From mtmorgan at fhcrc.org  Mon Dec 15 19:05:54 2008
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Mon, 15 Dec 2008 10:05:54 -0800
Subject: [Rd] install.packages and dependency version checking
In-Reply-To: <alpine.LFD.2.00.0812131539020.15227@gannet.stats.ox.ac.uk> (Brian
	Ripley's message of "Mon, 15 Dec 2008 17:35:14 +0000 (GMT)")
References: <alpine.LFD.2.00.0812131539020.15227@gannet.stats.ox.ac.uk>
Message-ID: <6phej09uxdp.fsf@gopher4.fhcrc.org>

Prof Brian Ripley <ripley at stats.ox.ac.uk> writes:

> 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.

Without XML in Imports: references in the package name space to
functions in XML rely on the user not adjusting their search
path. Often XML may well be 'infrastructure' that the end-user has no
use for, and should not be contributing to the possibility of
unexpected name collisions by cluttering their search path.

> 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.

Imports: (and imports() in NAMESPACE) gives the name space reliable
access to specific functions / classes; Depends: gives the user access
to (possibly a greater diversity of) functions.

> (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).)

To clarify, I guess you mean that IRanges 1.1.4 would be installed for
packages that specified, say, IRanges >= 1.1.0, but that the package
depending on 1.1.7 would not install. It would be a mistake to install
a package with unsatisfied dependencies.

> (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).
>
> -- 
> 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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793



[Rd] install.packages and dependency version checking
Martin Morgan