Standard non-standard evaluation problem with 2.10-0

[Gavin Simpson]

Dear List

I am getting an error when checking my analogue package with
R2.10.0-patched. The error comes when running a function within which I
use the standard non-standard evaluation method. I've distilled the
error and functions involved out into the following simple example to
illustrate the error:

## Dummy data to illustrate formula method
d <- data.frame(A = runif(10), B = runif(10), C = runif(10))
## simulate some missings
d[sample(10,3), 1] <- NA

foo <- function(formula, data = NULL,
                subset = NULL,
                na.action = na.pass, ...) {
    mf <- match.call()
    mf[[1]] <- as.name("model.frame")
    mt <- terms(formula, data = data, simplify = TRUE)
    mf[[2]] <- formula(mt, data = data)
    mf$na.action <- substitute(na.action)
    dots <- list(...)
    mf[[names(dots)]] <- NULL
    mf <- eval(mf,parent.frame())
    mf
}

## apply foo using formula
foo(~ . - B, data = d, na.action = na.pass,
    method = "missing", na.value = 0)
Error in mf[[names(dots)]] <- NULL :
  more elements supplied than there are to replace

If I debug(foo) and do:

Browse[2]> names(dots)
[1] "method"   "na.value"
Browse[2]> names(mf)
[1] ""          "formula"   "data"      "na.action" "method"  
[6] "na.value"
Browse[2]> mf[[names(dots)[1]]]
[1] "missing"
Browse[2]> mf[[names(dots)[2]]]
[1] 0

But
Browse[2]> mf[[names(dots)]]
Error in mf[[names(dots)]] : subscript out of bounds
Browse[2]> str(names(dots))
 chr [1:2] "method" "na.value"

I could have sworn I tested this during the beta test phase for 2.10.0 -
if I did I didn't get any errors at that time - and this code works fine
under R2.9.x branch. The package is now failing checks on CRAN and on my
local install.

Am I doing something patently stupid here? Has something changed in '[['
or 'names' that I'm now running foul of? I can probably work round this
by setting the individual names of 'mf' to NULL in two calls, but I'd
like to get to the bottom of the problem if at all possible.

Session Info:
R version 2.10.0 Patched (2009-11-01 r50276)
i686-pc-linux-gnu

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8  
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base    

other attached packages:
[1] analogue_0.6-21 MASS_7.2-48     lattice_0.17-25
[4] vegan_1.15-3  

loaded via a namespace (and not attached):
[1] grid_2.10.0  tools_2.10.0

Thanks in advance,

G
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson             [t] [phone]
 ECRC, UCL Geography,          [f] [phone]
 Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

[Gavin Simpson]

Dear list,

Prof Ripley has replied with the solution - I /was/ doing something
patently stupid.

The offending line:

mf[[names(dots)]] <- NULL

should have been

mf[names(dots)] <- NULL

That the offending line worked in R 2.9.x was the result of bug, which
has been fixed in the current version, and it was my mistake in using
'[[' where I meant '['.

All the best,

Gavin

On Tue, 2009-11-03 at 20:05 +0000, Gavin Simpson wrote:

> Dear List
>
> I am getting an error when checking my analogue package with
> R2.10.0-patched. The error comes when running a function within which I
> use the standard non-standard evaluation method. I've distilled the
> error and functions involved out into the following simple example to
> illustrate the error:
>
> ## Dummy data to illustrate formula method
> d <- data.frame(A = runif(10), B = runif(10), C = runif(10))
> ## simulate some missings
> d[sample(10,3), 1] <- NA
>
> foo <- function(formula, data = NULL,
>                 subset = NULL,
>                 na.action = na.pass, ...) {
>     mf <- match.call()
>     mf[[1]] <- as.name("model.frame")
>     mt <- terms(formula, data = data, simplify = TRUE)
>     mf[[2]] <- formula(mt, data = data)
>     mf$na.action <- substitute(na.action)
>     dots <- list(...)
>     mf[[names(dots)]] <- NULL
>     mf <- eval(mf,parent.frame())
>     mf
> }
>
> ## apply foo using formula
> foo(~ . - B, data = d, na.action = na.pass,
>     method = "missing", na.value = 0)
> Error in mf[[names(dots)]] <- NULL :
>   more elements supplied than there are to replace
>
> If I debug(foo) and do:
>
> Browse[2]> names(dots)
> [1] "method"   "na.value"
> Browse[2]> names(mf)
> [1] ""          "formula"   "data"      "na.action" "method"  
> [6] "na.value"
> Browse[2]> mf[[names(dots)[1]]]
> [1] "missing"
> Browse[2]> mf[[names(dots)[2]]]
> [1] 0
>
> But
> Browse[2]> mf[[names(dots)]]
> Error in mf[[names(dots)]] : subscript out of bounds
> Browse[2]> str(names(dots))
>  chr [1:2] "method" "na.value"
>
> I could have sworn I tested this during the beta test phase for 2.10.0 -
> if I did I didn't get any errors at that time - and this code works fine
> under R2.9.x branch. The package is now failing checks on CRAN and on my
> local install.
>
> Am I doing something patently stupid here? Has something changed in '[['
> or 'names' that I'm now running foul of? I can probably work round this
> by setting the individual names of 'mf' to NULL in two calls, but I'd
> like to get to the bottom of the problem if at all possible.
>
> Session Info:
> R version 2.10.0 Patched (2009-11-01 r50276)
> i686-pc-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
>  [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8  
>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C      
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods  
> [7] base    
>
> other attached packages:
> [1] analogue_0.6-21 MASS_7.2-48     lattice_0.17-25
> [4] vegan_1.15-3  
>
> loaded via a namespace (and not attached):
> [1] grid_2.10.0  tools_2.10.0
>
> Thanks in advance,
>
> G

--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson             [t] [phone]
 ECRC, UCL Geography,          [f] [phone]
 Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel