[Rd] sum() returns NA on a long *logical* vector when nb of TRUE values exceeds 2^31
Martin Maechler
maechler at stat.math.ethz.ch
Sat Jan 27 12:06:25 CET 2018
>>>>> Henrik Bengtsson <henrik.bengtsson at gmail.com>
>>>>> on Thu, 25 Jan 2018 09:30:42 -0800 writes:
> Just following up on this old thread since matrixStats 0.53.0 is now
> out, which supports this use case:
>> x <- rep(TRUE, times = 2^31)
>> y <- sum(x)
>> y
> [1] NA
> Warning message:
> In sum(x) : integer overflow - use sum(as.numeric(.))
>> y <- matrixStats::sum2(x, mode = "double")
>> y
> [1] 2147483648
>> str(y)
> num 2.15e+09
> No coercion is taking place, so the memory overhead is zero:
>> profmem::profmem(y <- matrixStats::sum2(x, mode = "double"))
> Rprofmem memory profiling of:
> y <- matrixStats::sum2(x, mode = "double")
> Memory allocations:
> bytes calls
> total 0
> /Henrik
Thank you, Henrik, for the reminder.
Back in June, I had mentioned to Hervé and R-devel that
'logical' should remain to be treated as 'integer' as in all
arithmetic in (S and) R. Hervé did mention the isum()
function in the C code which is relevant here .. which does have
a LONG INT counter already -- *but* if we consider that sum()
has '...' i.e. a conceptually arbitrary number of long vector
integer arguments that counter won't suffice even there.
Before talking about implementation / patch, I think we should
consider 2 possible goals of a change --- I agree the status quo
is not a real option
1) sum(x) for logical and integer x would return a double
in any case and overflow should not happen (unless for
the case where the result would be larger the
.Machine$double.max which I think will not be possible
even with "arbitrary" nargs() of sum.
2) sum(x) for logical and integer x should return an integer in
all cases there is no overflow, including returning
NA_integer_ in case of NAs.
If there would be an overflow it must be detected "in time"
and the result should be double.
The big advantage of 2) is that it is back compatible in 99.x %
of use cases, and another advantage that it may be a very small
bit more efficient. Also, in the case of "counting" (logical),
it is nice to get an integer instead of double when we can --
entirely analogously to the behavior of length() which returns
integer whenever possible.
The advantage of 1) is uniformity.
We should (at least provisionally) decide between 1) and 2) and then go for that.
It could be that going for 1) may have bad
compatibility-consequences in package space, because indeed we
had documented sum() would be integer for logical and integer arguments.
I currently don't really have time to
{work on implementing + dealing with the consequences}
for either ..
Martin
> On Fri, Jun 2, 2017 at 1:58 PM, Henrik Bengtsson
> <henrik.bengtsson at gmail.com> wrote:
>> I second this feature request (it's understandable that this and
>> possibly other parts of the code was left behind / forgotten after the
>> introduction of long vector).
>>
>> I think mean() avoids full copies, so in the meanwhile, you can work
>> around this limitation using:
>>
>> countTRUE <- function(x, na.rm = FALSE) {
>> nx <- length(x)
>> if (nx < .Machine$integer.max) return(sum(x, na.rm = na.rm))
>> nx * mean(x, na.rm = na.rm)
>> }
>>
>> (not sure if one needs to worry about rounding errors, i.e. where n %% 0 != 0)
>>
>> x <- rep(TRUE, times = .Machine$integer.max+1)
>> object.size(x)
>> ## 8589934632 bytes
>>
>> p <- profmem::profmem( n <- countTRUE(x) )
>> str(n)
>> ## num 2.15e+09
>> print(n == .Machine$integer.max + 1)
>> ## [1] TRUE
>>
>> print(p)
>> ## Rprofmem memory profiling of:
>> ## n <- countTRUE(x)
>> ##
>> ## Memory allocations:
>> ## bytes calls
>> ## total 0
>>
>>
>> FYI / related: I've just updated matrixStats::sum2() to support
>> logicals (develop branch) and I'll also try to update
>> matrixStats::count() to count beyond .Machine$integer.max.
>>
>> /Henrik
>>
>> On Fri, Jun 2, 2017 at 4:05 AM, Hervé Pagès <hpages at fredhutch.org> wrote:
>>> Hi,
>>>
>>> I have a long numeric vector 'xx' and I want to use sum() to count
>>> the number of elements that satisfy some criteria like non-zero
>>> values or values lower than a certain threshold etc...
>>>
>>> The problem is: sum() returns an NA (with a warning) if the count
>>> is greater than 2^31. For example:
>>>
>>> > xx <- runif(3e9)
>>> > sum(xx < 0.9)
>>> [1] NA
>>> Warning message:
>>> In sum(xx < 0.9) : integer overflow - use sum(as.numeric(.))
>>>
>>> This already takes a long time and doing sum(as.numeric(.)) would
>>> take even longer and require allocation of 24Gb of memory just to
>>> store an intermediate numeric vector made of 0s and 1s. Plus, having
>>> to do sum(as.numeric(.)) every time I need to count things is not
>>> convenient and is easy to forget.
>>>
>>> It seems that sum() on a logical vector could be modified to return
>>> the count as a double when it cannot be represented as an integer.
>>> Note that length() already does this so that wouldn't create a
>>> precedent. Also and FWIW prod() avoids the problem by always returning
>>> a double, whatever the type of the input is (except on a complex
>>> vector).
>>>
>>> I can provide a patch if this change sounds reasonable.
>>>
>>> Cheers,
>>> H.
>>>
>>> --
>>> Hervé Pagès
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