[datatable-help] mapply cannot modify in place when iterating over list of DTs
Matthew Dowle
mdowle at mdowle.plus.com
Fri Sep 20 20:18:44 CEST 2013
Does this sentence from the warning help?
" Also, in R<v3.1.0, list(DT1,DT2) copied the entire DT1 and DT2 (R's
list() used to copy named objects); please upgrade to R>=v3.1.0 if that
is biting. "
Matthew
On 20/09/13 19:01, Ricardo Saporta wrote:
> One warning per DT in the list
> (I added the line breaks)
> -Rick
> =============================================
> Warning messages:
>
> 1: In `[.data.table`(DT, , `:=`(c("Col3", "Col4"), list(C3, C4))) :
>
> Invalid .internal.selfref detected and fixed by taking a copy of the
> whole table so that := can add this new column by reference. At an
> earlier point, this data.table has been copied by R (or been created
> manually using structure() or similar). Avoid key<-, names<- and
> attr<- which in R currently (and oddly) may copy the whole data.table.
> Use set* syntax instead to avoid copying: ?set, ?setnames and
> ?setattr. Also, in R<v3.1.0, list(DT1,DT2) copied the entire DT1 and
> DT2 (R's list() used to copy named objects); please upgrade to
> R>=v3.1.0 if that is biting. If this message doesn't help, please
> report to datatable-help so the root cause can be fixed.
>
> 2: In `[.data.table`(DT, , `:=`(c("Col3", "Col4"), list(C3, C4))) :
>
> Invalid .internal.selfref detected and fixed by taking a copy of the
> whole table so that := can add this new column by reference. At an
> earlier point, this data.table has been copied by R (or been created
> manually using structure() or similar). Avoid key<-, names<- and
> attr<- which in R currently (and oddly) may copy the whole data.table.
> Use set* syntax instead to avoid copying: ?set, ?setnames and
> ?setattr. Also, in R<v3.1.0, list(DT1,DT2) copied the entire DT1 and
> DT2 (R's list() used to copy named objects); please upgrade to
> R>=v3.1.0 if that is biting. If this message doesn't help, please
> report to datatable-help so the root cause can be fixed.
> =============================================
>
>
>
>
> On Fri, Sep 20, 2013 at 12:49 PM, Matthew Dowle
> <mdowle at mdowle.plus.com <mailto:mdowle at mdowle.plus.com>> wrote:
>
>
> Hi,
>
> What's the warning?
>
> Matthew
>
>
>
> On 20/09/13 14:48, Ricardo Saporta wrote:
>> I've encountered the following issue iterating over a list of
>> data.tables.
>> The issue is only with mapply, not with lapply .
>>
>> Given a list of data.table's, mapply'ing over the list directly
>> cannot modify in place.
>>
>> Also if attempting to add a new column, we get an "Invalid
>> .internal.selfref" warning.
>> Modifying an existing column does not issue a warning, but still
>> fails to modify-in-place
>>
>> WORKAROUND:
>> ----------
>> The workaround is to iterate over an index to the list, then to
>> modify each data.table via list.of.DTs[[i]][ .. ]
>>
>> **Interestingly, this issue occurs with `mapply`, but not `lapply`.**
>>
>> EXAMPLE:
>> --------
>> # Given a list of DT's and two lists of vectors,
>> # we want to add the corresponding vectors as columns to the DT.
