[Rd] Bug with `[<-.POSIXlt` on specific OSes
Martin Maechler
m@ech|er @end|ng |rom @t@t@m@th@ethz@ch
Wed Oct 12 10:17:28 CEST 2022
>>>>> Kurt Hornik
>>>>> on Tue, 11 Oct 2022 16:44:13 +0200 writes:
>>>>> Davis Vaughan writes:
>> I've got a bit more information about this one. It seems like it
>> (only? not sure) appears when `TZ = "UTC"`, which is why I didn't see
>> it before on my Mac, which defaults to `TZ = ""`. I think this is at
>> least explainable by the fact that those "optional" fields aren't
>> technically needed when the time zone is UTC.
> Exactly. Debugging `[<-.POSIlt` with
> x <- as.POSIXlt(as.POSIXct("2013-01-31", tz = "America/Chicago"))
> Sys.setenv(TZ = "UTC")
> x[1] <- NA
> shows we get into
> value <- unclass(as.POSIXlt(value))
> if (ici) {
> for (n in names(x)) names(x[[n]]) <- nms
> }
> for (n in names(x)) x[[n]][i] <- value[[n]]
> where
> Browse[2]> names(value)
> [1] "sec" "min" "hour" "mday" "mon" "year" "wday" "yday" "isdst"
> Browse[2]> names(x)
> [1] "sec" "min" "hour" "mday" "mon" "year" "wday" "yday"
> [9] "isdst" "zone" "gmtoff"
> Without having looked at the code, the docs say
> ‘zone’ (Optional.) The abbreviation for the time zone in force at
> that time: ‘""’ if unknown (but ‘""’ might also be used for
> UTC).
> ‘gmtoff’ (Optional.) The offset in seconds from GMT: positive
> values are East of the meridian. Usually ‘NA’ if unknown,
> but ‘0’ could mean unknown.
> so perhaps we should fill with the values for the unknown case?
> -k
Well,
I think you both know I'm in the midst of dealing with these
issues, to fix both
[.POSIXlt and
[<-.POSIXlt
Yes, one needs a way to not only "fill" the partially filled
entries but also to *normalize* out-of-range values
(say negative seconds, minutes > 60, etc)
All this is available in our C code, but not on the R level,
so yesterday, I wrote a C function to be called via .Internal(.)
from a new R that provides this.
Provisionally called
balancePOXIXlt()
because it both balances the 9 to 11 list-components of POSIXlt
and it also puts all numbers of (sec, min, hour, mday, mon)
into a correct range (and also computes correctl wday and yday numbers).
but I'm happy for proposals of better names.
I had contemplated validatePOSIXlt() as alternative, but then
dismissed that as in some sense we now do agree that
"imbalanced" POSIXlt's are not really invalid ..
.. and yes, to Davis: Even though I've spent so many hours with
POSIXlt, POSIXct and Date during the last week, I'm still
surprised more often than I like by the effects of timezone
settings there.
Martin
>> I can reproduce this now on my personal Mac:
>> ```
>> x <- as.POSIXlt(as.POSIXct("2013-01-31", tz = "America/Chicago"))
>> Sys.setenv(TZ = "")
>> x[1] <- NA
>> x
>> #> [1] NA
>> x <- as.POSIXlt(as.POSIXct("2013-01-31", tz = "America/Chicago"))
>> Sys.setenv(TZ = "America/New_York")
>> x[1] <- NA
>> x
>> #> [1] NA
>> x <- as.POSIXlt(as.POSIXct("2013-01-31", tz = "America/Chicago"))
>> Sys.setenv(TZ = "UTC")
>> x[1] <- NA
>> #> Error in x[[n]][i] <- value[[n]] : replacement has length zero
>> x
>> #> [1] "2013-01-31 CST"
>> ```
>> Here are `sessionInfo()` and `Sys.getenv("TZ")` outputs for 3 GitHub
>> Actions platforms where the bug exists (note they all set `TZ = "UTC"`!):
>> Linux:
>> ```
>>> sessionInfo()
>> R version 4.2.1 (2022-06-23)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 18.04.6 LTS
>> Matrix products: default
>> BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
>> LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
>> locale:
>> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
>> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
>> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
>> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>> loaded via a namespace (and not attached):
>> [1] compiler_4.2.1
>>> Sys.getenv("TZ")
>> [1] "UTC"
>> ```
>> Mac:
>> ```
>>> sessionInfo()
>> R version 4.2.1 (2022-06-23)
>> Platform: x86_64-apple-darwin17.0 (64-bit)
>> Running under: macOS Big Sur ... 10.16
>> Matrix products: default
>> BLAS:
>> /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
>> LAPACK:
>> /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>> loaded via a namespace (and not attached):
>> [1] compiler_4.2.1
>>> Sys.getenv("TZ")
>> [1] "UTC"
>> ```
>> Windows:
>> This is the best I can get you, sorry (remote worker issues), but note that
>> it does also say `tz UTC` like the others.
