Updating packages for 1.8.0
===========================

Package maintainers should be aware of the following changes scheduled
to appear in 1.8.0.


1) print.coefmat (which was not a print method) has been deprecated and
replaced by printCoefmat.  By default NAs are not suppressed: should
this be desired call printCoefmat(..., na.print="").


2) codes() and codes<-() have been deprecated.  They did not use the
internal codes of an unordered factor, and in almost all cases
unclass/as.vector/as.integer was intended.  There is no replacment for 
codes<-(), but it appears to be unused on CRAN.


3) Multi-argument returns are deprecated.  Use a named list, e.g. replace

      return(pred, se)

by

      return(list(pred=pred, se=se))
.


4) Calling UseMethod with more than two arguments gives a warning, as
R-lang has long said it did.  Normally one argument suffices, and

       UseMethod("foo", x, ...)

is incorrect usage:  replace it by UseMethod("foo") unless you do not
want to dispatch on the first argument of the enclosing function.


5) The distinction between as.character(NA) and "NA" introduced in 1.5.0 
is now observed by sub, gsub, grep, regexpr, chartr, tolower, toupper, 
substr, substring, abbreviate and strsplit, but not by nchar. NA behaves 
as `unknown': any comparison with NA is has NA results.


6) The S3 methods format.dist() and plot.hclust() are removed from the mva
namespace.


7) The QC facilities in package tools have substantially been enhanced, and
hence might report problems not found previously.  Analyzing \usage
sections no longer misses replacement functions or S3 replacement
methods, and no longer ignores variables and data sets.  Code for
computation on S3 methods now knows about internal S3 generics and S3
group generics.  S4 classes and methods are tested where appropriate.
There is some support for namespace renaming.  Function checkDocFiles()
(renamed from checkDocArgs()) now also determines 'over-documented'
arguments which are given in the \arguments section but not in \usage.
There is some code/documentation consistency checking for data sets and
S4 classes.


8) Additional Rd markup is now available, including \concept for concept
index entries to be used by help.search(), \preformatted, as well as
commands for emphasizing and quoting text, for indicating the usage of
an S4 method, and for indicating specific kinds of text.


9) .Random.seed is only looked for in the workspace, so R code in
packages should use constructs like

    exists(".Random.seed", envir=.GlobalEnv, inherits = FALSE)
    seed.save <- get(".Random.seed", envir=.GlobalEnv, inherits = FALSE)
    assign(".Random.seed",  seed.save, envir=.GlobalEnv)


10) The header file <R_ext/Mathlib.h> has been removed: it was replaced by
<Rmath.h> in R 1.2.0.