From ligges at statistik.tu-dortmund.de  Thu Sep 22 13:54:18 2011
From: ligges at statistik.tu-dortmund.de (Uwe Ligges)
Date: Thu, 22 Sep 2011 13:54:18 +0200
Subject: [Rd] R check error / update.packages
In-Reply-To: <025b01cc7919$03675a30$0a360e90$@sabbe@ugent.be>
References: <025b01cc7919$03675a30$0a360e90$@sabbe@ugent.be>
Message-ID: <4E7B21EA.2020903@statistik.tu-dortmund.de>

This is an infelicity in a recent glmnet release, I will follow up off 
list in a minute.

Best,
Uwe Ligges



On 22.09.2011 13:16, Nick Sabbe wrote:
> While building/checking a package of mine that depends on glmnet, I got the
> following message:
>
>
>
> * checking whether the name space can be loaded with stated dependencies
> ...Warn
>
> ing: running command
> '"C:/Users/nisabbe/Documents/R/R-2.13.1/bin/i386/Rterm.exe"
>
>   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
>
> --
>
> 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]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] R check error / update.packages
Uwe Ligges