>>
>> ## ---------------- ##
>> ## SAMPLE DATA: ##
>> ## ---------------- ##
>> # list of data.tables
>> list.DT <- list(
>> DT1=data.table(Col1=111:115, Col2=121:125),
>> DT2=data.table(Col1=211:215, Col2=221:225)
>> )
>>
>> # lists of columns to add
>> list.Col3 <- list(131:135, 231:235)
>> list.Col4 <- list(141:145, 241:245)
>>
>>
>> ## ------------------------------------ ##
>> ## Iterating over the list elements ##
>> ## adding a new column ##
>> ## ------------------------------------ ##
>> ## Will issue warning and ##
>> ## will fail to modify in place ##
>> ## ------------------------------------ ##
>> mapply (
>> function(DT, C3, C4)
>> DT[, c("Col3", "Col4") := list(C3, C4)],
>> list.DT, # iterating over the list
>> list.Col3, list.Col4,
>> SIMPLIFY=FALSE
>> )
>>
>> ## Note the lack of change
>> list.DT
>>
>>
>> ## ------------------------------------ ##
>> ## Iterating over an index ##
>> ## ------------------------------------ ##
>> mapply (
>> function(i, C3, C4)
>> list.DT[[i]] [, c("Col3", "Col4") := list(C3, C4)],
>> seq(list.DT), # iterating over an index to the list
>> list.Col3, list.Col4,
>> SIMPLIFY=FALSE
>> )
>>
>> ## Note each DT _has_ been modified
>> list.DT
>>
>> ## ------------------------------------ ##
>> ## Iterating over the list elements ##
>> ## modifying existing column ##
>> ## ------------------------------------ ##
>> ## No warning issued, but ##
>> ## Will fail to modify in place ##
>> ## ------------------------------------ ##
>> mapply (
>> function(DT, C3, C4)
>> DT[, c("Col3", "Col4") := list(Col3*1e3, Col4*1e4)],
>>
>> list.DT, # iterating over the list
>> list.Col3, list.Col4,
>> SIMPLIFY=FALSE
>> )
>>
>> ## Note the lack of change (compare with output from `mapply`)
>> list.DT
>>
>> ## ------------------------------------ ##
>> ## ##
>> ## `lapply` works as expected. ##
>> ## ##
>> ## ------------------------------------ ##
>> ## NOW WITH lapply
>> lapply(list.DT,
>> function(DT)
>> DT[, newCol := LETTERS[1:5]]
>> )
>>
>> ## Note the new column:
>> list.DT
>>
>>
>>
>> # ========================== #
>>
>> ## NON-WORKAROUNDS ##
>> ##
>> ## I also tried all of the following alternatives
>> ## in hopes of being able to iterate over the list
>> ## directly, using `mapply`.
>> ## None of these worked.
>>
>> # (1) Creating the DTs First, then creating the list from them
>> DT1 <- data.table(Col1=111:115, Col2=121:125)
>> DT2 <- data.table(Col1=211:215, Col2=221:225)
>>
>> list.DT <- list(DT1=DT1,DT2=DT2 )
>>
>>
>> # (2) Same as 1, and using `copy()` in the call to `list()`
>> list.DT <- list(DT1=copy(DT1),
>> DT2=copy(DT2) )
>>
>> # (3) lapply'ing `copy` and then iterating over that list
>> list.DT <- lapply(list.DT, copy)
>>
>> # (4) Not naming the list elements
>> list.DT <- list(DT1, DT2)
>> # and tried
>> list.DT <- list(copy(DT1), copy(DT2))
>>
>> ## All of the above still failed to modify in place
>> ## (and also issued the same warning if trying to add a column)
>> ## when iterating using mapply
>>
>> mapply(function(DT, C3, C4)
>> DT[, c("Col3", "Col4") := list(C3, C4)],
>> list.DT, list.Col3, list.Col4,
>> SIMPLIFY=FALSE)
>>
>>
>> # ========================== #
>>
>>
>> Ricardo Saporta
>> Rutgers University, New Jersey
>> e: saporta at rutgers.edu <mailto:saporta at rutgers.edu>
>>
>>
>>
>> _______________________________________________
>> datatable-help mailing list
>> datatable-help at lists.r-forge.r-project.org <mailto:datatable-help at lists.r-forge.r-project.org>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/datatable-help/attachments/20130920/7c560937/attachment-0001.html>
More information about the datatable-help
mailing list