conflicted does not shows conflict with base R function

[vasili111]

For example this code:

library(conflicted)

library(geepack)
library(PairedData)
library(Matrix)

timeorder <- rep(1:5, 6)
tvar <- timeorder + rnorm(length(timeorder))
idvar <- rep(1:6, each=5)
uuu <- rep(rnorm(6), each=5)
yvar <- 1 + 2*tvar + uuu + rnorm(length(tvar))
simdat <- data.frame(idvar, timeorder, tvar, yvar)

mod1 <- geeglm(yvar~tvar, id=idvar, data=simdat, corstr="ar1")

summary(mod1)

output:

Error: [conflicted] `summary` found in 2 packages.
Either pick the one you want with `::` 
* Matrix::summary
* PairedData::summary
Or declare a preference with `conflict_prefer()`
* conflict_prefer("summary", "Matrix")
* conflict_prefer("summary", "PairedData")

In fact there are 3 sammary functions here: base::summary, Matrix::summary and PairedData::summary. But only Matrix::summary and PairedData::summary are reported. Is it bug or there is any solution for it?

[hadley]

Minimal reprex:

library(conflicted)

library(PairedData)
#> Loading required package: MASS
#> Loading required package: gld
#> Loading required package: mvtnorm
#> Loading required package: lattice
#> Loading required package: ggplot2
library(Matrix)

summary
#> Error: [conflicted] `summary` found in 2 packages.
#> Either pick the one you want with `::` 
#> * Matrix::summary
#> * PairedData::summary
#> Or declare a preference with `conflict_prefer()`
#> * conflict_prefer("summary", "Matrix")
#> * conflict_prefer("summary", "PairedData")

^{Created on 2021-11-16 by the reprex package (v2.0.1)}

[hadley]

I think the issue here is that neither Matrix::summary nor PairedData::summary conflict with base::summary, but they conflict with each other.

[hadley]

Even more minimal reprex:

conflicted::conflict_scout(c("base", "PairedData", "Matrix"))
#> 37 conflicts:
#> * `all.equal`  : [Matrix]
#> * `as.array`   : [Matrix]
#> * `as.matrix`  : [Matrix]
#> * `chol`       : [Matrix]
#> * `chol2inv`   : base, Matrix
#> * `colMeans`   : [Matrix]
#> * `colSums`    : [Matrix]
#> * `crossprod`  : [Matrix]
#> * `determinant`: [Matrix]
#> * `diag`       : [Matrix]
#> * `diag<-`     : [Matrix]
#> * `diff`       : [Matrix]
#> * `drop`       : [Matrix]
#> * `format`     : [Matrix]
#> * `isSymmetric`: [Matrix]
#> * `mean`       : [Matrix]
#> * `norm`       : [Matrix]
#> * `plot`       : [PairedData]
#> * `print`      : [Matrix]
#> * `qr`         : [Matrix]
#> * `qr.coef`    : [Matrix]
#> * `qr.fitted`  : [Matrix]
#> * `qr.Q`       : [Matrix]
#> * `qr.qty`     : [Matrix]
#> * `qr.qy`      : [Matrix]
#> * `qr.R`       : [Matrix]
#> * `qr.resid`   : [Matrix]
#> * `rcond`      : base, Matrix
#> * `rowMeans`   : [Matrix]
#> * `rowSums`    : [Matrix]
#> * `solve`      : [Matrix]
#> * `summary`    : PairedData, Matrix
#> * `t`          : [Matrix]
#> * `tcrossprod` : [Matrix]
#> * `unname`     : [Matrix]
#> * `which`      : [Matrix]
#> * `zapsmall`   : [Matrix]

^{Created on 2021-11-25 by the reprex package (v2.0.1)}

Which reveals another problems with the superset handling

[hadley]

I think it should actually be this:

conflicted::conflict_scout(c("base", "PairedData", "Matrix"))
#> 3 conflicts:
#> * `chol2inv`: base, Matrix
#> * `rcond`   : base, Matrix
#> * `summary` : base, PairedData, Matrix

^{Created on 2021-11-25 by the reprex package (v2.0.1)}

And the first two aren't right either because Matrix's rcond and chol2inv are just S4 generic versions of the base functions so shouldn't technically be conflicts either

[hadley]

Now we get:

conflicted::conflict_scout(c("base", "PairedData", "Matrix"))
#> 1 conflict:
#> * `summary`: base, PairedData, Matrix

^{Created on 2021-11-25 by the reprex package (v2.0.1)}