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
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>
--
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