R devel - May 2020 - [External] Feature Request: User Prompt + Message First Execution when "Managing Search Path Conflicts"

Dear R Developers,

###
# Context:
###

When managing Search Path Conflicts (See:
https://developer.r-project.org/Blog/public/2019/03/19/managing-search-path-conflicts/index.html),
with:

options(conflicts.policy = "strict")

We get the following behaviour when loading a package (Eg: dplyr):

library(dplyr)
## Error: Conflicts attaching package ?dplyr?:
##
## The following objects are masked from ?package:stats?:
##
##     filter, lag
##
## The following objects are masked from ?package:base?:
##
##     intersect, setdiff, setequal, union

So we would have to solve the conflict by writing:

library(dplyr,
        mask.ok = c("filter", "lag",
                    "intersect", "setdiff",
"setequal",
                    "union"))

So my feature request proposals:

###
# Feature Request 1: Interactive Session
###

Would it be possible to raise an input prompt, which asks user for an
action to be taken as regards conflicts?

This would make the package loading process more dynamic when being
loaded for first time in an interactive session (Eg: R Notebook). An
example:

The first time the package is loaded:

options(conflicts.policy = "strict", conflicts.policy.ask = TRUE)

library(dplyr)

Executes iteratively the code, in order to ask the user for action
(See toy example):

opt <- readline(prompt="1: mask.ok; 2: exclude. Choose: ")

if (opt == "1"){

  txt <- sprintf(
    fmt = "conflictRules(pkg = '%s' , mask.ok =
'%s')",
    "package.name",
    "variable.name"
  )

  eval(parse(text = txt))

  message(txt)

} else if(opt == "2"){

  txt <- sprintf(
    fmt = "conflictRules(pkg = '%s' , exclude =
'%s')",
    "package.name",
    "variable.name"
  )

  eval(parse(text = txt))

  message(txt)

}

And afterwards, a message is printed with the selected
"conflictRules()" Configuration for the dynamic setup.

The user will only have to put the printed pre-configured
"conflictRules()" setup into his code, and when re-executing, the
input prompt asking for action will not be raised back again.

Such behaviour is similar in spirit to how 'conflicted' R package
works, which prints for example, for dplyr::filter :

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

Where the user will only have to copy "conflict_prefer("filter",
"dplyr")" and paste it into his script. The difference, is that
with:
options(conflicts.policy = "strict", conflicts.policy.ask = TRUE),
such message is printed at package load.

I would put the required code within the library() function with the
following conditional:
...
if (length(conflicts)) {
   if(getOption("conflicts.policy.ask") == TRUE){
      ...
   }
}
...

###
# Feature Request 2: Source Execution
###

Another alternative, which could apply when executing the .R file from
source, would be to suggest the user a default conflictRules() setup:

options(conflicts.policy = "strict")
library(dplyr)

# Error: Conflicts attaching package ?dplyr?:
#
# The following objects are masked from ?package:stats?:
#
#     filter, lag
#
# The following objects are masked from ?package:base?:
#
#     intersect, setdiff, setequal, union
#
# Declare preference with `conflictRules()` before loading:
#     * conflictRules("dplyr", mask.ok = list(stats = TRUE, base =
TRUE))
#     * conflictRules("dplyr", mask.ok = list(stats =
c("filter",
"lag"), base = c("intersect", "setdiff",
"setequal", "union")))
#     * conflictRules("dplyr", exclude = c("filter",
"lag",
"intersect", "setdiff", "setequal",
"union"))

In this case, the error message would have to be extended with
sensible suggested defaults.

Thanks,
Juan

You can get what you are asking for now in R 4.0.0 with
globalCallingHandlers and using the packageConflictError object that
is signaled. This should get you started:

```
options(conflicts.policy = "strict")

packageConflictError

handle_conflicts <- function(e) {
     cat(conditionMessage(e))
     opt <- readline(prompt="1: mask.ok; 2: exclude. Choose: ")
     if (opt == "1")
         conflictRules(e$package, mask.ok = as.character(unlist(e$conflicts)))
     else if (opt == "2")
         conflictRules(e$package, exclude = as.character(unlist(e$conflicts)))
     stop("unresolved conflicts") ## ideal invode a restart here
}

globalCallingHandlers(packageConflictError = handle_conflicts)

library(dplyr)
```

An IDE could provide a more sophisticated interface, like a dialog
allowing separate choices for each conflict. But this is best left up
to the IDE or the user.

The one addition to library that might be worth considering is to
provide a restart for the handler to invoke.

