From ripley at stats.ox.ac.uk  Sat Oct 20 16:50:41 2012
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Sat, 20 Oct 2012 15:50:41 +0100 (BST)
Subject: [Rd] R-2.15.1 CMD CHECK output: "Call Sequence"
In-Reply-To: <F7EACB21-9D34-4F5B-87EA-D72597E96971@garvan.org.au>
References: <F7EACB21-9D34-4F5B-87EA-D72597E96971@garvan.org.au>
Message-ID: <alpine.LFD.2.02.1210201414120.11586@auk.stats.ox.ac.uk>

On Sat, 20 Oct 2012, Mark Cowley wrote:

> Hi guRus,

> i'm running R-2.15.1 and the R CMD CHECK output appears to have 
> changed substantially, in that instead of pointing me to the

Changed since when?   This has been the behaviour for years with the 
error quoted.

> offending functions or files, I get lots of 'call sequence' traces 
> as below.

It is an offending _package_, and it tells you which one in

> Error: package/namespace load failed for ?metaGSEA?

Package 'metaGSEA' seems not to be installed properly.  It also tells 
you that 'library' is involved, so it looks like it is a package load 
and not a namespace load.

You have not told us if ?metaGSEA? is the package under test or a 
dependent.  Given that in earlier 'check' output which you excised the 
loading of the package under test was checked, the latter looks more 
plausible.

> I've been using R CMD CHECK for years & never seen anything like 
> this before. This is on a pretty fresh OSX 10.8 Mountain Lion 
> installation, where I installed R from CRAN via pkg. Is this a 
> problem unique to me?

Maybe not, but unusual.  It is a lot harder to get a package installed 
non-functionally these days, but it can happen if it were installed 
with a different version or architecture, or if binary packages are 
involved.

>
> cheers,
> Mark
>
> heres' a snippet from testing one of my packages under development:
>
> * checking for unstated dependencies in R code ... WARNING
> Error: package/namespace load failed for ?metaGSEA?
> Call sequence:
> 2: stop(gettextf("package/namespace load failed for %s", sQuote(package)),
>      call. = FALSE, domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
> Execution halted
> See the information on DESCRIPTION files in the chapter ?Creating R
> packages? of the ?Writing R Extensions? manual.
> * checking S3 generic/method consistency ... WARNING
> Error: package/namespace load failed for ?metaGSEA?
> Call sequence:
> 2: stop(gettextf("package/namespace load failed for %s", sQuote(package)),
>      call. = FALSE, domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
> Execution halted
> See section ?Generic functions and methods? of the ?Writing R
> Extensions? manual.
> * checking replacement functions ... WARNING
> Error: package/namespace load failed for ?metaGSEA?
> Call sequence:
> 2: stop(gettextf("package/namespace load failed for %s", sQuote(package)),
>      call. = FALSE, domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
> Execution halted
> The argument of a replacement function which corresponds to the right
> hand side must be named ?value?.
> * checking foreign function calls ... WARNING
> Error: package/namespace load failed for ?metaGSEA?
> Call sequence:
> 2: stop(gettextf("package/namespace load failed for %s", sQuote(package)),
>      call. = FALSE, domain = NA)
> 1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
> Execution halted
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595


[Rd] R-2.15.1 CMD CHECK output: "Call Sequence"
Prof Brian Ripley