R devel - Jun 2017 - sum() returns NA on a long *logical* vector when nb of TRUE values exceeds 2^31

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

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

>>>>> Herv? Pag?s <hpages at fredhutch.org>
>>>>>     on Fri, 2 Jun 2017 04:05:15 -0700 writes:
    > 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.

This sounds very reasonable,  thank you Herv?, for the report,
and even more for a (small) patch.

Martin

    > Cheers, H.

    > -- 
    > Herv? Pag?s

    > Program in Computational Biology Division of Public Health
    > Sciences Fred Hutchinson Cancer Research Center 1100
    > Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA
    > 98109-1024

    > E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax:
    > (206) 667-1319

    > ______________________________________________
    > R-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-devel

>>>>> Martin Maechler <maechler at stat.math.ethz.ch>
>>>>>     on Tue, 6 Jun 2017 09:45:44 +0200 writes:
>>>>> Herv? Pag?s <hpages at fredhutch.org>
>>>>>     on Fri, 2 Jun 2017 04:05:15 -0700 writes:
    >> 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.

    > This sounds very reasonable, thank you Herv?, for the
    > report, and even more for a (small) patch.

I was made aware of the fact, that R treats logical and
integer very often identically in the C code, and in general we
even mention that logicals are treated as 0/1/NA integers in
arithmetic.

For the present case that would mean that we should also
safe-guard against *integer* overflow in sum(.)  and that is
not something we have done / wanted to do in the past...  Speed
being one reason.

So this ends up being more delicate than I had thought at first,
because changing  sum(<logical>)  only would mean that

  sum(LOGI)   	  		  and
  sum(as.integer(LOGI))

would start differ for a logical vector LOGI.

So, for now this is something that must be approached carefully,
and the R Core team may want discuss "in private" first.

I'm sorry for having raised possibly unrealistic expectations.
Martin

    > Martin

    >> Cheers, H.

    >> -- 
    >> Herv? Pag?s

    >> Program in Computational Biology Division of Public
    >> Health Sciences Fred Hutchinson Cancer Research Center
    >> 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA
    >> 98109-1024

    >> E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax:
    >> (206) 667-1319

    >> ______________________________________________
    >> R-devel at r-project.org mailing list
    >> https://stat.ethz.ch/mailman/listinfo/r-devel

    > ______________________________________________
    > R-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-devel

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

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
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fredhutch.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel