Dear all,
For my package "ref" I have implemented extensive regression testing. It now
fails to compile since primitives "dim" and "dimnames" (and their assignment
methods) no longer allow for additional arguments. I was using an additional
argument "ref" with several methods. For "].refdata" it still works, with
"dim.refdata" no longer. Could you please allow for additional arguments for
the following generic functions (or primitives):
dim <- function (x, ...)
UseMethod("dim")
"dim<-" <- function (x, ..., value)
UseMethod("dim<-")
dimnames <- function (x, ...)
UseMethod("dimnames")
"dimnames<-" <- function (x, ..., value)
UseMethod("dimnames<-")
row.names <- function (x, ...)
UseMethod("row.names")
"row.names<-" <- function (x, ..., value)
UseMethod("row.names<-")
names <- function (x, ...)
UseMethod("names")
"names<-" <- function (x, ..., value)
UseMethod("names<-")
BTW: why does get("dim") returns
function (x) .Primitive("dim")
and args() works on it,
while get("[") returns
.Primitive("[")
and args() doesn't work on it?
Furthermore, until now "rownames", "colnames" have been convenience wrappers
for "dimnames". Consequently implementing "dimnames" and "dimnames<-" would
indirectly implement "rownames", "colnames" and their assignment methods. This
no longer works for classes inheriting from "data.frame" because the assignment
methods no longer work via "dimnames<-". I can imagine that this change breaks
existing code in other packages as well - without formally throwing errors at
package check time (as I said, I have unusually strict regression testing
included in the example section, that other packages may not have). If it is
really necessary to treat data.frames differently, I'd recommend to change
"rownames" and "colnames" accordingly, in order to have symmetry between
accessor and assignment functions. That would mean defining "names" and
"row.names" and their assignment methods for any classes inheriting from
data.frame, instead of "dimnames", correct? Maybe *all* package maintainers
should be warned about this or R CMD CHECK should check whether anyone defines
"dimnames" or "dimnames<-" for any class inheriting from "data.frame".
Best regards
Jens Oehlschlägel
> -----Ursprüngliche Nachricht-----
> Von: [EMAIL PROTECTED]
> Gesendet: 08.04.07 16:50:29
> An: [EMAIL PROTECTED]
> CC: [EMAIL PROTECTED],[EMAIL PROTECTED]
> Betreff: Package ref_0.92.tar.gz did not pass R CMD check
> Dear package maintainer,
>
> this notification has been generated automatically.
> Your package ref_0.92.tar.gz did not pass 'R CMD check' on
> Windows and will be omitted from the corresponding CRAN directory
> (CRAN/bin/windows/contrib/2.5/).
> Please check the attached log-file and consider to resubmit a version
> with increased version number that passes R CMD check on Windows.
> R version 2.5.0 alpha (2007-04-05 r41063)
>
> All the best,
> Uwe Ligges
> (Maintainer of binary packages for Windows)
>
>
> <hr>
> * using log directory 'd:/Rcompile/CRANpkg/local/2.5/ref.Rcheck'
> * using R version 2.5.0 alpha (2007-04-05 r41063)
> * checking for file 'ref/DESCRIPTION' ... OK
> * this is package 'ref' version '0.92'
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking whether package 'ref' can be installed ... OK
> * checking package directory ... OK
> * checking for portable file names ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking top-level files ... OK
> * checking index information ... OK
> * checking package subdirectories ... OK
> * checking R files for non-ASCII characters ... OK
> * checking R files for syntax errors ... OK
> * checking whether the package can be loaded ... OK
> * checking whether the package can be loaded with stated dependencies ... OK
> * checking for unstated dependencies in R code ... OK
> * checking S3 generic/method consistency ... WARNING
> dim:
> function(x)
> dim.refdata:
> function(x, ref)
>
> dimnames:
> function(x)
> dimnames.refdata:
> function(x, ref)
>
> dimnames<-:
> function(x, value)
> dimnames<-.refdata:
> function(x, ref, value)
>
> See section 'Generic functions and methods' of the 'Writing R Extensions'
> manual.
> * checking replacement functions ... OK
> * checking foreign function calls ... OK
> * checking R code for possible problems ... OK
> * checking Rd files ... OK
> * checking Rd cross-references ... OK
> * checking for missing documentation entries ... OK
> * checking for code/documentation mismatches ... OK
> * checking Rd \usage sections ... OK
> * creating ref-Ex.R ... OK
> * checking examples ... ERROR
> Running examples in 'ref-Ex.R' failed.
