R devel - Aug 2020 - M[cbind()] <- assignment with Matrix object loses attributes

? Does this constitute a bug, or is there something I'm missing? 
assigning sub-elements of a sparse Matrix via M[X]<-..., where X is a 
2-column matrix, appears to drop user-assigned attributes. I dug around 
in the R code for Matrix trying to find the relevant machinery but my 
brain started to hurt too badly ...

 ?? Will submit this as a bug if it seems warranted.

library(Matrix)
m1 <- matrix(1:9,3,3)
m1 <- Matrix(m1)
attr(m1,"junk") <- 12
stopifnot(isTRUE(attr(m1,"junk")==12))? ## OK
m1[cbind(1:2,2:3)] <- 1
stopifnot(isTRUE(attr(m1,"junk")==12)) ## not OK
attr(m1,"junk") ## NULL


## note I have to use the ugly stopifnot(isTRUE(...)) because a missing 
attribute returns NULL, an assignment to NULL returns NULL, and 
stopifnot(NULL) doesn't stop ...


 ?? cheers

 ???? Ben Bolker

Hi Ben,

I had some problems reproducing this.
As far as I can tell *all* indexed assignments drop attributes.
(Maybe we have different versions).

I'm not an expert on S4, but I'm unenthusiastic about mixing slot (S4)
semantics with attribute (S3) semantics.
And str() excludes attributes, but attributes() includes slots.
Highlighting the problems here...

I think R should generate an error or a warning, if a user tries to
assign attributes to S4 objects.

In saying that, mixing OO design with numerical linear algebra is a gold mine...


On Tue, Aug 11, 2020 at 1:23 PM Ben Bolker <bbolker at gmail.com>
wrote:
>
>    Does this constitute a bug, or is there something I'm missing?
> assigning sub-elements of a sparse Matrix via M[X]<-..., where X is a
> 2-column matrix, appears to drop user-assigned attributes. I dug around
> in the R code for Matrix trying to find the relevant machinery but my
> brain started to hurt too badly ...
>
>     Will submit this as a bug if it seems warranted.
>
> library(Matrix)
> m1 <- matrix(1:9,3,3)
> m1 <- Matrix(m1)
> attr(m1,"junk") <- 12
> stopifnot(isTRUE(attr(m1,"junk")==12))  ## OK
> m1[cbind(1:2,2:3)] <- 1
> stopifnot(isTRUE(attr(m1,"junk")==12)) ## not OK
> attr(m1,"junk") ## NULL
>
>
> ## note I have to use the ugly stopifnot(isTRUE(...)) because a missing
> attribute returns NULL, an assignment to NULL returns NULL, and
> stopifnot(NULL) doesn't stop ...
>
>
>     cheers
>
>       Ben Bolker
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

Thanks for taking a look!

    Hmm, really?  In `R Under development (unstable) (2020-08-14 
r79020)`, doing the indexed assignment with a regular matrix (as opposed 
to a Matrix) appears to preserve attributes.

m1 <- matrix(1:9,3,3)
attr(m1,"junk") <- 12
stopifnot(isTRUE(attr(m1,"junk")==12)) ## OK
m1[cbind(1:2,2:3)] <- 1
stopifnot(isTRUE(attr(m1,"junk")==12)) ## OK
attr(m1,"junk")  ## 12

    Do you lose attributes with this code? It would surprise me if this 
had changed in recent versions but I guess anything's possible ...

On 8/22/20 3:36 AM, Abby Spurdle wrote:
> Hi Ben,
> 
> I had some problems reproducing this.
> As far as I can tell *all* indexed assignments drop attributes.
> (Maybe we have different versions).
> 
> I'm not an expert on S4, but I'm unenthusiastic about mixing slot
(S4)
> semantics with attribute (S3) semantics.
> And str() excludes attributes, but attributes() includes slots.
> Highlighting the problems here...
> 
> I think R should generate an error or a warning, if a user tries to
> assign attributes to S4 objects.
> 
> In saying that, mixing OO design with numerical linear algebra is a gold
mine...
> 
> 
> On Tue, Aug 11, 2020 at 1:23 PM Ben Bolker <bbolker at gmail.com>
wrote:
>>
>>     Does this constitute a bug, or is there something I'm missing?
>> assigning sub-elements of a sparse Matrix via M[X]<-..., where X is
a
>> 2-column matrix, appears to drop user-assigned attributes. I dug around
>> in the R code for Matrix trying to find the relevant machinery but my
>> brain started to hurt too badly ...
>>
>>      Will submit this as a bug if it seems warranted.
>>
>> library(Matrix)
>> m1 <- matrix(1:9,3,3)
>> m1 <- Matrix(m1)
>> attr(m1,"junk") <- 12
>> stopifnot(isTRUE(attr(m1,"junk")==12))  ## OK
>> m1[cbind(1:2,2:3)] <- 1
>> stopifnot(isTRUE(attr(m1,"junk")==12)) ## not OK
>> attr(m1,"junk") ## NULL
>>
>>
>> ## note I have to use the ugly stopifnot(isTRUE(...)) because a missing
>> attribute returns NULL, an assignment to NULL returns NULL, and
>> stopifnot(NULL) doesn't stop ...
>>
>>
>>      cheers
>>
>>        Ben Bolker
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel