of cases. I think Steve's suggestion is really the right way to go: if you're going to be setting lots of debug flags, then keep track of them yourself, and use your records to unset them. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how do you know which functions are being debugged?
On Fri, Oct 23, 2009 at 2:52 PM, Duncan Murdoch wrote: > On 10/23/2009 2:49 PM, Andrew Yee wrote: >> >> Thanks everyone for the responses. As a suggestion, wouldn't it be >> useful, >> that when you run isdebugged() without any parameters, it would just >> report >> back the functions that are being flagged for debugging? > > Could you give an example of what the answer would look like? Not all > functions have names, not all names are unique, ... > One could use the formal argument list of the function, i.e. the output of args, when there is no notion of name since that is always available. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how do you know which functions are being debugged?
Hi,
On Oct 23, 2009, at 2:39 PM, Gabor Grothendieck wrote:
On Fri, Oct 23, 2009 at 2:34 PM, Duncan Murdoch
wrote:
On 10/23/2009 2:27 PM, Gabor Grothendieck wrote:
I have often wanted to get such a list as well without having to
write
code myself. If a function which automatically iterated over all
possible objects and listed out the ones that being debugged were
available in the core it would be useful. Even if its slow this
would
be used at debug time and not a production time so it would not be
too
bad. Even a heuristic that checked likely locations, e.g. just the
global environment, but not all locations might be useful.
If you look at the code in setBreakpoint, it does a search for
functions in
lots of places (but not everywhere). You could start from that.
Generally speaking, it's quite hard to think of a way to express
what the
answer would look like to a perfectly general function like you're
asking
for. Suppose a function lives in the parent environment of the
environment
of an expression that was returned in the result of a call to lm
that is a
local variable in the function that called the function where you
are asking
the question: how would you return that as an answer??? In a
language with
pointers, you'd just return a pointer to it, but R doesn't have
those.
I agree its problematic but it would still be useful since after you
have debugged a number of functions its easy to forget which ones are
being debugged.
If this is something you just want to use on your own functions that
are set to `debug`, why not just make write a debug wraps the
base::debug and does some keeps track of which functions you're
debugging in some global environment variable (of your creation).
You should probably use something beside "substitute" here, but:
R> .DLIST <- character()
R> debug <- function(fun, text="", condition=NULL) {
.DLIST <<- c(.DLIST, substitute(fun))
base::debug(fun, text=text, condition=condition)
}
R> myfun <- function(something) {
a <- length(something)
b <- sum(something)
b
}
R> debug(myfun)
R> debug(myfun)
R> .DLIST
[[1]]
myfun
R> myfun(1:10)
debugging in: myfun(1:10)
debug: {
a <- length(something)
b <- sum(something)
b
}
Browse[2]> n
debug: a <- length(something)
Browse[2]> n
debug: b <- sum(something)
Browse[2]> n
debug: b
Browse[2]> n
exiting from: myfun(1:10)
[1] 55
You can define your own undebug function accordingly.
Would that do what you want?
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] how do you know which functions are being debugged?
On 10/23/2009 2:49 PM, Andrew Yee wrote: Thanks everyone for the responses. As a suggestion, wouldn't it be useful, that when you run isdebugged() without any parameters, it would just report back the functions that are being flagged for debugging? Could you give an example of what the answer would look like? Not all functions have names, not all names are unique, ... Duncan Murdoch Andrew On Fri, Oct 23, 2009 at 2:12 PM, Yihui Xie wrote: Oops... I forgot to mention that 'envir' (or 'pos') should be specified in ls()/get() in my last reply if you are looking for debugged functions in environments other than ".GlobalEnv". Regards, Yihui -- Yihui Xie Phone: 515-294-6609 Web: http://yihui.name Department of Statistics, Iowa State University 3211 Snedecor Hall, Ames, IA On Fri, Oct 23, 2009 at 1:02 PM, Duncan Murdoch wrote: > On 10/23/2009 1:28 PM, Andrew Yee wrote: >> >> This is kind of a dumb question: I know you can use isdebugged() to find >> out if a specific function is flagged for debugging, but is there a way to >> list all the functions that are flagged for debugging? > > No, R doesn't keep any master list, it sets a flag in each one. So you > could iterate over all visible objects to find the ones that have the flag > set (and this is quite slow, there are a lot of places to look), but there > would always be the chance that one was hiding somewhere you didn't look. > > Duncan Murdoch > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how do you know which functions are being debugged?
