From j@ri@ok@@nen @ending from oulu@fi  Fri Aug 24 09:12:13 2018
From: j@ri@ok@@nen @ending from oulu@fi (Jari Oksanen)
Date: Fri, 24 Aug 2018 07:12:13 +0000
Subject: [Rd] conflicted: an alternative conflict resolution strategy
In-Reply-To: <adf26ba5-6b0a-e7ad-f8e3-50abdf7d0493@gmail.com>
References: <CABdHhvHyV7YXUp9fChvpH-Q7cpW81XhbfNDP8_KwzMFPmAJyHQ@mail.gmail.com>
 <adf26ba5-6b0a-e7ad-f8e3-50abdf7d0493@gmail.com>
Message-ID: <EF40A9BC-8A83-44A9-9736-9C752BF2C41D@oulu.fi>

If you have to load two packages which both export the same name in their namespaces, namespace does not help in resolving which synonymous function to use. Neither does it help to have a package instead of a script as long as you end up loading two namespaces with name conflicts. The order of importing namespaces can also be difficult to control, because you may end up loading a namespace already when you start your R with a saved workspace. Moving a function to another package may be a transitional issue which disappears when both packages are at their final stages, but if you use the recommend deprecation stage, the same names can live together for a long time. So this package is a good idea, and preferably base R should be able to handle the issue of choosing between exported synonymous functions.

This has bitten me several times in package development, and with growing CRAN it is a growing problem. Package authors often have poor control of the issue, as they do not know what packages users use. Now we can only have a FAQ that tells that a certain error message does not come from a function in our package, but from some other package having a synonymous function that was used instead.

cheers, Jari Oksanen

On 23 Aug 2018, at 23:46 pm, Duncan Murdoch <murdoch.duncan at gmail.com<mailto:murdoch.duncan at gmail.com>> wrote:

First, some general comments:

This sounds like a useful package.

I would guess it has very little impact on runtime efficiency except when attaching a new package; have you checked that?

I am not so sure about your heuristics.  Can they be disabled, so the user is always forced to make the choice?  Even when a function is intended to adhere to the superset principle, they don't always get it right, so a really careful user should always do explicit disambiguation.

And of course, if users wrote most of their long scripts as packages instead of as long scripts, the ambiguity issue would arise far less often, because namespaces in packages are intended to solve the same problem as your package does.

One more comment inline about a typo, possibly in an error message.

Duncan Murdoch

On 23/08/2018 2:31 PM, Hadley Wickham wrote:
Hi all,
I?d love to get your feedback on the conflicted package, which provides an
alternative strategy for resolving ambiugous function names (i.e. when
multiple packages provide identically named functions). conflicted 0.1.0
is already on CRAN, but I?m currently preparing a revision
(<https://github.com/r-lib/conflicted>), and looking for feedback.
As you are no doubt aware, R?s default approach means that the most
recently loaded package ?wins? any conflicts. You do get a message about
conflicts on load, but I see a lot newer R users experiencing problems
caused by function conflicts. I think there are three primary reasons:
-   People don?t read messages about conflicts. Even if you are
    conscientious and do read the messages, it?s hard to notice a single
    new conflict caused by a package upgrade.
-   The warning and the problem may be quite far apart. If you load all
    your packages at the top of the script, it may potentially be 100s
    of lines before you encounter a conflict.
-   The error messages caused by conflicts are cryptic because you end
    up calling a function with utterly unexpected arguments.
For these reasons, conflicted takes an alternative approach, forcing the
user to explicitly disambiguate any conflicts:
    library(conflicted)
    library(dplyr)
    library(MASS)
    select
    #> Error: [conflicted] `select` found in 2 packages.
    #> Either pick the one you want with `::`
    #> * MASS::select
    #> * dplyr::select
    #> Or declare a preference with `conflicted_prefer()`
    #> * conflict_prefer("select", "MASS")
    #> * conflict_prefer("select", "dplyr")

I don't know if this is a typo in your r-devel message or a typo in the error message, but you say `conflicted_prefer()` in one place and conflict_prefer() in the other.

conflicted works by attaching a new ?conflicted? environment just after
the global environment. This environment contains an active binding for
any ambiguous bindings. The conflicted environment also contains
bindings for `library()` and `require()` that rebuild the conflicted
environemnt suppress default reporting (but are otherwise thin wrapeprs
around the base equivalents).
conflicted also provides a `conflict_scout()` helper which you can use
to see what?s going on:
    conflict_scout(c("dplyr", "MASS"))
    #> 1 conflict:
    #> * `select`: dplyr, MASS
conflicted applies a few heuristics to minimise false positives (at the
cost of introducing a few false negatives). The overarching goal is to
ensure that code behaves identically regardless of the order in which
packages are attached.
-   A number of packages provide a function that appears to conflict
    with a function in a base package, but they follow the superset
    principle (i.e. they only extend the API, as explained to me by
    Herv? Pages).
    conflicted assumes that packages adhere to the superset principle,
    which appears to be true in most of the cases that I?ve seen. For
    example, the lubridate package provides `as.difftime()` and `date()`
    which extend the behaviour of base functions, and provides S4
    generics for the set operators.
        conflict_scout(c("lubridate", "base"))
        #> 5 conflicts:
        #> * `as.difftime`: [lubridate]
        #> * `date`       : [lubridate]
        #> * `intersect`  : [lubridate]
        #> * `setdiff`    : [lubridate]
        #> * `union`      : [lubridate]
    There are two popular functions that don?t adhere to this principle:
    `dplyr::filter()` and `dplyr::lag()` :(. conflicted handles these
    special cases so they correctly generate conflicts. (I sure wish I?d
    know about the subset principle when creating dplyr!)
        conflict_scout(c("dplyr", "stats"))
        #> 2 conflicts:
        #> * `filter`: dplyr, stats
        #> * `lag`   : dplyr, stats
-   Deprecated functions should never win a conflict, so conflicted
    checks for use of `.Deprecated()`. This rule is very useful when
    moving functions from one package to another. For example, many
    devtools functions were moved to usethis, and conflicted ensures
    that you always get the non-deprecated version, regardess of package
    attach order:
        head(conflict_scout(c("devtools", "usethis")))
        #> 26 conflicts:
        #> * `use_appveyor`       : [usethis]
        #> * `use_build_ignore`   : [usethis]
        #> * `use_code_of_conduct`: [usethis]
        #> * `use_coverage`       : [usethis]
        #> * `use_cran_badge`     : [usethis]
        #> * `use_cran_comments`  : [usethis]
        #> ...
Finally, as mentioned above, the user can declare preferences:
    conflict_prefer("select", "MASS")
    #> [conflicted] Will prefer MASS::select over any other package
    conflict_scout(c("dplyr", "MASS"))
    #> 1 conflict:
    #> * `select`: [MASS]
I?d love to hear what people think about the general idea, and if there
are any obviously missing pieces.
Thanks!
Hadley


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[Rd] conflicted: an alternative conflict resolution strategy
Jari Oksanen