[Rd] install.packages and dependency version checking
Prof Brian Ripley
ripley at stats.ox.ac.uk
Mon Dec 15 18:35:14 CET 2008
I've started to implement checks for package versions on dependencies in
install.packages(). However, this is revealing a number of
(A) We do not check versions when loading namespaces, ahd the namespace
registry does not contain version information. So that for example
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
(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
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
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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