[Rd] Dependencies on recommended packages

From: Nick Sabbe <nick.sabbe_at_ugent.be>
Date: Fri, 01 Jun 2012 11:19:49 +0200


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

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