>> ```
>> version R version 4.2.1 (2022-06-23 ucrt)
>> os Windows Server x64 (build 20348)
>> system x86_64, mingw32
>> ui RTerm
>> language (EN)
>> collate English_United States.utf8
>> ctype English_United States.utf8
>> tz UTC
>> date 2022-10-11
>> ```
>> And here is my Mac where the bug doesn't show up by default because `TZ =
>> ""`:
>> ```
>>> sessionInfo()
>> R version 4.2.1 (2022-06-23)
>> Platform: x86_64-apple-darwin17.0 (64-bit)
>> Running under: macOS Big Sur ... 10.16
>> Matrix products: default
>> BLAS:
>> /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
>> LAPACK:
>> /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>> loaded via a namespace (and not attached):
>> [1] compiler_4.2.1
>>> Sys.getenv("TZ")
>> [1] ""
>>> Sys.timezone()
>> [1] "America/New_York"
>> ```
>> -Davis
>> On Thu, Oct 6, 2022 at 9:33 AM Davis Vaughan <davis using rstudio.com> wrote:
>>> Hi all,
>>>
>>> I have found another POSIXlt bug while I've been fiddling around with it.
>>> This one only appears on specific OSes, because it has to do with the fact
>>> that the `gmtoff` field is optional, and isn't always used on all OSes. It
>>> also doesn't seem to be specific to r-devel, I think it has been there
>>> awhile.
>>>
>>> Here is the bug:
>>>
>>> ```
>>> x <- as.POSIXlt(as.POSIXct("2013-01-31", tz = "America/Chicago"))
>>>
>>> # Oh no!
>>> x[1] <- NA
>>> #> Error in x[[n]][i] <- value[[n]] : replacement has length zero
>>> ```
>>>
>>> If you look at the objects, you can see that `x` has a `gmtoff` field, but
>>> `NA` (when converted to POSIXlt, which is what `[<-.POSIXlt` does) does not:
>>>
>>> ```
>>> unclass(x)
>>> #> $sec
>>> #> [1] 0
>>> #>
>>> #> $min
>>> #> [1] 0
>>> #>
>>> #> $hour
>>> #> [1] 0
>>> #>
>>> #> $mday
>>> #> [1] 31
>>> #>
>>> #> $mon
>>> #> [1] 0
>>> #>
>>> #> $year
>>> #> [1] 113
>>> #>
>>> #> $wday
>>> #> [1] 4
>>> #>
>>> #> $yday
>>> #> [1] 30
>>> #>
>>> #> $isdst
>>> #> [1] 0
>>> #>
>>> #> $zone
>>> #> [1] "CST"
>>> #>
>>> #> $gmtoff
>>> #> [1] -21600
>>> #>
>>> #> attr(,"tzone")
>>> #> [1] "America/Chicago" "CST" "CDT"
>>>
>>> unclass(as.POSIXlt(NA))
>>> #> $sec
>>> #> [1] NA
>>> #>
>>> #> $min
>>> #> [1] NA
>>> #>
>>> #> $hour
>>> #> [1] NA
>>> #>
>>> #> $mday
>>> #> [1] NA
>>> #>
>>> #> $mon
>>> #> [1] NA
>>> #>
>>> #> $year
>>> #> [1] NA
>>> #>
>>> #> $wday
>>> #> [1] NA
>>> #>
>>> #> $yday
>>> #> [1] NA
>>> #>
>>> #> $isdst
>>> #> [1] -1
>>> #>
>>> #> attr(,"tzone")
>>> #> [1] "UTC"
>>> ```
>>>
>>> The problem seems to be that `[<-.POSIXlt` assumes that if the field was
>>> there in `x` then it must also be there in `value`:
>>>
>>> https://github.com/wch/r-source/blob/e10a971dee6a0ab851279c183cc21954d66b3be4/src/library/base/R/datetime.R#L1303-L1304
>>>
>>> But this isn't the case for the `NA` value that was converted to POSIXlt.
>>>
>>> I can't reproduce this on my personal Mac, but it affects the Linux, Mac,
>>> and Windows machines we use for the lubridate CI checks through GitHub
>>> Actions.
>>>
>>> Thanks,
>>> Davis
>>>
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