> The error most likely occurred in:
>
> > ### * refdata
> >
> > flush(stderr()); flush(stdout())
> >
> > ### Name: refdata
> > ### Title: subsettable reference to matrix or data.frame
> > ### Aliases: refdata [.refdata [<-.refdata [[.refdata [[<-.refdata
> > ### $.refdata $<-.refdata dim.refdata dim<-.refdata dimnames.refdata
> > ### dimnames<-.refdata print.refdata
> > ### Keywords: programming manip
> >
> > ### ** Examples
> >
> >
> > ## Simple usage Example
> > x <- cbind(1:5, 5:1) # take a matrix or data frame
> > rx <- refdata(x) # wrap it into an refdata object
> > rx # see the autoprinting
> refdata (matrix) with [5,2] of [5,2]
> use x[] to get the complete actual subset
> use x[...] for standard extraction
> use x[..., ref=TRUE] to get a newly indexed refdata object
> use x[...] <- value to overwrite x with a refdata object containing a new env
> containing a modified dataset
> use x[..., ref=TRUE] <- value to modify the original dataset
> > rm(x) # delete original to save memory
> > rx[] # extract all data
> [,1] [,2]
> [1,] 1 5
> [2,] 2 4
> [3,] 3 3
> [4,] 4 2
> [5,] 5 1
> > rx[-1, ] # extract part of data
> [,1] [,2]
> [1,] 2 4
> [2,] 3 3
> [3,] 4 2
> [4,] 5 1
> > rx2 <- rx[-1, , ref=TRUE] # create refdata object referencing part of data
> > (only index, no data is duplicated)
> > rx2 # compare autoprinting
> refdata (matrix) with [4,2] of [5,2]
> use x[] to get the complete actual subset
> use x[...] for standard extraction
> use x[..., ref=TRUE] to get a newly indexed refdata object
> use x[...] <- value to overwrite x with a refdata object containing a new env
> containing a modified dataset
> use x[..., ref=TRUE] <- value to modify the original dataset
> > rx2[] # extract 'all' data
> [,1] [,2]
> [1,] 2 4
> [2,] 3 3
> [3,] 4 2
> [4,] 5 1
> > rx2[-1, ] # extract part of (part of) data
> [,1] [,2]
> [1,] 3 3
> [2,] 4 2
> [3,] 5 1
> > cat("for more examples look the help pages\n")
> for more examples look the help pages
> >
> > ## Not run:
> > ##D # Memory saving demos
> > ##D square.matrix.size <- 1000
> > ##D recursion.depth.limit <- 10
> > ##D non.referenced.matrix <-
> > matrix(1:(square.matrix.size*square.matrix.size), nrow=square.matrix.size,
> > ncol=square.matrix.size)
> > ##D rownames(non.referenced.matrix) <- paste("a",
> > seq(length=square.matrix.size), sep="")
> > ##D colnames(non.referenced.matrix) <- paste("b",
> > seq(length=square.matrix.size), sep="")
> > ##D referenced.matrix <- refdata(non.referenced.matrix)
> > ##D recurse.nonref <- function(m, depth.limit=10){
> > ##D x <- m[1,1] # need read access here to create local copy
> > ##D gc()
> > ##D cat("depth.limit=", depth.limit, " memory.size=", memsize.wrapper(),
> > "\n", sep="")
> > ##D if (depth.limit)
> > ##D Recall(m[-1, -1, drop=FALSE], depth.limit=depth.limit-1)
> > ##D invisible()
> > ##D }
> > ##D recurse.ref <- function(m, depth.limit=10){
> > ##D x <- m[1,1] # read access, otherwise nothing happens
> > ##D gc()
> > ##D cat("depth.limit=", depth.limit, " memory.size=", memsize.wrapper(),
> > "\n", sep="")
> > ##D if (depth.limit)
> > ##D Recall(m[-1, -1, ref=TRUE], depth.limit=depth.limit-1)
> > ##D invisible()
> > ##D }
> > ##D gc()
> > ##D memsize.wrapper()
> > ##D recurse.ref(referenced.matrix, recursion.depth.limit)
> > ##D gc()
> > ##D memsize.wrapper()
> > ##D recurse.nonref(non.referenced.matrix, recursion.depth.limit)
> > ##D gc()
> > ##D memsize.wrapper()
> > ##D rm(recurse.nonref, recurse.ref, non.referenced.matrix,
> > referenced.matrix, square.matrix.size, recursion.depth.limit)
> > ##D
> > ## End(Not run)
> > cat("for even more examples look at regression.test.refdata()\n")
> for even more examples look at regression.test.refdata()
> > regression.test.refdata() # testing correctness of refdata functionality
> testing refdata with matrix
> Error in identical(dim(rx3, ref = TRUE), dim(x)) :
> 2 arguments passed to 'dim' which requires 1
> Execution halted
>
>
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