214update.txt

Updating packages for 2.14.0
===========================+

Package maintainers should be aware of the following changes scheduled
to appear in 2.14.0 on 31 October 2011.

Lazy-loading
============

All packages will be lazy-loaded.  Please remove any LazyLoad field
from the DESCRIPTION file: false values will give a warning on
installation.

Very few packages were affected by this: in most cases they had
top-level code with side-effects, something 'Writing R Extensions' has
warned about for many years.


Namespaces
==========

All packages will have a namespace, and R CMD INSTALL will create a
NAMESPACE file if one is not supplied (and R CMD build will add one,
using the same code).

The automatically-generated NAMESPACE file works well in the vast
majority of cases (well over 1000 packages on CRAN), but should be
regarded as a starting point for updating the package.  Known issues
include:

- The default namespace exports all symbols (even those names starting
  with '.'): you probably want to be much more selective.

- If you have a .First.lib() function, it is run as .onAssign.  In
  many cases this is only used to load compiled code and can be
  replaced by a useDynLib directive in the NAMESPACE file.  In others
  the .First.lib() function should be renamed as .onAssign() or
  .onLoad(): in a few cases it needs to split into two functions.

  There are exceptions where it has been found that .First.lib should
  be run as .onLoad: these are listed in object
  base::.Firstlib_as_onLoad.

- The package environment is sealed, so you cannot use it to store
  changing values.  Use a separate environment instead: there are
  examples in package 'grDevices' for example.

- There may be scoping issues.  If as for package 'quantreg' you make
  use of a function t() from package SparseM, the namespace needs to
  import SparseM (or just the functions used from SparseM).  This is
  most common where S4 generics which mask functions in 'base' are to
  be used.

- If the package defines S3 methods for generics in other packages
  such as 'stats', it should import the generic and register the
  method with an S3method directive.

- Packages which set S4 methods which create an S4 generic by taking
  over a function in another package (notably plot()) need to import
  the function they take over, e.g. by importFrom(graphics, plot).
  (This may appear to work without in R 2.14.x, but the package will
  then not install in R 2.13.x.)


Vignette sources
================

The preferred location for vignette sources is now directory
'vignettes' and not 'inst/doc'.  If you want to maintain compatibility
with R <= 2.13.x for the time being, do at least make use of a
.Rinstignore file to avoid installing anything other than the vignette
.Rnw (etc) and .pdf files, plus any other files needed for end-users
to run the vignette code.

If you know a priori that the vignettes cannot be re-made on CRAN
(e.g. because you use unusual LaTeX files), set the BuildVignettes
field in the DESCRIPTION file to a false value.  (The R code in the
vignettes as extracted by Stangle still needs to be runnable.)


Deprecation
===========

Using mean(x) and sd(x) directly on data frames (or also matrices,
for sd) x, is deprecated, and produces warnings now.
Both uses have been relatively widespread, and should be replaced
by sapply(), vapply() or, for mean, colMeans().