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 haltedsessionInfo()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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
-- Brian D. Ripley, rip...@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
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