[R-pkg-devel] Error creating union class: object ‘.__C__compMatrix’ not found
renozao
renoz@o @end|ng |rom protonm@||@com
Wed Apr 29 19:16:41 CEST 2020
Thank you Martin,
Looks like the mMatrix class defined in Matrix is not exported in 3.6.3, maybe it is now exported in the current R-devel.
In this case I'd rather use a conditional import and definition.
I'll try that route.
Bests,
Renaud
Sent with ProtonMail Secure Email.
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Saturday, April 18, 2020 12:36 PM, Martin Maechler <maechler using stat.math.ethz.ch> wrote:
> > > > > > renozao
> > > > > > on Wed, 8 Apr 2020 16:19:59 +0000 writes:
>
> > Thank you William for the reproducible example.
>
> > Currently I using the following (same as in William's example):
>
> > setClassUnion("mMatrix", c("Matrix", "matrix"))
>
>
> > Martin, are the changes made in the union class handling affecting the way we should declare them?
>
> > Thank you.
>
> > Bests,
>
> > Renaud
>
>
> Thank you, Renaud, and Bill Dunlap.
>
> There is obviously a bit of a problem there, but it may well be
> "only" a problem in error handling.
>
> As Bill's trace(get, ..) shows, R tries to get
> "#HAS_DUPLICATE_CLASS_NAMES" which is indeed an indication of the problem:
>
> You are trying to REdefine a class union that already exists
> identically in the Matrix package:
> In the R-forge development version of 'Matrix', it is
> line 717 of Matrix/R/AllClass.R (and that will be close also
> in the CRAN version of Matrix).
>
> So at least for you, Renaud, the solution to the problem is easy:
> Just don't do what you should not do: What you want is already
> part of Matrix.... and after searching: It's been part of
> Matrix since ca. July 2012 ...
>
> -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> But yes, there's a buglet in the 'methods' package currently,
> which leads to a misleading error message
> (It's arguable if it should give an error which it did not previously;
> I think it would be quite a good idea to give at least a
> warning as you are masking class definition of the Matrix
> package which is in your search() path or at least among the
> loaded namespaces at this time).
>
> Best,
> Martin
>
> > ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
>
> > On Wednesday, April 8, 2020 11:19 AM, William Dunlap <wdunlap using tibco.com> wrote:
>
>
> >> Use trace() to get a bit more detail - .__C_compMatrix is looked for in the wrong environment with inherits=FALSE.
>
> >>
>
> >>> setClassUnion("mMatrix", c("Matrix", "matrix"))
>
> >> Tracing get(name, envir = env) on entry
>
> >> x=".AllMTable", envir="<environment: 0x21dcf10>", topenv="<environment: namespace:methods>", inherits=TRUE
>
> >> Tracing get(name, envir = env) on entry
>
> >> x=".MTable", envir="<environment: 0x2238cf0>", topenv="<environment: namespace:methods>", inherits=TRUE
>
> >> Tracing get(name, envir = env) on entry
>
> >> x=".AllMTable", envir="<environment: 0x21dcf10>", topenv="<environment: namespace:methods>", inherits=TRUE
>
> >> Tracing get("#HAS_DUPLICATE_CLASS_NAMES", envir = .classTable) on entry
>
> >> x="#HAS_DUPLICATE_CLASS_NAMES", envir="<environment: 0x2787710>", topenv="<environment: base>", inherits=TRUE
>
> >> Tracing get(name, envir = env) on entry
>
> >> x=".AllMTable", envir="<environment: 0x21dcf10>", topenv="<environment: namespace:methods>", inherits=TRUE
>
> >> Tracing get(name, envir = env) on entry
>
> >> x=".MTable", envir="<environment: 0x2238cf0>", topenv="<environment: namespace:methods>", inherits=TRUE
>
> >> Tracing get(name, envir = env) on entry
>
> >> x=".MTable", envir="<environment: 0x21dcf10>", topenv="<environment: namespace:methods>", inherits=TRUE
>
> >> Tracing get(".SigLength", envir = env) on entry
>
> >> x=".SigLength", envir="<environment: 0x21dcf10>", topenv="<environment: namespace:methods>", inherits=TRUE
>
> >> Tracing get(".SigLength", envir = env) on entry
>
> >> x=".SigLength", envir="<environment: 0x21dcf10>", topenv="<environment: namespace:methods>", inherits=TRUE
>
> >> Tracing get(name, envir = env) on entry
>
> >> x=".MTable", envir="<environment: 0x2238cf0>", topenv="<environment: namespace:methods>", inherits=TRUE
>
> >> Tracing get(".SigLength", envir = env) on entry
>
> >> x=".SigLength", envir="<environment: 0x2238cf0>", topenv="<environment: namespace:methods>", inherits=TRUE
>
> >> Tracing get(".SigLength", envir = env) on entry
>
> >> x=".SigLength", envir="<environment: 0x2238cf0>", topenv="<environment: namespace:methods>", inherits=TRUE
>
> >> Tracing get(cname, envir = cwhere, inherits = FALSE) on entry
>
> >> x=".__C__compMatrix", envir="<environment: R_GlobalEnv>", topenv="<environment: R_GlobalEnv>", inherits=FALSE
>
> >> Error in get(cname, envir = cwhere, inherits = FALSE) :
>
> >> object '.__C__compMatrix' not found
>
> >> ...
