From smckinney at bccrc.ca  Wed Nov 29 21:01:14 2006
From: smckinney at bccrc.ca (Steven McKinney)
Date: Wed, 29 Nov 2006 12:01:14 -0800
Subject: [Rd] rm() deletes 'c' if c('a','b') is the argument (PR#9399)
References: <20061129183537.0F42D5734F@slim.kubism.ku.dk>
	<0BE438149FF2254DB4199E2682C8DFEB0235F9FA@crcmail1.BCCRC.CA>
	<456DDC20.3000002@med.umich.edu>
Message-ID: <0BE438149FF2254DB4199E2682C8DFEB0235F9FB@crcmail1.BCCRC.CA>

The argument should indeed be made.

I think the documentation for rm() needs
to be changed to:

Arguments:

      ...: the object to be removed, supplied individually.  Multiple objects
           must be supplied via the list argument. 



>From the rm() help page:

rm    (..., list = character(0), pos = -1,
       envir = as.environment(pos), inherits = FALSE)
Arguments

...	 the objects to be removed, supplied individually and/or as a character vector




> class(c('a', 'b'))
[1] "character"
> 
> length(c('a', 'b'))
[1] 2
> is.vector(c('a', 'b'))
[1] TRUE
> 

By all appearances, c('a', 'b') seems
to be a character vector.  I'm not the
most knowledgeable R programmer, so I'm not
sure what I'm missing here.

I haven't delved deeply into the rm() source code, but
this looks like a logical bug.  The documentation
needs to be modified to fit the current function
behaviour, or the current function behaviour needs
to be modified to fit the documentation.

> rm(c('a', 'b'))
Warning message:
remove: variable "c" was not found 

Why is "c" ending up in the list of items to remove? 
(see PS: below)

> unlist(list('a', 'b'))
[1] "a" "b"
> class(unlist(list('a', 'b')))
[1] "character"
> is.vector(unlist(list('a', 'b')))
[1] TRUE
> a <- 1
> b <- 2
> rm(unlist(list('a', 'b')))
Warning messages:
1: remove: variable "unlist" was not found 
2: remove: variable "list("a", "b")" was not found 
> ls()
[1] "a"            "b"            "d"            "getMonograph" "last.warning" "myfun"       
> 

Does the rm() doc need modification?

Presently it appears that the doc should read

Arguments:

      ...: the object to be removed, supplied individually.  Multiple objects
           must be supplied via the list argument. 




PS:

Does it have anything to do with this
type of behaviour?  Is this essentially
what is happening in the match.call()
in rm()?

> sapply(substitute(c('a', 'b')), as.character)
[1] "c" "a" "b"

> rm
function (..., list = character(0), pos = -1, envir = as.environment(pos), 
    inherits = FALSE) 
{
    names <- sapply(match.call(expand.dots = FALSE)$..., as.character)
    if (length(names) == 0) 
        names <- character(0)
    list <- .Primitive("c")(list, names)
    .Internal(remove(list, envir, inherits))
}
<environment: namespace:base>
> sapply(c('a', 'b'), as.character)
  a   b 
"a" "b" 
> sapply(substitute(c('a', 'b')), as.character)
[1] "c" "a" "b"
> match.call
function (definition = NULL, call = sys.call(sys.parent()), expand.dots = TRUE) 
.Internal(match.call(definition, call, expand.dots))
<environment: namespace:base>



Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney at bccrc.ca

tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3
Canada




-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
Sent: Wed 11/29/2006 11:14 AM
To: Steven McKinney
Cc: hanl2 at wyeth.com; r-devel at stat.math.ethz.ch; R-bugs at biostat.ku.dk
Subject: Re: [Rd] rm() deletes 'c' if c('a','b') is the argument (PR#9399)
 
That's because you are not using rm() correctly. From the help page:

Arguments:

      ...: the objects to be removed, supplied individually and/or as a
           character vector

     list: a character vector naming objects to be removed.

So if you pass an unnamed argument, rm() will assume you have some 
objects in the .GlobalEnv with those names that you would like to 
remove. If you want to pass a character vector, you have to name it 
because the first argument is '...'.

 > a <- 1:5
 > b <- 2:10
 > c <- "not a good variable name"
 > rm(list=c("a","b"))
 > c
[1] "not a good variable name"

 > a <- 1:5
 > b <- 2:10
 > c <- "still not a good variable name"
 > rm(a,b)
 > c
[1] "still not a good variable name"

 > a <- 1:5
 > b <- 2:10
 > c <- "still not a good variable name"
 > rm("a","b")
 > c
[1] "still not a good variable name"


NB: 'c' is not a good variable name because you are masking an existing 
function.

An argument could be made that the explanation for the first argument is 
not very exact.

Best,

Jim



Steven McKinney wrote:
> Same behaviour seen on Apple Mac OSX 10.4.8 platform:
> 
> 
>>sessionInfo()
> 
> R version 2.4.0 Patched (2006-10-31 r39758) 
> powerpc-apple-darwin8.8.0 
> 
> locale:
> en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
> 
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"  "base"     
> 
> other attached packages:
>     XML 
> "1.2-0" 
> 
>>ls()
> 
> [1] "getMonograph" "last.warning" "myfun"       
> 
>>a <- 1
>>b <- 2
>>c <- letters
>>a
> 
> [1] 1
> 
>>b
> 
> [1] 2
> 
>>c
> 
>  [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s" "t" "u" "v" "w" "x" "y" "z"
> 
>>rm(c('a', 'b'))
>>a
> 
> Error: object "a" not found
> 
>>b
> 
> Error: object "b" not found
> 
>>c
> 
> .Primitive("c")
> 
>>ls()
> 
> [1] "getMonograph" "last.warning" "myfun"       
> 
>>a <- 1
>>b <- 2
>>d <- letters
>>ls()
> 
> [1] "a"            "b"            "d"            "getMonograph" "last.warning" "myfun"       
> 
>>rm(c('a', 'b'))
> 
> Warning message:
> remove: variable "c" was not found 
> 
>>ls()
> 
> [1] "d"            "getMonograph" "last.warning" "myfun"       
> 
> 
> Steven McKinney
> 
> Statistician
> Molecular Oncology and Breast Cancer Program
> British Columbia Cancer Research Centre
> 
> email: smckinney at bccrc.ca
> 
> tel: 604-675-8000 x7561
> 
> BCCRC
> Molecular Oncology
> 675 West 10th Ave, Floor 4
> Vancouver B.C. 
> V5Z 1L3
> Canada
> 
> 
> 
> 
> -----Original Message-----
> From: r-devel-bounces at r-project.org on behalf of hanl2 at wyeth.com
> Sent: Wed 11/29/2006 10:35 AM
> To: r-devel at stat.math.ethz.ch
> Cc: R-bugs at biostat.ku.dk
> Subject: [Rd] rm() deletes 'c' if c('a','b') is the argument (PR#9399)
>  
> Full_Name: Lixin Han
> Version: 2.4.0
> OS: Windows 2000
> Submission from: (NULL) (155.94.110.222)
> 
> 
> A character vector c('a','b') is supplied to rm().  As a result, 'c' is deleted
> unintentionally.
> 
> 
>>a <- 1:5
>>b <- 'abc'
>>c <- letters
>>ls()
> 
> [1] "a" "b" "c"
> 
>>rm(c('a','b'))
>>ls()
> 
> character(0)
> 
> 
> ______________________________________________
> 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


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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[Rd] rm() deletes 'c' if c('a','b') is the argument (PR#9399)
Steven McKinney