Hi all,
I came across an issue in using the Matrix package which made it that I
could only subset Matrices using the numeric class, but could not using
integers. Steps to reproduce the problem:
library(Matrix)
# this class has *nothing* to do with Matrix
setClass("MyClass",
representation(myvalue = "numeric"),
prototype(myvalue = NA_real_))
# this class also has nothing to do with Matrix
setClassUnion("NumOrMyClass", c("numeric",
"MyClass"))
# this is to demonstrate creating and subsetting a specific Matrix
m <- new("dgCMatrix", i = c(2L, 0L, 1L, 2L, 0L, 1L), p = c(0L, 1L,
2L, 4L,
4L, 6L),
Dim = c(3L, 5L), Dimnames = list(NULL, NULL), x = c(2, 1, 2, 1, 2, 1),
factors = list())
# this next line fails:
m[1:2, 1:2]
The last line fails consistently with R 3.6.1 and Matrix 1.2-17 on a
variety of operating systems and computers (tested with ubuntu 19.10 &
windows 10). I'll note at this point that without the class union I defined
above, the rest of the code works perfectly fine.
There are 2 workarounds I've come up with. Firstly, one could change the
last line to
m[as.numeric(1:2), as.numeric(1:2)]
or as.numeric(seq()) or c(1, 2), etc.
The other workaround is to change setClassUnion("NumOrMyClass",
c("numeric", "MyClass")) to
setClassUnion("NumOrMyClass", c("numeric",
"double", "integer", "MyClass")), which I believe
should be the recommended
workaround here.
The underlying issue, though, is that I would not have expected *anything*
that I write to get in the way of Matrix; in fact, the classes that I
defined have nothing to do with Matrix at all. So, I have some fears that
this might be a bigger problem, possibly either in Methods or in Base.
1. Can others confirm that this is in fact an issue as I believe it to be?
2. If it is a legitimate issue, have others seen it manifested working with
other packages that are not Matrix? In this case, I believe that the class
union I defied is somehow interfering with the "index" class union in
Matrix, R/AllClass.R, line 809
3. Why should the class union I defined interfere with the inner workings
of a separate package?
4. Is this a bug in Base or Methods?
Thank you for your time!
Sincerely,
Ezra
[[alternative HTML version deleted]]
>>>>> Ezra Tucker >>>>> on Mon, 11 Nov 2019 21:47:41 +0000 writes:> Hi all, > > I came across an issue in using the Matrix package which made it that I > could only subset Matrices using the numeric class, but could not using > integers. Steps to reproduce the problem: > > library(Matrix) > > # this class has *nothing* to do with Matrix > setClass("MyClass", > representation(myvalue = "numeric"), > prototype(myvalue = NA_real_)) > # this class also has nothing to do with Matrix > setClassUnion("NumOrMyClass", c("numeric", "MyClass")) > > # this is to demonstrate creating and subsetting a specific Matrix > m <- new("dgCMatrix", i = c(2L, 0L, 1L, 2L, 0L, 1L), p = c(0L, 1L, 2L, 4L, > 4L, 6L), > Dim = c(3L, 5L), Dimnames = list(NULL, NULL), x = c(2, 1, 2, 1, 2, 1), > factors = list()) > # this next line fails: > m[1:2, 1:2] > > The last line fails consistently with R 3.6.1 and Matrix 1.2-17 on a > variety of operating systems and computers (tested with ubuntu 19.10 & > windows 10). I'll note at this point that without the class union I defined > above, the rest of the code works perfectly fine. > > There are 2 workarounds I've come up with. Firstly, one could change the > last line to > m[as.numeric(1:2), as.numeric(1:2)] > or as.numeric(seq()) or c(1, 2), etc. > > The other workaround is to change setClassUnion("NumOrMyClass", > c("numeric", "MyClass")) to setClassUnion("NumOrMyClass", c("numeric", > "double", "integer", "MyClass")), which I believe should be the recommended > workaround here. > > The underlying issue, though, is that I would not have expected *anything* > that I write to get in the way of Matrix; in fact, the classes that I > defined have nothing to do with Matrix at all. So, I have some fears that > this might be a bigger problem, possibly either in Methods or in Base. > > 1. Can others confirm that this is in fact an issue as I believe it to be?yes, others have confirmed this is an issue .. (unfortunately not in this R-devel thread). Thank you, Ezra, very much for your helpful report, including a simple reproducible example.