From lawrence.michael at gene.com  Thu Apr 19 18:40:09 2018
From: lawrence.michael at gene.com (Michael Lawrence)
Date: Thu, 19 Apr 2018 09:40:09 -0700
Subject: [Rd] odd assignInNamespace / setGeneric interaction
In-Reply-To: <CAF8bMcYh3MQs+BA0kL7FqDeEwaCNW2cOPKSDBVws_KsEXCoxvA@mail.gmail.com>
References: <CAF8bMcZKhy_7nZm3Weoabi5fbbF=9Z8ciPK1LVd8Wt_p8HZshw@mail.gmail.com>
 <CAOQ5NyeeYGAD9NyfQepdHmcRfjWppJepeZebSYiRO-ZCJqi9_Q@mail.gmail.com>
 <23256.25200.216197.166249@stat.math.ethz.ch>
 <CAF8bMcYh3MQs+BA0kL7FqDeEwaCNW2cOPKSDBVws_KsEXCoxvA@mail.gmail.com>
Message-ID: <CAOQ5Nye4PT6mZL8+jutMb2v-ySe4pdsiuLWDHLkejy_T6hNs2w@mail.gmail.com>

To clarify, I am going to fix the issue in the methods package
(actually I already have but need to test further). There's no intent
to change the behavior of q().

On Thu, Apr 19, 2018 at 8:39 AM, William Dunlap <wdunlap at tibco.com> wrote:
> The problem is not specific to redefining the q function, but to
> the interaction of assignInNamespace and setGeneric.  The
> latter requires, roughtly, that the environment of the function
> being replaced by an S4 generic is (or is the descendent of)
> the environment in which it lives.
>
> E.g., the following demonstrates the problem
>
> % R --quiet --vanilla
>> assignInNamespace("plot", function(x, ...) stop("No plotting allowed!"),
>> getNamespace("graphics"))
>> library(stats4)
> Error: package or namespace load failed for ?stats4? in loadNamespace(name):
>  there is no package called ?.GlobalEnv?
>
> and defining the bogus plot function in the graphics namespace avoids the
> problem
>
> % R --quiet --vanilla
>>  assignInNamespace("plot", with(getNamespace("graphics"), function(x, ...)
>> stop("No plotting allowed!")), getNamespace("graphics"))
>> library(stats4)
>>
>
> I suppose poeple who use assignInNamespace get what they deserve.
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Thu, Apr 19, 2018 at 2:33 AM, Martin Maechler
> <maechler at stat.math.ethz.ch> wrote:
>>
>> >>>>> Michael Lawrence <lawrence.michael at gene.com>
>> >>>>>     on Wed, 18 Apr 2018 14:16:37 -0700 writes:
>>
>>     > Hi Bill,
>>     > Ideally, your coworker would just make an alias (or shortcut or
>>     > whatever) for R that passed --no-save to R. I'll try to look into
>> this
>>     > though.
>>
>>     > Michael
>>
>> Yes, indeed!
>>
>> As some of you know, I've been using R (for ca 23 years now)
>> almost only from ESS (Emacs Speaks Statistics).
>>
>> There, I've activated '--no-save' for ca 20 years or so,
>> nowadays (since Emacs has adopted "custom") I have had this in
>> my ~/.emacs  custom lines
>>
>>  '(inferior-R-args "--no-restore-history --no-save ")
>>
>> standalone (to paste into your own ~/.emacs ) :
>>
>> (custom-set-variables '(inferior-R-args "--no-restore-history --no-save
>> "))
>>
>> --------
>>
>> The current fashionable IDE to R,
>> Rstudio, also allows to set such switches by its GUI:
>>
>> Menu [Tools]
>>   --> (bottom) entry [Global Options]
>>     --> the first sidebar entry  [R General]:
>>     Look for two lines mentioning "workspace" or ".RData" and
>>     change to 'save never' ( == --no-save),
>>     and nowadays I also recommend my students to not *read*
>>     these, i.e., '--no-restore'
>>
>> ---
>>
>> @Michael: I'm not sure what you're considering.  I feel that in
>>  general, there are already too many R startup tweaking
>>  possibilities, notably via environment variables.
>> [e.g., the current ways to pre-determine the active .libPaths() in R,
>>  and the fact the R calls R again during 'R CMD check' etc,
>>  sometimes drives me crazy when .libPaths() become incompatible
>>  for too many reasons .... yes, I'm diverting: that's another story]
>>
>> If we'd want to allow using (yet  another!) environment variable
>> here, I'd at least would  make sure they are not consulted when
>> explicit --no-save or --vanilla, etc are used.
>>
>> Martin
>>
>>
>>     > On Wed, Apr 18, 2018 at 1:38 PM, William Dunlap via R-devel
>>     > <r-devel at r-project.org> wrote:
>>     >> A coworker got tired of having to type 'yes' or 'no' after quitting
>> R: he
>>     >> never wanted to save the R workspace when quitting.  So he added
>>     >> assignInNamespace lines to his .Rprofile file to replace base::q
>> with
>>     >> one that, by default, called the original with save="no"..
>>     >>
>>     >> utils::assignInNamespace(".qOrig", base::q, "base")
>>     >> utils::assignInNamespace("q", function(save = "no", ...)
>>     >> base:::.qOrig(save = save, ...), "base")
>>     >>
>>     >> This worked fine until he decide to load the distr package:
>>     >>
>>     >> > suppressPackageStartupMessages(library(distr))
>>     >> Error: package or namespace load failed for ?distr? in
>>     >> loadNamespace(name):
>>     >> there is no package called ?.GlobalEnv?
>>     >>
>>     >> distr calls setGeneric("q"), which indirectly causes the
>> environment
>>     >> of base::q, .GlobalEnv, to be loaded as a namespace, causing the
>> error.
>>     >> Giving his replacement q function the environment
>> getNamespace("base")
>>     >> avoids the problem.
>>     >>
>>     >> I can reproduce the problem by making a package that just calls
>>     >> setGeneric("as.hexmode",...) and a NAMEPACE file with
>>     >> exportMethods("as.hexmode").  If my .Rprofile puts a version of
>> as.hexmode
>>     >> with environment .GlobalEnv into the base namespace, then I get the
>> same
>>     >> error when trying to load the package.
>>     >>
>>     >> I suppose this is mostly a curiosity and unlikely to happen to most
>> people
>>     >> but it did confuse us for a while.
>>     >>
>>     >> Bill Dunlap
>>     >> TIBCO Software
>>     >> wdunlap tibco.com
>>     >>
>>     >> [[alternative HTML version deleted]]
>>     >>
>>     >> ______________________________________________
>>     >> R-devel at r-project.org mailing list
>>     >> https://stat.ethz.ch/mailman/listinfo/r-devel
>>     >>
>>
>>     > ______________________________________________
>>     > R-devel at r-project.org mailing list
>>     > https://stat.ethz.ch/mailman/listinfo/r-devel
>
>



[Rd] odd assignInNamespace / setGeneric interaction
Michael Lawrence