R devel - May 2019 - rbind has confusing result for custom sub-class (possible bug?)

On Sun, May 26, 2019 at 4:06 AM Michael Chirico
<michaelchirico4 at gmail.com> wrote:
>
> Have finally managed to come up with a fix after checking out sys.calls()
> from within the as.Date.IDate debugger, which shows something like:
>
> [[1]] rbind(DF, DF)
> [[2]] rbind(deparse.level, ...)
> [[3]] `[<-`(`*tmp*`, ri, value = 18042L)
> [[4]] `[<-.Date`(`*tmp*`, ri, value = 18042L)
> [[5]] as.Date(value)
> [[6]] as.Date.IDate(value)
>
> I'm not sure why [<- is called, I guess the implementation is to
assign to
> the output block by block? Anyway, we didn't have a [<- method. And
> [<-.Date looks like:
>
> value <- unclass(as.Date(value)) # <- converts to double
> .Date(NextMethod(.Generic), oldClass(x)) # <- restores 'IDate'
class
>
> So we can fix our bug by defining a [<- class; the question that I still
> don't see answered in documentation or source code is, why/where is
[<-
> called, exactly?
>
Your rbind(DF, DF) call dispatches to base::rbind.data.frame().  The
`[<-` call is this line:
value[[jj]][ri] <- if (is.factor(xij)) as.vector(xij) else xij

That's where the storage.mode changes from integer to double.

debug: value[[jj]][ri] <- if (is.factor(xij)) as.vector(xij) else xij
Browse[2]>
debug: xij
Browse[2]> storage.mode(xij)
[1] "integer"
Browse[2]> value[[jj]][ri]
[1] "2019-05-26"
Browse[2]> storage.mode(value[[jj]][ri])
[1] "integer"
Browse[2]>
debug: if (!is.null(nm <- names(xij))) names(value[[jj]])[ri] <- nm
Browse[2]> storage.mode(value[[jj]][ri])
[1] "double"

> Mike C
>
> On Sun, May 26, 2019 at 1:16 PM Michael Chirico <michaelchirico4 at
gmail.com>
> wrote:
>
> > Debugging this issue:
> >
> > https://github.com/Rdatatable/data.table/issues/2008
> >
> > We have custom class 'IDate' which inherits from
'Date' (it just forces
> > integer storage for efficiency, hence, I).
> >
> > The concatenation done by rbind, however, breaks this and returns a
double:
> >
> > library(data.table)
> > DF = data.frame(date = as.IDate(Sys.Date()))
> > storage.mode(rbind(DF, DF)$date)
> > # [1] "double"
> >
> > This is specific to base::rbind (data.table's rbind returns an
integer as
> > expected); in ?rbind we see:
> >
> > The method dispatching is not done via UseMethod(), but by C-internal
> > dispatching. Therefore there is no need for, e.g., rbind.default.
> > The dispatch algorithm is described in the source file
> > (?.../src/main/bind.c?) as
> > 1. For each argument we get the list of possible class memberships
from
> > the class attribute.
> > 2. *We inspect each class in turn to see if there is an applicable
> > method.*
> > 3. If we find an applicable method we make sure that it is identical
to
> > any method determined for prior arguments. If it is identical, we
proceed,
> > otherwise we immediately drop through to the default code.
> >
> > It's not clear what #2 means -- an applicable method *for what*?
Glancing
> > at the source code would suggest it's looking for rbind.IDate:
> >
> > https://github.com/wch/r-source/blob/trunk/src/main/bind.c#L1051-L1063
> >
> > const char *generic = ((PRIMVAL(op) == 1) ? "cbind" :
"rbind"); // should
> > be rbind here
> > const char *s = translateChar(STRING_ELT(classlist, i)); // iterating
over
> > the classes, should get to IDate first
> > sprintf(buf, "%s.%s", generic, s); // should be rbind.IDate
> >
> > but adding this method (or even exporting it) is no help [ simply
defining
> > rbind.IDate = function(...) as.IDate(NextMethod()) ]
> >
> > Lastly, it appears that as.Date.IDate is called, which is causing the
type
> > conversion:
> >
> > debug(data.table:::as.Date.IDate)
> > rbind(DF, DF) # launches debugger
> > x
> > # [1] "2019-05-26" <-- singleton, so apparently applied
to DF$date, not
> > c(DF$date, DF$date)
> > undebug(data.table:::as.Date.IDate)
> >
> > I can't really wrap my head around why as.Date is being called
here, and
> > even allowing that, why the end result is still the original class [
> > class(rbind(DF, DF)$date) == c('IDate', 'Date') ]
> >
> > So, I'm beginning to think this might be a bug. Am I missing
something?
> >
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


