[Rd] package incompatibility under 2.5.0 (please respond directly, I am not on r-devel)

[Jens Oehlschlägel]

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: Uwe.Ligges at R-Project.org
> Gesendet: 08.04.07 16:50:29
> An: joehl at web.de
> CC: Uwe.Ligges at R-Project.org,olafm at kimberly.tako.de
> 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
> 
>