R devel - Apr 2015 - Formula evaluation, environments and attached packages

Hi!

Some time ago, I replaced calls to library() with calls to
requireNamespace() in my package logmult, in order to follow the new
CRAN policies. But I just noticed it broke jackknife/bootstrap using
several workers via package parallel.

The reason is that I'm running model replicates on the workers, and the
formula includes non-standard terms like Mult() which are provided by
gnm. If gnm is not attached to the global namespace, these functions are
not found.

What would be the best solution to fix this? I tried changing the
environment of the formula to be gnm's namespace, but so far I failed.

Here's a reproducer using only gnm:
> dat <- structure(c(326, 688, 343, 98, 38, 116, 84, 48, 241, 584, 909, 
+ 403, 110, 188, 412, 681, 3, 4, 26, 85), .Dim = 4:5, .Dimnames =
structure(list(
+     Eye = c("Blue", "Light", "Medium",
"Dark"), Hair = c("Fair",
+     "Red", "Medium", "Dark",
"Black")), .Names = c("Eye", "Hair"
+ )), class="table")
> 
> f <- Freq ~ Eye + Hair + Mult(Eye, Hair)
> gnm::gnm(f, family=poisson, data=dat)
Error in which(sapply(variables, function(x) { : 
  error in evaluating the argument 'x' in selecting a method for
function 'which':
Error in get(as.character(FUN), mode = "function", envir = envir) : 
  object 'Mult' of mode 'function' was not found

# Failed attempt by setting the environment
> environment(f) <- loadNamespace("gnm")
> environment(f)                        
<environment: namespace:gnm>
> gnm::gnm(f, family=poisson, data=dat)
Error in which(sapply(variables, function(x) { : 
  error in evaluating the argument 'x' in selecting a method for
function 'which':
Error in get(as.character(FUN), mode = "function", envir = envir) : 
  object 'Mult' of mode 'function' was not found


Thanks for your help

Hi Milan,

I expect I may be able to do something about the way the terms are
evaluated, to ensure the evaluation is done in the gnm namespace (while
still ensuring the variables can be found!).

In the meantime, I think the following will work:

Mult <- gnm::Mult
 f <- Freq ~ Eye + Hair + Mult(Eye, Hair)
gnm::gnm(f, family=poisson, data=dat)

Hope that helps,

Heather

On Wed, Apr 29, 2015, at 05:57 PM, Milan Bouchet-Valat
wrote:
> Hi!
> 
> Some time ago, I replaced calls to library() with calls to
> requireNamespace() in my package logmult, in order to follow the new
> CRAN policies. But I just noticed it broke jackknife/bootstrap using
> several workers via package parallel.
> 
> The reason is that I'm running model replicates on the workers, and the
> formula includes non-standard terms like Mult() which are provided by
> gnm. If gnm is not attached to the global namespace, these functions are
> not found.
> 
> What would be the best solution to fix this? I tried changing the
> environment of the formula to be gnm's namespace, but so far I failed.
> 
> Here's a reproducer using only gnm:
> 
> > dat <- structure(c(326, 688, 343, 98, 38, 116, 84, 48, 241, 584,
909,
> + 403, 110, 188, 412, 681, 3, 4, 26, 85), .Dim = 4:5, .Dimnames >
structure(list(
> +     Eye = c("Blue", "Light", "Medium",
"Dark"), Hair = c("Fair",
> +     "Red", "Medium", "Dark",
"Black")), .Names = c("Eye", "Hair"
> + )), class="table")
> > 
> > f <- Freq ~ Eye + Hair + Mult(Eye, Hair)
> > gnm::gnm(f, family=poisson, data=dat)
> Error in which(sapply(variables, function(x) { : 
>   error in evaluating the argument 'x' in selecting a method for
function
>   'which':
> Error in get(as.character(FUN), mode = "function", envir = envir)
:
>   object 'Mult' of mode 'function' was not found
> 
> # Failed attempt by setting the environment
> > environment(f) <- loadNamespace("gnm")
> > environment(f)                        
> <environment: namespace:gnm>
> > gnm::gnm(f, family=poisson, data=dat)
> Error in which(sapply(variables, function(x) { : 
>   error in evaluating the argument 'x' in selecting a method for
function
>   'which':
> Error in get(as.character(FUN), mode = "function", envir = envir)
:
>   object 'Mult' of mode 'function' was not found
> 
> 
> Thanks for your help

Le mercredi 29 avril 2015 ? 18:27 +0100, Heather Turner a ?crit
:
> Hi Milan,
> 
> I expect I may be able to do something about the way the terms are
> evaluated, to ensure the evaluation is done in the gnm namespace (while
> still ensuring the variables can be found!).
> 
> In the meantime, I think the following will work:
> 
> Mult <- gnm::Mult
>  f <- Freq ~ Eye + Hair + Mult(Eye, Hair)
> gnm::gnm(f, family=poisson, data=dat)
Indeed, that's a good trick, waiting for a more general solution.


Regards
> Hope that helps,
> 
> Heather
> 
> On Wed, Apr 29, 2015, at 05:57 PM, Milan Bouchet-Valat wrote:
> > Hi!
> > 
> > Some time ago, I replaced calls to library() with calls to
> > requireNamespace() in my package logmult, in order to follow the new
> > CRAN policies. But I just noticed it broke jackknife/bootstrap using
> > several workers via package parallel.
> > 
> > The reason is that I'm running model replicates on the workers,
and the
> > formula includes non-standard terms like Mult() which are provided by
> > gnm. If gnm is not attached to the global namespace, these functions
are
> > not found.
> > 
> > What would be the best solution to fix this? I tried changing the
> > environment of the formula to be gnm's namespace, but so far I
failed.
> > 
> > Here's a reproducer using only gnm:
> > 
> > > dat <- structure(c(326, 688, 343, 98, 38, 116, 84, 48, 241,
584, 909,
> > + 403, 110, 188, 412, 681, 3, 4, 26, 85), .Dim = 4:5, .Dimnames >
> structure(list(
> > +     Eye = c("Blue", "Light", "Medium",
"Dark"), Hair = c("Fair",
> > +     "Red", "Medium", "Dark",
"Black")), .Names = c("Eye", "Hair"
> > + )), class="table")
> > > 
> > > f <- Freq ~ Eye + Hair + Mult(Eye, Hair)
> > > gnm::gnm(f, family=poisson, data=dat)
> > Error in which(sapply(variables, function(x) { : 
> >   error in evaluating the argument 'x' in selecting a method
for function
> >   'which':
> > Error in get(as.character(FUN), mode = "function", envir =
envir) :
> >   object 'Mult' of mode 'function' was not found
> > 
> > # Failed attempt by setting the environment
> > > environment(f) <- loadNamespace("gnm")
> > > environment(f)                        
> > <environment: namespace:gnm>
> > > gnm::gnm(f, family=poisson, data=dat)
> > Error in which(sapply(variables, function(x) { : 
> >   error in evaluating the argument 'x' in selecting a method
for function
> >   'which':
> > Error in get(as.character(FUN), mode = "function", envir =
envir) :
> >   object 'Mult' of mode 'function' was not found
> > 
> > 
> > Thanks for your help