[R] warning on generic function when building R package

[David Stevens]

Sorry to be a late comer to this problem but I'm having a similar 
issue.  My function is called by ode from deSolve

ADM1_C <- function(t,state,parameters,...){

with(as.list(c(state,parameters)), {
   # do some stuff here and return a list containing a vector of 
derivatives to ode
...
})
}
in which 't' is a time and 'state' and 'parameters' are numeric vectors 
with each element named. When I invoke the solver,

times <- d.df$time
out <- as.data.frame(ode(y = state,times = times,func = ADM1_C,parms = 
parameters))

I get ~three Note:s for each value in 'state'  (sometimes more). The 
calculation is successful but the issue is a little puzzling.
Here's 'state'
state
      Ssu      Saa      Sfa      Sva      Sbu     Spro Sac      Sh2     
Sch4      Sic
0.300000 0.001000 0.300000 0.300000 0.300000 0.300000 0.300000 0.000001 
0.000010 0.040000
      Sin       Si       Xc      Xch      Xpr      Xli Xsu      Xaa      
Xfa      Xc4
0.010000 0.020000 0.300000 0.026000 0.300000 0.030000 0.400000 1.100000 
0.200000 0.410000
     Xpro      Xac      Xh2       Xi  Scation   Sanion Sva_m    Sbu_m   
Spro_m    Sac_m
0.137000 0.700000 0.010000 5.000000 0.040000 0.020000 0.090000 0.090000 
0.074000 0.169000
  Shco3_m     Snh3  Sgas_h2 Sgas_ch4 Sgas_co2
0.009700 0.016000 0.020000 0.020000 0.037600

The messages are something like this ...
Note: no visible binding for global variable 'Sin'
Note: no visible binding for global variable 'Snh3'
Note: no visible binding for global variable 'Scation'
Note: no visible binding for global variable 'Shco3_m'
.... (~130 rows of these messages)

Neither Duncan's nor Jim's solution solved the problem.  I can't change 
(at least I don't think so) how ode(...) calls the function except via 
the documentation. Any ideas? Does it matter? Could it be ode strips out 
the names, but only sometimes?

signed Grasping at Straws (David)

David K Stevens, P.E., Ph.D.
Professor and Head, Environmental Engineering
Civil and Environmental Engineering
Utah Water Research Laboratory
8200 Old Main Hill
Logan, UT  84322-8200
435 797 3229 - voice
435 797 1363 - fax
david.stevens at usu.edu


On 10/19/2015 2:32 PM, carol white via R-help wrote:
> In effect, this works
> but whether I use x or x.init, y or y.init in plot.func, I get
>   
> no visible binding for global variable ‘x.init’no visible binding for global variable ‘y.init’
> Regards,
>
>       On Monday, October 19, 2015 9:59 PM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
>     
>
>   On 19/10/2015 3:50 PM, carol white wrote:
>> Thanks Murdoch.
>>
>> defining
>> plot.func<- function(x=x.init, y=y.init, arg3, arg4, "title", col, arg5)
>>
>> and if plot doesn't take the exact parameters of plot.func but modified
>> of these parameters
>> plot(x=x.pt,y=y.pt,xlim = c(0, 10), ylim = c(0,1), xlab= "xlab",
>> ylab="ylab", main = "title", col = col,type = "l")
>>
>> then, how to define and invoke to be consisent?
> I don't really understand your question, but this is all about the
> function header for plot.func, not the call you make to plot().  You
> need to name the first argument as "x", you need to include "..." as an
> open argument, and you need a legal header.  So this would be okay:
>
>
> plot.func<- function(x=x.init, y=y.init, arg3, arg4,
>                      main = "title", # can't skip the arg name
>                      col, arg5,
>                      ...)  {          # can't skip the dots
>
> Duncan Murdoch
>
>> Regards,
>>
>> On Monday, October 19, 2015 7:45 PM, Duncan Murdoch
>> <murdoch.duncan at gmail.com> wrote:
>>
>>
>> On 19/10/2015 1:29 PM, carol white via R-help wrote:
>>
>>> Hi,I have invoked plot in a function (plot.func) as follows but when I
>> check the built package, I get a warning:
>>> plot(x.pt,y.pt,xlim = c(0, 10), ylim = c(0,1), xlab= "xlab",
>> ylab="ylab", main = "title", col = col,type = "l")
>>> R CMD check my.package
>>> checking S3 generic/method consistency ... WARNING
>>> plot:
>>>    function(x, ...)
>>> plot.func:
>>>    function(x.pt, y.pt, arg3, arg4, "title", col, arg5)
>>>
>>> See section ‘Generic functions and methods’ in the ‘Writing R
>>> Extensions’ manual.
>>> Which plot argument is illegitimate or missing and how to eliminate
>> the warning?
>>
>>
>> The first argument to plot.func needs to be called "x" if you want to
>> use it as a method.  Method signatures need to be consistent with the
>> generic signature.
>>
>> Duncan Murdoch
>>
>>
>>
>>
>
>
>    
> 	[[alternative HTML version deleted]]
>
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