-- 
Joshua Ulrich  |  about.me/joshuaulrich
FOSS Trading  |  www.fosstrading.com
R/Finance 2019 | www.rinfinance.com

On Sun, May 26, 2019 at 6:47 AM Joshua Ulrich <josh.m.ulrich at gmail.com>
wrote:
>
> On Sun, May 26, 2019 at 4:06 AM Michael Chirico
> <michaelchirico4 at gmail.com> wrote:
> >
> > Have finally managed to come up with a fix after checking out
sys.calls()
> > from within the as.Date.IDate debugger, which shows something like:
> >
> > [[1]] rbind(DF, DF)
> > [[2]] rbind(deparse.level, ...)
> > [[3]] `[<-`(`*tmp*`, ri, value = 18042L)
> > [[4]] `[<-.Date`(`*tmp*`, ri, value = 18042L)
> > [[5]] as.Date(value)
> > [[6]] as.Date.IDate(value)
> >
> > I'm not sure why [<- is called, I guess the implementation is
to assign to
> > the output block by block? Anyway, we didn't have a [<- method.
And
> > [<-.Date looks like:
> >
> > value <- unclass(as.Date(value)) # <- converts to double
> > .Date(NextMethod(.Generic), oldClass(x)) # <- restores
'IDate' class
> >
> > So we can fix our bug by defining a [<- class; the question that I
still
> > don't see answered in documentation or source code is, why/where
is [<-
> > called, exactly?
> >
> Your rbind(DF, DF) call dispatches to base::rbind.data.frame().  The
> `[<-` call is this line:
> value[[jj]][ri] <- if (is.factor(xij)) as.vector(xij) else xij
>
> That's where the storage.mode changes from integer to double.
>
> debug: value[[jj]][ri] <- if (is.factor(xij)) as.vector(xij) else xij
> Browse[2]>
> debug: xij
> Browse[2]> storage.mode(xij)
> [1] "integer"
> Browse[2]> value[[jj]][ri]
> [1] "2019-05-26"
> Browse[2]> storage.mode(value[[jj]][ri])
> [1] "integer"
> Browse[2]>
> debug: if (!is.null(nm <- names(xij))) names(value[[jj]])[ri] <- nm
> Browse[2]> storage.mode(value[[jj]][ri])
> [1] "double"
>
To be clear, I don't think this is a bug in rbind() or
rbind.data.frame().  The confusion is that rbind.data.frame() calls
`[<-` for each column of the data.frame, and there is no `[<-.IDate`
method.  So the parent class method is dispatched, which converts the
storage mode to double.