>
> >>
>
> >> Bill Dunlap
>
> >> TIBCO Software
>
> >> wdunlap tibco.com
>
> >>
>
> >> On Wed, Apr 8, 2020 at 7:52 AM William Dunlap <wdunlap using tibco.com> wrote:
>
> >>
>
> >>> % R-devel --vanilla --quiet
>
> >>>> library(Matrix)
>
> >>>> setClassUnion("mMatrix", c("Matrix", "matrix"))
>
> >>> Error in get(cname, envir = cwhere, inherits = FALSE) :
>
> >>> object '.__C__compMatrix' not found
>
> >>> Error in setClassUnion("mMatrix", c("Matrix", "matrix")) :
>
> >>> unable to create union class: could not set members "Matrix"
>
> >>>> sessionInfo()
>
> >>> R Under development (unstable) (2020-04-07 r78175)
>
> >>> Platform: x86_64-pc-linux-gnu (64-bit)
>
> >>> Running under: Ubuntu 16.04.6 LTS
>
> >>>
>
> >>> Matrix products: default
>
> >>> BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.18.so
>
> >>>
>
> >>> locale:
>
> >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>
> >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>
> >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>
> >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>
> >>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>
> >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> >>>
>
> >>> attached base packages:
>
> >>> [1] stats graphics grDevices utils datasets methods base
>
> >>>
>
> >>> other attached packages:
>
> >>> [1] Matrix_1.2-18
>
> >>>
>
> >>> loaded via a namespace (and not attached):
>
> >>> [1] compiler_4.1.0 grid_4.1.0 lattice_0.20-41
>
> >>>
>
> >>> Bill Dunlap
>
> >>> TIBCO Software
>
> >>> wdunlap tibco.com
>
> >>>
>
> >>> On Wed, Apr 8, 2020 at 7:35 AM Martin Maechler <maechler using stat.math.ethz.ch> wrote:
>
> >>>
>
> >>>>>>>>> renozao
>
> >>>>>>>>> on Mon, 30 Mar 2020 21:20:43 +0000 writes:
>
> >>>>
>
> >>>> > Hi,
>
> >>>> > when R CMD check is run under R-devel (2020-03-29 r78108) I get the following error at installation:
>
> >>>>
>
> >>>> > Error in get(cname, envir = cwhere, inherits = FALSE) :
>
> >>>> > object ‘.__C__compMatrix’ not found
>
> >>>> > Error in setClassUnion("mMatrix", c("Matrix", "matrix")) :
>
> >>>> > unable to create union class: could not set members "Matrix"
>
> >>>>
>
> >>>> > This does not happen on R 3.6.3.
>
> >>>>
>
> >>>> > I tried with Matrix listed in Depends but I still get the same error.
>
> >>>>
>
> >>>> > Is this linked to some changes in union classes or the Matrix package?
>
> >>>>
>
> >>>> > Thank you.
>
> >>>>
>
> >>>> > Bests,
>
> >>>> > Renaud
>
> >>>>
>
> >>>> Hi Renaud,
>
> >>>> One reason you got no response here, is because we don't even
>
> >>>> know about which package you are talking.
>
> >>>>
>
> >>>> So there's nothing, anybody can reproduce from your posting.
>
> >>>>
>
> >>>> There have been changes in R's dealing with class unions etc,
>
> >>>> notably even *relating* to an earlier bug report on class unions
>
> >>>> exactly for such a case which was *triggered* when people built
>
> >>>> on such Matrix classes.
>
> >>>>
>
> >>>> But we would really want to be able to reproduce what you are seeing..
>
> >>>>
>
> >>>> Best regards,
>
> >>>> Martin Maechler
>
> >>>>
>
> >>>> ETH Zurich, R Core Team *and* maintainer("Matrix")
>
> >>>>
>
> >>>> ______________________________________________
>
> >>>> R-package-devel using r-project.org mailing list
>
> >>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> > [[alternative HTML version deleted]]
>
>
> > ______________________________________________
>
> > R-package-devel using r-project.org mailing list
>
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
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