Thanks everyone for the responses. As a suggestion, wouldn't it be useful, that when you run isdebugged() without any parameters, it would just report back the functions that are being flagged for debugging? Andrew On Fri, Oct 23, 2009 at 2:12 PM, Yihui Xie wrote: > Oops... I forgot to mention that 'envir' (or 'pos') should be > specified in ls()/get() in my last reply if you are looking for > debugged functions in environments other than ".GlobalEnv". > > Regards, > Yihui > -- > Yihui Xie > Phone: 515-294-6609 Web: http://yihui.name > Department of Statistics, Iowa State University > 3211 Snedecor Hall, Ames, IA > > > > On Fri, Oct 23, 2009 at 1:02 PM, Duncan Murdoch > wrote: > > On 10/23/2009 1:28 PM, Andrew Yee wrote: > >> > >> This is kind of a dumb question: I know you can use isdebugged() to > find > >> out if a specific function is flagged for debugging, but is there a way > to > >> list all the functions that are flagged for debugging? > > > > No, R doesn't keep any master list, it sets a flag in each one. So you > > could iterate over all visible objects to find the ones that have the > flag > > set (and this is quite slow, there are a lot of places to look), but > there > > would always be the chance that one was hiding somewhere you didn't look. > > > > Duncan Murdoch > > > > __ > > R-help@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how do you know which functions are being debugged?
On Fri, Oct 23, 2009 at 2:34 PM, Duncan Murdoch wrote: > On 10/23/2009 2:27 PM, Gabor Grothendieck wrote: >> >> I have often wanted to get such a list as well without having to write >> code myself. If a function which automatically iterated over all >> possible objects and listed out the ones that being debugged were >> available in the core it would be useful. Even if its slow this would >> be used at debug time and not a production time so it would not be too >> bad. Even a heuristic that checked likely locations, e.g. just the >> global environment, but not all locations might be useful. > > If you look at the code in setBreakpoint, it does a search for functions in > lots of places (but not everywhere). You could start from that. > > Generally speaking, it's quite hard to think of a way to express what the > answer would look like to a perfectly general function like you're asking > for. Suppose a function lives in the parent environment of the environment > of an expression that was returned in the result of a call to lm that is a > local variable in the function that called the function where you are asking > the question: how would you return that as an answer??? In a language with > pointers, you'd just return a pointer to it, but R doesn't have those. I agree its problematic but it would still be useful since after you have debugged a number of functions its easy to forget which ones are being debugged. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how do you know which functions are being debugged?
On 10/23/2009 2:27 PM, Gabor Grothendieck wrote: I have often wanted to get such a list as well without having to write code myself. If a function which automatically iterated over all possible objects and listed out the ones that being debugged were available in the core it would be useful. Even if its slow this would be used at debug time and not a production time so it would not be too bad. Even a heuristic that checked likely locations, e.g. just the global environment, but not all locations might be useful. If you look at the code in setBreakpoint, it does a search for functions in lots of places (but not everywhere). You could start from that. Generally speaking, it's quite hard to think of a way to express what the answer would look like to a perfectly general function like you're asking for. Suppose a function lives in the parent environment of the environment of an expression that was returned in the result of a call to lm that is a local variable in the function that called the function where you are asking the question: how would you return that as an answer??? In a language with pointers, you'd just return a pointer to it, but R doesn't have those. Duncan Murdoch On Fri, Oct 23, 2009 at 2:02 PM, Duncan Murdoch wrote: On 10/23/2009 1:28 PM, Andrew Yee wrote: This is kind of a dumb question: I know you can use isdebugged() to find out if a specific function is flagged for debugging, but is there a way to list all the functions that are flagged for debugging? No, R doesn't keep any master list, it sets a flag in each one. So you could iterate over all visible objects to find the ones that have the flag set (and this is quite slow, there are a lot of places to look), but there would always be the chance that one was hiding somewhere you didn't look. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how do you know which functions are being debugged?