Someone may argue that this is an issue with `[<-.Date`, and that it
shouldn't convert the storage.mode from integer to
double.
>
> > Mike C
> >
> > On Sun, May 26, 2019 at 1:16 PM Michael Chirico <michaelchirico4 at
gmail.com>
> > wrote:
> >
> > > Debugging this issue:
> > >
> > > https://github.com/Rdatatable/data.table/issues/2008
> > >
> > > We have custom class 'IDate' which inherits from
'Date' (it just forces
> > > integer storage for efficiency, hence, I).
> > >
> > > The concatenation done by rbind, however, breaks this and returns
a double:
> > >
> > > library(data.table)
> > > DF = data.frame(date = as.IDate(Sys.Date()))
> > > storage.mode(rbind(DF, DF)$date)
> > > # [1] "double"
> > >
> > > This is specific to base::rbind (data.table's rbind returns
an integer as
> > > expected); in ?rbind we see:
> > >
> > > The method dispatching is not done via UseMethod(), but by
C-internal
> > > dispatching. Therefore there is no need for, e.g., rbind.default.
> > > The dispatch algorithm is described in the source file
> > > (?.../src/main/bind.c?) as
> > > 1. For each argument we get the list of possible class
memberships from
> > > the class attribute.
> > > 2. *We inspect each class in turn to see if there is an
applicable
> > > method.*
> > > 3. If we find an applicable method we make sure that it is
identical to
> > > any method determined for prior arguments. If it is identical, we
proceed,
> > > otherwise we immediately drop through to the default code.
> > >
> > > It's not clear what #2 means -- an applicable method *for
what*? Glancing
> > > at the source code would suggest it's looking for
rbind.IDate:
> > >
> > >
https://github.com/wch/r-source/blob/trunk/src/main/bind.c#L1051-L1063
> > >
> > > const char *generic = ((PRIMVAL(op) == 1) ? "cbind" :
"rbind"); // should
> > > be rbind here
> > > const char *s = translateChar(STRING_ELT(classlist, i)); //
iterating over
> > > the classes, should get to IDate first
> > > sprintf(buf, "%s.%s", generic, s); // should be
rbind.IDate
> > >
> > > but adding this method (or even exporting it) is no help [ simply
defining
> > > rbind.IDate = function(...) as.IDate(NextMethod()) ]
> > >
> > > Lastly, it appears that as.Date.IDate is called, which is causing
the type
> > > conversion:
> > >
> > > debug(data.table:::as.Date.IDate)
> > > rbind(DF, DF) # launches debugger
> > > x
> > > # [1] "2019-05-26" <-- singleton, so apparently
applied to DF$date, not
> > > c(DF$date, DF$date)
> > > undebug(data.table:::as.Date.IDate)
> > >
> > > I can't really wrap my head around why as.Date is being
called here, and
> > > even allowing that, why the end result is still the original
class [
> > > class(rbind(DF, DF)$date) == c('IDate', 'Date') ]
> > >
> > > So, I'm beginning to think this might be a bug. Am I missing
something?
> > >
> >
> >         [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
>
> --
> Joshua Ulrich  |  about.me/joshuaulrich
> FOSS Trading  |  www.fosstrading.com
> R/Finance 2019 | www.rinfinance.com


-- 
Joshua Ulrich  |  about.me/joshuaulrich
FOSS Trading  |  www.fosstrading.com
R/Finance 2019 | www.rinfinance.com

Yes, thanks for following up on thread here. And thanks again for clearing
things up, your email was a finger snap of clarity on the whole issue.

I'll add that actually it was data.table's code at fault on the storage
conversion -- note that if you use an arbitrary sub-class 'foo' with no
methods defined, it'll stay integer.

That's because [<- calls as.Date and then as.Date.IDate, and that method
(ours) has as.numeric(); earlier I had recognized that if we commented that
line, the issue was "fixed" but I still wasn't understanding the
root cause.

My last curiosity on this issue will be in my follow-up thread.

