Re: [Rd] Outdated dependencies and install.packages()

From: Peter Dalgaard <P.Dalgaard_at_biostat.ku.dk>
Date: Thu, 21 Aug 2008 10:53:58 +0200

Martin Maechler wrote:
>>>>>> "PD" == Peter Dalgaard <P.Dalgaard@biostat.ku.dk>
>>>>>> on Wed, 20 Aug 2008 17:06:36 +0200 writes:
>>>>>>
>
> PD> Prof Brian Ripley wrote:
> >> On Wed, 20 Aug 2008, Peter Dalgaard wrote:
> >>
> >>> This looks like a buglet:
> >>>
> >>>> install.packages("lme4", depend=TRUE, lib="~/Rlibrary/")
> >>> --- Please select a CRAN mirror for use in this session ---
> >>> [...snip...]
> >>> ** preparing package for lazy loading
> >>> Error: package 'Matrix' 0.999375-4 was found, but >= 0.999375.11 is
> >>> required by 'lme4'
> >>> Execution halted
> >>> ERROR: lazy loading failed for package 'lme4'
> >>> ** Removing '/home/bs/pd/Rlibrary/lme4'
> >>> ** Restoring previous '/home/bs/pd/Rlibrary/lme4'
> >>>
> >>> and the DESCRIPTION file for lme 4 does have
> >>>
> >>> Depends: methods, R(≥ 2.7.0), Matrix(≥ 0.999375-11), lattice
> >>> <http://cran.r-project.org/web/packages/lattice/index.html>
> >>>
> >>>
> >>> Looks like we're either not checking the version requirement of
> >>> dependencies, or something is making 4 > 11... (from my reading of the
> >>> code, it is the former, but I could have missed something).
> >>
> >> We don't check version requirements of dependencies in
> >> install.packages(). That's a minefield related to having multiple
> >> versions of a package on a system and which gets loaded/namespace
> >> loaded, so you can easily have the needed version but pick up a
> >> different one.
> >>
> >> Depending on whether lazy-loading is in place (and various other
> >> issues) you may or may not need the dependencies to install the
> >> package. It's also a problem that you can update dependencies to
> >> incompatible ones, so the versions available at installation are only
> >> part of the story.
> >>
> >> I don't see why the message reports .11 not -11, but that may be
> >> related to "package_version" classes.
> >>
> >>> We should at least document the behaviour.
> >>
> >> I am not sure where you think it should be documented and is not.
> >> But for install.packages():
> >>
> >> dependencies: logical indicating to also install uninstalled packages
> >> on which these packages depend/suggest/import (and so on
> >> recursively). Not used if 'repos = NULL'. Can also be a
> >> character vector, a subset of 'c("Depends", "Imports",
> >> "Suggests")'.
> >>
> >> 'uninstalled' seems pretty clear to me.
> >>
> PD> It isn't. Matrix 0.999375-11 was 'uninstalled'. The above could just
> PD> mean that if you installed it, it wouldn't be installed again.
>
> PD> Something like "Notice that version dependencies are not checked." would
> PD> help. (Assuming that people read the help page.)
>
> Or even more:
>
> "
> Notice that version dependencies are not checked such that
> outdated versions of installed packages are \emph{not} updated.
> Consider using \code{\link{update.packages}()} before
> \code{install.packages()}.
> "
>
> Note that --- thanks to Kate Mullen's nice help.request() proposal ---
> one of my top "TODOs" for R-devel is
> to finish a generalization of the current
> update.packages()
> function (that I have not quite finished)
> which will allow to only look for updates of specified set of
> packages rather than all packages in a given lib.loc
> {something that should *not* be triggered by a help.request()
> for a user (as ours) who has ~ 2000 R packages installed}.
>
> Martin
>
That's essentially what happened to me (not with 2000 packages, though). I was looking into the lme4/aod issue - reinstall lme4 - Matrix out of date - update.packages() - wait for an hour or so for gtk2 and friends to be updated on my laptop...

-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard_at_biostat.ku.dk)              FAX: (+45) 35327907

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