install.packages and dependency version checking

I've started to implement checks for package versions on dependencies in
install.packages().  However, this is revealing a number of
problems/misconceptions.


(A) We do not check versions when loading namespaces, ahd the namespace
registry does not contain version information.  So that for example
(rtracklayer)

Depends: R (>= 2.7.0), Biobase, methods, RCurl
Imports: XML (>= 1.98-0), IRanges, Biostrings

will never check the version of namespace XML that is loaded, either
already loaded or resulting from loading this package's namespace.  For
this to be operational we would need to extend the syntax of the
imports() and importsFrom() directive in a NAMESPACE file to allow
version restrictions. I am not sure this is worth doing, as an
alternative is to put the imported package in Depends.

The version dependence will in a future release cause an update of XML
when rtracklayer is installed, if needed (and available).

(B) Things like (package stam)

Depends: R (>= 2.7.0), GO.db (>= 2.1.3), Biobase (>= 1.99.5), pamr (>=
        1.37.0), cluster (>= 1.11.10), annaffy (>= 1.11.5), methods (>=
        2.7.0), utils (>= 2.7.0)

are redundant: the versions of method and utils are always the same as
that of R.

And there is no point in having a package in both Depends: and Imports:,
as Biostrings has.

(C) There is no check on the version of a package suggested by
Suggests:, unless the package itself provides one (and I found no
instances).

(D) We can really only handle >= dependencies on package versions (but
then I can see no other ops in use).  install.packages() will find the
latest version available on the repositories, and we possibly need to
check version requirements on the same dependency many times.  Given
that BioC has a penchant for having version dependencies on unavailable
versions (e.g. last week on IRanges (>= 1.1.7) with 1.1.4 available), we
may be able to satisfy the requirements of some packages and not others.
(In that case the strategy used is to install the latest available
version if the one installed does not suffice for those we can satisfy,
and report the problem(s).)

(E) One of the arguments that has been used to do this version checking
at install time is to avoid installing packages that cannot work. It
would be possible to extend the approach to do so, but I am going to
leave that to those who advocated it.


The net effect of the current changes will be that if there is a
dependence that is already installed but a later version is available
and will help satisfy a >= dependence, it will be added to the list of
packages to be installed.  As we have seen with Matrix this last week,
that can have downsides in stopping previously functional packages working.

This is work in progress: there is no way to write a test suite that
will encapsulate all the possible scenarios so weneed to get experience
until 2.9.0 is released.  Please report any quirks to R-devel if they
are completely reproducible (and preferably with the code change needed
to fix them, since the chance of anyone else being able to reproduce
them are fairly slim).