Mike C

On Mon, May 27, 2019, 10:25 PM Joshua Ulrich <josh.m.ulrich at gmail.com>
wrote:
> On Sun, May 26, 2019 at 6:47 AM Joshua Ulrich <josh.m.ulrich at
gmail.com>
> wrote:
> >
> > On Sun, May 26, 2019 at 4:06 AM Michael Chirico
> > <michaelchirico4 at gmail.com> wrote:
> > >
> > > Have finally managed to come up with a fix after checking out
> sys.calls()
> > > from within the as.Date.IDate debugger, which shows something
like:
> > >
> > > [[1]] rbind(DF, DF)
> > > [[2]] rbind(deparse.level, ...)
> > > [[3]] `[<-`(`*tmp*`, ri, value = 18042L)
> > > [[4]] `[<-.Date`(`*tmp*`, ri, value = 18042L)
> > > [[5]] as.Date(value)
> > > [[6]] as.Date.IDate(value)
> > >
> > > I'm not sure why [<- is called, I guess the implementation
is to
> assign to
> > > the output block by block? Anyway, we didn't have a [<-
method. And
> > > [<-.Date looks like:
> > >
> > > value <- unclass(as.Date(value)) # <- converts to double
> > > .Date(NextMethod(.Generic), oldClass(x)) # <- restores
'IDate' class
> > >
> > > So we can fix our bug by defining a [<- class; the question
that I
> still
> > > don't see answered in documentation or source code is,
why/where is [<-
> > > called, exactly?
> > >
> > Your rbind(DF, DF) call dispatches to base::rbind.data.frame().  The
> > `[<-` call is this line:
> > value[[jj]][ri] <- if (is.factor(xij)) as.vector(xij) else xij
> >
> > That's where the storage.mode changes from integer to double.
> >
> > debug: value[[jj]][ri] <- if (is.factor(xij)) as.vector(xij) else
xij
> > Browse[2]>
> > debug: xij
> > Browse[2]> storage.mode(xij)
> > [1] "integer"
> > Browse[2]> value[[jj]][ri]
> > [1] "2019-05-26"
> > Browse[2]> storage.mode(value[[jj]][ri])
> > [1] "integer"
> > Browse[2]>
> > debug: if (!is.null(nm <- names(xij))) names(value[[jj]])[ri] <-
nm
> > Browse[2]> storage.mode(value[[jj]][ri])
> > [1] "double"
> >
> To be clear, I don't think this is a bug in rbind() or
> rbind.data.frame().  The confusion is that rbind.data.frame() calls
> `[<-` for each column of the data.frame, and there is no `[<-.IDate`
> method.  So the parent class method is dispatched, which converts the
> storage mode to double.
>
> Someone may argue that this is an issue with `[<-.Date`, and that it
> shouldn't convert the storage.mode from integer to double.
> >
> > > Mike C
> > >
> > > On Sun, May 26, 2019 at 1:16 PM Michael Chirico <
> michaelchirico4 at gmail.com>
> > > wrote:
> > >
> > > > Debugging this issue:
> > > >
> > > > https://github.com/Rdatatable/data.table/issues/2008
> > > >
> > > > We have custom class 'IDate' which inherits from
'Date' (it just
> forces
> > > > integer storage for efficiency, hence, I).
> > > >
> > > > The concatenation done by rbind, however, breaks this and
returns a
> double:
> > > >
> > > > library(data.table)
> > > > DF = data.frame(date = as.IDate(Sys.Date()))
> > > > storage.mode(rbind(DF, DF)$date)
> > > > # [1] "double"
> > > >
> > > > This is specific to base::rbind (data.table's rbind
returns an
> integer as
> > > > expected); in ?rbind we see:
> > > >
> > > > The method dispatching is not done via UseMethod(), but by
C-internal
> > > > dispatching. Therefore there is no need for, e.g.,
rbind.default.
> > > > The dispatch algorithm is described in the source file
> > > > (?.../src/main/bind.c?) as
> > > > 1. For each argument we get the list of possible class
memberships
> from
> > > > the class attribute.
> > > > 2. *We inspect each class in turn to see if there is an
applicable
> > > > method.*
> > > > 3. If we find an applicable method we make sure that it is
identical
> to
> > > > any method determined for prior arguments. If it is
identical, we
> proceed,
> > > > otherwise we immediately drop through to the default code.
> > > >
> > > > It's not clear what #2 means -- an applicable method
*for what*?
> Glancing
> > > > at the source code would suggest it's looking for
rbind.IDate:
> > > >
> > > >
> https://github.com/wch/r-source/blob/trunk/src/main/bind.c#L1051-L1063
> > > >
> > > > const char *generic = ((PRIMVAL(op) == 1) ?
"cbind" : "rbind"); //
> should
> > > > be rbind here
> > > > const char *s = translateChar(STRING_ELT(classlist, i)); //
> iterating over
> > > > the classes, should get to IDate first
> > > > sprintf(buf, "%s.%s", generic, s); // should be
rbind.IDate
> > > >
> > > > but adding this method (or even exporting it) is no help [
simply
> defining
> > > > rbind.IDate = function(...) as.IDate(NextMethod()) ]
> > > >
> > > > Lastly, it appears that as.Date.IDate is called, which is
causing
> the type
> > > > conversion:
> > > >
> > > > debug(data.table:::as.Date.IDate)
> > > > rbind(DF, DF) # launches debugger
> > > > x
> > > > # [1] "2019-05-26" <-- singleton, so apparently
applied to DF$date,
> not
> > > > c(DF$date, DF$date)
> > > > undebug(data.table:::as.Date.IDate)
> > > >
> > > > I can't really wrap my head around why as.Date is being
called here,
> and
> > > > even allowing that, why the end result is still the original
class [
> > > > class(rbind(DF, DF)$date) == c('IDate',
'Date') ]
> > > >
> > > > So, I'm beginning to think this might be a bug. Am I
missing
> something?
> > > >
> > >
> > >         [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-devel at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >
> >
> > --
> > Joshua Ulrich  |  about.me/joshuaulrich
> > FOSS Trading  |  www.fosstrading.com
> > R/Finance 2019 | www.rinfinance.com
>
>
>
> --
> Joshua Ulrich  |  about.me/joshuaulrich
> FOSS Trading  |  www.fosstrading.com
> R/Finance 2019 | www.rinfinance.com
>
	[[alternative HTML version deleted]]