Best,

luke

On Wed, 20 May 2020, Juan Telleria Ruiz de Aguirre wrote:
> Dear R Developers,
>
> ###
> # Context:
> ###
>
> When managing Search Path Conflicts (See:
>
https://developer.r-project.org/Blog/public/2019/03/19/managing-search-path-conflicts/index.html),
> with:
>
> options(conflicts.policy = "strict")
>
> We get the following behaviour when loading a package (Eg: dplyr):
>
> library(dplyr)
> ## Error: Conflicts attaching package ?dplyr?:
> ##
> ## The following objects are masked from ?package:stats?:
> ##
> ##     filter, lag
> ##
> ## The following objects are masked from ?package:base?:
> ##
> ##     intersect, setdiff, setequal, union
>
> So we would have to solve the conflict by writing:
>
> library(dplyr,
>        mask.ok = c("filter", "lag",
>                    "intersect", "setdiff",
"setequal",
>                    "union"))
>
> So my feature request proposals:
>
> ###
> # Feature Request 1: Interactive Session
> ###
>
> Would it be possible to raise an input prompt, which asks user for an
> action to be taken as regards conflicts?
>
> This would make the package loading process more dynamic when being
> loaded for first time in an interactive session (Eg: R Notebook). An
> example:
>
> The first time the package is loaded:
>
> options(conflicts.policy = "strict", conflicts.policy.ask = TRUE)
>
> library(dplyr)
>
> Executes iteratively the code, in order to ask the user for action
> (See toy example):
>
> opt <- readline(prompt="1: mask.ok; 2: exclude. Choose: ")
>
> if (opt == "1"){
>
>  txt <- sprintf(
>    fmt = "conflictRules(pkg = '%s' , mask.ok =
'%s')",
>    "package.name",
>    "variable.name"
>  )
>
>  eval(parse(text = txt))
>
>  message(txt)
>
> } else if(opt == "2"){
>
>  txt <- sprintf(
>    fmt = "conflictRules(pkg = '%s' , exclude =
'%s')",
>    "package.name",
>    "variable.name"
>  )
>
>  eval(parse(text = txt))
>
>  message(txt)
>
> }
>
> And afterwards, a message is printed with the selected
> "conflictRules()" Configuration for the dynamic setup.
>
> The user will only have to put the printed pre-configured
> "conflictRules()" setup into his code, and when re-executing, the
> input prompt asking for action will not be raised back again.
>
> Such behaviour is similar in spirit to how 'conflicted' R package
> works, which prints for example, for dplyr::filter :
>
> Error: [conflicted] `filter` found in 2 packages.
> Either pick the one you want with `::`
> * dplyr::filter
> * stats::filter
> Or declare a preference with `conflict_prefer()`
> * conflict_prefer("filter", "dplyr")
> * conflict_prefer("filter", "stats")
>
> Where the user will only have to copy
"conflict_prefer("filter",
> "dplyr")" and paste it into his script. The difference, is
that with:
> options(conflicts.policy = "strict", conflicts.policy.ask =
TRUE),
> such message is printed at package load.
>
> I would put the required code within the library() function with the
> following conditional:
> ...
> if (length(conflicts)) {
>   if(getOption("conflicts.policy.ask") == TRUE){
>      ...
>   }
> }
> ...
>
> ###
> # Feature Request 2: Source Execution
> ###
>
> Another alternative, which could apply when executing the .R file from
> source, would be to suggest the user a default conflictRules() setup:
>
> options(conflicts.policy = "strict")
> library(dplyr)
>
> # Error: Conflicts attaching package ?dplyr?:
> #
> # The following objects are masked from ?package:stats?:
> #
> #     filter, lag
> #
> # The following objects are masked from ?package:base?:
> #
> #     intersect, setdiff, setequal, union
> #
> # Declare preference with `conflictRules()` before loading:
> #     * conflictRules("dplyr", mask.ok = list(stats = TRUE, base
= TRUE))
> #     * conflictRules("dplyr", mask.ok = list(stats =
c("filter",
> "lag"), base = c("intersect", "setdiff",
"setequal", "union")))
> #     * conflictRules("dplyr", exclude = c("filter",
"lag",
> "intersect", "setdiff", "setequal",
"union"))
>
> In this case, the error message would have to be extended with
> sensible suggested defaults.
>
> Thanks,
> Juan
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
-- 
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa                  Phone:             319-335-3386
Department of Statistics and        Fax:               319-335-3017
    Actuarial Science
241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu

> An IDE could provide a more sophisticated interface, like a dialog
> allowing separate choices for each conflict. But this is best left up
> to the IDE or the user.
An IDE (or other user interface) should not alter the behavior of R,
especially the installing/loading/attaching of packages.

There are some possible exceptions:
(1) The global option for width.
(2) Output that would normally appear in a separate window.
(3) Maybe others...

But only as non-defaults, with consent from the user.
Also, while exception (2) may have an intuitive appeal, it's risky
business...

Thank you Mr. Tierney!

Using globalCallingHandlers() to directly handle
"packageConflictError" is an excellent idea!

The benefits I see for such an implementation are:
* The patch would be contained within the Conflict Error Handler,
which should reduce any side effects with an eventual implementation.
* And by making its usage optional, by setting for example
options(conflicts.policy.ask = TRUE), in should neither affect any
packages nor other base code.

Hope it allows R Users to work in a more agile manner, and guide R
Students through best practices of variable conflict handling in an
educative manner.

Thanks,
Juan
> You can get what you are asking for now in R 4.0.0 with
> globalCallingHandlers and using the packageConflictError object that
> is signaled. This should get you started:
>
> ```
> options(conflicts.policy = "strict")
>
> packageConflictError
>
> handle_conflicts <- function(e) {
>      cat(conditionMessage(e))
>      opt <- readline(prompt="1: mask.ok; 2: exclude. Choose:
")
>      if (opt == "1")
>          conflictRules(e$package, mask.ok =
as.character(unlist(e$conflicts)))
>      else if (opt == "2")
>          conflictRules(e$package, exclude =
as.character(unlist(e$conflicts)))
>      stop("unresolved conflicts") ## ideal invode a restart here
> }
>
> globalCallingHandlers(packageConflictError = handle_conflicts)
>
> library(dplyr)
> ```
>
> An IDE could provide a more sophisticated interface, like a dialog
> allowing separate choices for each conflict. But this is best left up
> to the IDE or the user.
>
> The one addition to library that might be worth considering is to
> provide a restart for the handler to invoke.
>
> Best,
>
> luke
>