From hpages at fredhutch.org  Tue Jan 30 22:30:18 2018
From: hpages at fredhutch.org (=?UTF-8?B?SGVydsOpIFBhZ8Oocw==?=)
Date: Tue, 30 Jan 2018 13:30:18 -0800
Subject: [Rd] sum() returns NA on a long *logical* vector when nb of
 TRUE values exceeds 2^31
In-Reply-To: <23148.23857.970768.727765@stat.math.ethz.ch>
References: <5931466B.1060407@fredhutch.org>
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 <CAFDcVCQv19O2zBybkRHh6G58AMa0GjQRZcHnD3WEnQACnuM7Uw@mail.gmail.com>
 <23148.23857.970768.727765@stat.math.ethz.ch>
Message-ID: <3d97d7d0-ef1b-90a7-ed1e-16af5461abc0@fredhutch.org>

Hi Martin, Henrik,

Thanks for the follow up.

@Martin: I vote for 2) without *any* hesitation :-)

(and uniformity could be restored at some point in the
future by having prod(), rowSums(), colSums(), and others
align with the behavior of length() and sum())

Cheers,
H.


On 01/27/2018 03:06 AM, Martin Maechler wrote:
>>>>>> 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 Herv? and R-devel that
> 'logical' should remain to be treated as 'integer' as in all
> arithmetic in (S and) R.     Herv? 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, Herv? Pag?s <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.
>      >>>
>      >>> --
>      >>> Herv? Pag?s
>      
> 

-- 
Herv? Pag?s

Program in Computational Biology
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[Rd] sum() returns NA on a long *logical* vector when nb of TRUE values exceeds 2^31
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