[Rd] R check error / update.packages

From: Nick Sabbe <nick.sabbe_at_ugent.be>
Date: Thu, 22 Sep 2011 13:16:02 +0200

While building/checking a package of mine that depends on glmnet, I got the following message:  

ing: running command

 R_DEFAULT_PACKAGES=NULL --vanilla --slave -f C:\Users\nisabbe\AppData\Local\Tem

p\RtmpZpjj07\Rin121ae93' had status 1

 WARNING Error: .onLoad failed in loadNamespace() for 'glmnet', details:

  call: cat("Loaded glmnet", installed.packages()["glmnet", "Version"],

  error: could not find function "installed.packages"

Execution halted  

A namespace must be able to be loaded with just the base namespace

loaded: otherwise if the namespace gets loaded by a saved object, the

session will be unable to start.  

Probably some imports need to be declared in the NAMESPACE file.  

I have not changed anything to my dependencies (since my last successful build the day before yesterday), and to my knowledge, I have not changed anything relevant. I am using R 2.13.1 (unchanged since the last successful build) on Windows 7 32bit. When starting a vanilla R terminal, the function installed.packages is present and can be run. Apart from this, I do not get any warnings or errors (e.g. the examples run fine). Also, as far as I can tell, I've never had the warning wrt status 1 (up to today), but it is unclear whether one is just the consequence of the other. Note: the sources for this package can be found on R-Forge: https://r-forge.r-project.org/R/?group_id=1130

The namespace itself contains as its import statement: import(glmnet, rgl, Matrix, snowfall)

Can someone please help me avoid this warning, as I prefer 0 errors 0 warnings.    

On a related note, while trying to alleviate the problem, I ran update.packages, which led me to another problem: apparently, packages that are loaded at the time of update.packages are not updated and may end up broken (this was the case for lattice and Hmisc, for me). Luckily my colleague had gone through the same troubles and pointed me to the solution. I can imagine it to be hard to define exactly which packages should or shouldn't be updated, but it would be nice if the update.packages at least issued a warning against this.    

Nick Sabbe


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