# [Rd] Outdated dependencies and install.packages()

Martin Maechler maechler at stat.math.ethz.ch
Thu Aug 21 09:39:13 CEST 2008

>>>>> "PD" == Peter Dalgaard <P.Dalgaard at 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...]
>>> Error: package 'Matrix' 0.999375-4 was found, but >= 0.999375.11 is
>>> required by 'lme4'
>>> Execution halted
>>> ** 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.
>>
>> 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.
\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