I have often wanted to get such a list as well without having to write code myself. If a function which automatically iterated over all possible objects and listed out the ones that being debugged were available in the core it would be useful. Even if its slow this would be used at debug time and not a production time so it would not be too bad. Even a heuristic that checked likely locations, e.g. just the global environment, but not all locations might be useful. On Fri, Oct 23, 2009 at 2:02 PM, Duncan Murdoch wrote: > On 10/23/2009 1:28 PM, Andrew Yee wrote: >> >> This is kind of a dumb question: I know you can use isdebugged() to find >> out if a specific function is flagged for debugging, but is there a way to >> list all the functions that are flagged for debugging? > > No, R doesn't keep any master list, it sets a flag in each one. So you > could iterate over all visible objects to find the ones that have the flag > set (and this is quite slow, there are a lot of places to look), but there > would always be the chance that one was hiding somewhere you didn't look. > > Duncan Murdoch > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how do you know which functions are being debugged?
Oops... I forgot to mention that 'envir' (or 'pos') should be specified in ls()/get() in my last reply if you are looking for debugged functions in environments other than ".GlobalEnv". Regards, Yihui -- Yihui Xie Phone: 515-294-6609 Web: http://yihui.name Department of Statistics, Iowa State University 3211 Snedecor Hall, Ames, IA On Fri, Oct 23, 2009 at 1:02 PM, Duncan Murdoch wrote: > On 10/23/2009 1:28 PM, Andrew Yee wrote: >> >> This is kind of a dumb question: I know you can use isdebugged() to find >> out if a specific function is flagged for debugging, but is there a way to >> list all the functions that are flagged for debugging? > > No, R doesn't keep any master list, it sets a flag in each one. So you > could iterate over all visible objects to find the ones that have the flag > set (and this is quite slow, there are a lot of places to look), but there > would always be the chance that one was hiding somewhere you didn't look. > > Duncan Murdoch > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how do you know which functions are being debugged?
On 10/23/2009 1:28 PM, Andrew Yee wrote: This is kind of a dumb question: I know you can use isdebugged() to find out if a specific function is flagged for debugging, but is there a way to list all the functions that are flagged for debugging? No, R doesn't keep any master list, it sets a flag in each one. So you could iterate over all visible objects to find the ones that have the flag set (and this is quite slow, there are a lot of places to look), but there would always be the chance that one was hiding somewhere you didn't look. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how do you know which functions are being debugged?
list all objects first; use a loop (explicitly or not) to check whether (1) your objects are functions (2) functions are debugged > f = function(x) x > g = 1 > x = ls() > debug(f) > sapply(x[sapply(x, function(i) is.function(get(i)))], isdebugged) f TRUE > undebug(f) > sapply(x[sapply(x, function(i) is.function(get(i)))], isdebugged) f FALSE Regards, Yihui -- Yihui Xie Phone: 515-294-6609 Web: http://yihui.name Department of Statistics, Iowa State University 3211 Snedecor Hall, Ames, IA On Fri, Oct 23, 2009 at 12:28 PM, Andrew Yee wrote: > This is kind of a dumb question: I know you can use isdebugged() to find > out if a specific function is flagged for debugging, but is there a way to > list all the functions that are flagged for debugging? > Thanks, > Andrew > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
