From ligges at statistik.tu-dortmund.de  Fri Jun  1 12:10:17 2012
From: ligges at statistik.tu-dortmund.de (Uwe Ligges)
Date: Fri, 01 Jun 2012 12:10:17 +0200
Subject: [Rd] Dependencies on recommended packages
In-Reply-To: <027001cd3fd7$b179a3f0$146cebd0$@ugent.be>
References: <027001cd3fd7$b179a3f0$146cebd0$@ugent.be>
Message-ID: <4FC89509.70000@statistik.tu-dortmund.de>

Does it still happen with R-2.15.0 patched? Maybe an old version of 
Matrix in a library that is first in the search path? Unfortunately 
glmnet does not import from Matrix and search path issues are likely to 
happen. This needs to be sorted out on R-forge , I think.

Best,
Uwe Ligges




On 01.06.2012 11:19, Nick Sabbe wrote:
> Dear all,
>
>
>
> I've recently had some issues getting my package to successfully "check".
>
> This was on R-Forge, so it's not obvious for me to provide SessionInfo or
> the likes (if necessary, Stefan can chime in?).
>
>
>
> After some research (mainly by Stefan Theussler, driving force behind
> R-Forge), this turned out to be the root cause:
>
> On R-Forge, the version of R installed was the latest release (2.15.0),
> which includes Matrix 1.0-5 as a recommended package.
>
>
>
> My own package depends upon glmnet, which itself depends upon Matrix 1.0-6.
>
> (Note: to avoid issues with that, as a test I've also included an explicit
> dependency upon Matrix 1.0-6 in my own package, but this didn't change
> anything).
>
>
>
> During build and most of R CMD check (with the -as-cran flag), everything
> worked out fine (which suggests to me that among others, Matrix 1.0-6 is
> present and can be loaded, since one of the checks is that the package and
> all its dependencies can be loaded), but while running the examples, somehow
> loading of the package failed, with an error message that Matrix 1.0-6 could
> not be loaded. Here's the relevant part of the log:
>
>> library('addendum')
>
> Loading required package: glmnet
>
> Error: package 'Matrix' 1.0-5 was found, but>= 1.0.6 is required by
> 'glmnet'
>
> Execution halted
>
> Run time: 92.43 seconds.
>
>
>
> There are some issues with this comparison, but in the Windows build/check
> chain on R-Forge, R2.15.0 patched was installed (including Matrix 1.0-6) and
> the build _was_ successful.
>
>
>
> Stefan suspected this to be an artifact of Matrix being a recommended
> package (so R CMD check would somehow prefer the version installed with R),
> and to a certain degree the successful build/check with R patched confirms
> this suspicion.
>
> I've neither read up on this nor tried other options, but if this is indeed
> the case then I suggest to alter this behaviour. Unless, of course, there is
> any reason to treat "recommended" packages any different wrt versioning and
> R CMD check.
>
>
>
>
>
> I suspect other people may run into this sooner or later.
>
> If not or if my/our analysis is wrong/incomplete I will gladly stand
> corrected.
>
> I'll leave it to you gurus to judge.
>
>
>
> Thanks for R! (And another shout out to Stefan, who diligently helped me)
>
>
>
>
>
> Nick Sabbe
>
> --
>
> ping: nick.sabbe at ugent.be
>
> link:<http://biomath.ugent.be/>  http://biomath.ugent.be
>
> wink: A1.056, Coupure Links 653, 9000 Gent
>
> ring: 09/264.59.36
>
>
>
> -- Do Not Disapprove
>
>
>
>
> 	[[alternative HTML version deleted]]
>
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[Rd] Dependencies on recommended packages
Uwe Ligges