> 2. If it is a legitimate issue, have others seen it manifested working with > other packages that are not Matrix? In this case, I believe that the class > union I defied is somehow interfering with the "index" class union in > Matrix, R/AllClass.R, line 809> 3. Why should the class union I defined interfere with the inner workings > of a separate package?There is no good reason ...> 4. Is this a bug in Base or Methods?This is a bug in "base R", in package 'methods'. The R core team had taken the issue up, already two weeks ago, but unfortunately did not get to address this in a definitive way. ==> I'll remind us about it ! Martin Maechler ETH Zurich and R Core> Thank you for your time! > > Sincerely, > Ezra
I've been working on this and will hopefully get a fix checked in today. On Wed, Nov 27, 2019 at 3:53 AM Martin Maechler <maechler at stat.math.ethz.ch> wrote:> > >>>>> Ezra Tucker > >>>>> on Mon, 11 Nov 2019 21:47:41 +0000 writes: > > > Hi all, > > > > I came across an issue in using the Matrix package which made it that I > > could only subset Matrices using the numeric class, but could not using > > integers. Steps to reproduce the problem: > > > > library(Matrix) > > > > # this class has *nothing* to do with Matrix > > setClass("MyClass", > > representation(myvalue = "numeric"), > > prototype(myvalue = NA_real_)) > > # this class also has nothing to do with Matrix > > setClassUnion("NumOrMyClass", c("numeric", "MyClass")) > > > > # this is to demonstrate creating and subsetting a specific Matrix > > m <- new("dgCMatrix", i = c(2L, 0L, 1L, 2L, 0L, 1L), p = c(0L, 1L, 2L, 4L, > > 4L, 6L), > > Dim = c(3L, 5L), Dimnames = list(NULL, NULL), x = c(2, 1, 2, 1, 2, 1), > > factors = list()) > > # this next line fails: > > m[1:2, 1:2] > > > > The last line fails consistently with R 3.6.1 and Matrix 1.2-17 on a > > variety of operating systems and computers (tested with ubuntu 19.10 & > > windows 10). I'll note at this point that without the class union I defined > > above, the rest of the code works perfectly fine. > > > > There are 2 workarounds I've come up with. Firstly, one could change the > > last line to > > m[as.numeric(1:2), as.numeric(1:2)] > > or as.numeric(seq()) or c(1, 2), etc. > > > > The other workaround is to change setClassUnion("NumOrMyClass", > > c("numeric", "MyClass")) to setClassUnion("NumOrMyClass", c("numeric", > > "double", "integer", "MyClass")), which I believe should be the recommended > > workaround here. > > > > The underlying issue, though, is that I would not have expected *anything* > > that I write to get in the way of Matrix; in fact, the classes that I > > defined have nothing to do with Matrix at all. So, I have some fears that > > this might be a bigger problem, possibly either in Methods or in Base. > > > > 1. Can others confirm that this is in fact an issue as I believe it to be? > > yes, others have confirmed this is an issue .. (unfortunately > not in this R-devel thread). > > Thank you, Ezra, very much for your helpful report, including a > simple reproducible example. > > > 2. If it is a legitimate issue, have others seen it manifested working with > > other packages that are not Matrix? In this case, I believe that the class > > union I defied is somehow interfering with the "index" class union in > > Matrix, R/AllClass.R, line 809 > > > 3. Why should the class union I defined interfere with the inner workings > > of a separate package? > > There is no good reason ... > > > 4. Is this a bug in Base or Methods? > > This is a bug in "base R", in package 'methods'. > > The R core team had taken the issue up, already two weeks ago, > but unfortunately did not get to address this in a definitive > way. ==> I'll remind us about it ! > > Martin Maechler > ETH Zurich and R Core > > > > Thank you for your time! > > > > Sincerely, > > Ezra > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel-- Michael Lawrence Senior Scientist, Bioinformatics and Computational Biology Genentech, A Member of the Roche Group Office +1 (650) 225-7760 michafla at gene.com Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube