From lawrence.michael at gene.com  Wed Jan 31 21:41:47 2018
From: lawrence.michael at gene.com (Michael Lawrence)
Date: Wed, 31 Jan 2018 12:41:47 -0800
Subject: [Rd] bug [methods]: double execution of `insertSource` within
 the same session does not work
In-Reply-To: <CAOQ5Nyf5MrBLfq2T-dRDDpfGxthqyv=wGthu7TxZy_f7JWTy4g@mail.gmail.com>
References: <CA+ZF6Z+z_tFLSq9KFy_6sX35gXRTr4qknSLELBX6GRLAck8SGw@mail.gmail.com>
 <CAOQ5Nyf5MrBLfq2T-dRDDpfGxthqyv=wGthu7TxZy_f7JWTy4g@mail.gmail.com>
Message-ID: <CAOQ5NydS_5D5pb28pco_dPd5y+BciWYcADJnF2h=XrgAU4_VNQ@mail.gmail.com>

The issue should be resolved in R-devel. It was actually deeper and more
important than this obscure insertSource() function. names() was not doing
the right thing on S4 objects derived from "environment".

On Mon, Jan 29, 2018 at 11:02 AM, Michael Lawrence <michafla at gene.com>
wrote:

> Thanks, I will fix this.
>
> On Mon, Jan 29, 2018 at 8:06 AM, Demetrio Rodriguez T. <
> demetrio.rodriguez.t at gmail.com> wrote:
>
>> Hello everyone,
>>
>>
>> I hope this reaches someone at all. It's my first bug report to the
>> R-core,
>> and, apparently, bugzilla is locked from new reports for now.
>>
>> I was using `methods::insertSource` to debug and successfully fix another
>> package, until it suddenly stopped working. I figured out, that it is
>> because I am using it on the same function multiple times within one
>> session. It also produces warnings even during the first call, but somehow
>> still works. Below I provide a reproducible example:
>>
>> SETUP:
>> ```bash
>> demetrio at laptop:[folder_structure]/Bugreports/methods_insertSource$ ls -a
>> .  ..  gmapsdistance_fix.R  methods_insertSource.R
>> ```
>>
>> file `gmapsdistance_fix.R`
>> ```R
>> gmapsdistance = function(param) {
>>     print('I am a bug report, my params are:')
>>     print(param)
>> }
>> ```
>>
>>
>> file `methods_insertSource.R`
>> ```R
>> library(gmapsdistance)  # works with any package
>>
>> methods::insertSource('gmapsdistance_fix.R',
>>     package = 'gmapsdistance',
>>     functions = 'gmapsdistance',
>>     force = T
>> )
>> buggy = gmapsdistance('Works?')
>> ```
>>
>>
>> TO REPRODUCE:
>> in that directory `R --vanilla` then
>> ```R
>> > source('methods_insertSource.R')
>> Modified functions inserted through trace(): gmapsdistance
>> [1] "I am a bug report, my params are:"
>> [1] "Works?"
>> Warning message:
>> In methods::insertSource("gmapsdistance_fix.R", package =
>> "gmapsdistance",
>> :
>>   cannot insert these (not found in source): "gmapsdistance"
>> # Works, but gives the warning that it does not
>>
>> # repeat:
>> > source('methods_insertSource.R')
>> Error in assign(this, thisObj, envir = envwhere) :
>>   cannot change value of locked binding for 'gmapsdistance'
>> In addition: Warning message:
>> In methods::insertSource("gmapsdistance_fix.R", package =
>> "gmapsdistance",
>> :
>>   cannot insert these (not found in source): "gmapsdistance"
>>
>> # does not work, and gets even more confusing: so is it that the object is
>> not find, or is it about a locked object?
>> ```
>>
>> I think it's a bug.
>>
>> --------------------- BUG REPORT END ------------------------
>>
>>
>> I looked into it a bit myself, in case you are interested:
>>
>> ```R
>> # lines 20-22
>>     if (is(source, "environment"))
>>         env <- source
>>     else env <- evalSource(source, package, FALSE)
>>     # We're in the second case I guess
>>
>> # Browse[2]> env
>> # Object of class "sourceEnvironment"
>> # Source environment created  2017-12-01 05:19:51
>> # For package "gmapsdistance"
>> # From source file "gmapsdistancefix.R"
>>
>>
>> # later, before line 52:
>> x = env
>> Browse[2]> package
>> [1] "gmapsdistance"
>>
>> # evaluate 52
>> packageSlot(env) <- package
>>
>> # objects x and env are still identical
>> # Browse[2]> class(env)
>> # [1] "sourceEnvironment"
>> # attr(,"package")
>> # [1] "methods"
>> # Browse[2]> class(x)
>> # [1] "sourceEnvironment"
>> # attr(,"package")
>> # [1] "methods"
>>
>> # Browse[2]> env
>> # Object of class "sourceEnvironment"
>> # Source environment created  2017-12-01 05:19:51
>> # For package "gmapsdistance"
>> # From source file "gmapsdistancefix.R"
>> # Browse[2]> x
>> # Object of class "sourceEnvironment"
>> # Source environment created  2017-12-01 05:19:51
>> # For package "gmapsdistance"
>> # From source file "gmapsdistancefix.R"
>>
>> # so:
>> Browse[2]>  names(env)
>> NULL
>>
>> # which is why 53-60 do not work:
>> allObjects <- names(env)
>> if (!missing(functions)) {
>>     notThere <- is.na(match(functions, allObjects))
>>     if (any(notThere)) {
>>         warning(gettextf("cannot insert these (not found in source): %s",
>>             paste("\"", functions[notThere], "\"", sep = "",
>>                 collapse = ", ")), domain = NA)
>>     }
>> }
>> ```
>>
>> Looking forward to your feedback!
>>
>> Cheers,
>> Demetrio
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>

	[[alternative HTML version deleted]]



[Rd] bug [methods]: double execution of `insertSource` within the same session does not work
Michael Lawrence