[Bioc-devel] peculiar warning in BiocOncoTK

[Martin Morgan]

I'd guess that 'car' is trying to use globalVariables() with saying Imports: utils in the DESCRIPTION and / or importFrom(utils, globalVariables) in the NAMESPACE?

Martin

On 12/19/19, 2:22 PM, "Bioc-devel on behalf of Vincent Carey" <bioc-devel-bounces using r-project.org on behalf of stvjc using channing.harvard.edu> wrote:

    I can't get a handle on this apparent issue with 'car' -- there is some
    
    indication of this globalVariables error at
    https://rdrr.io/github/hadley/tibble/f/revdep/problems.md  but I don't see
    an explanation.  The pernicious aspect of this, which seems limited
    
    to mac, is that it stops the "possible problems" process, and various notes
    
    are not emitted that should be.
    
    
    * checking whether the namespace can be loaded with stated dependencies ...
    WARNING
    
    Error in globalVariables(".groups") :
    
      could not find function "globalVariables"
    
    Error: unable to load R code in package ‘car’
    
    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.
    
    * checking whether the namespace can be unloaded cleanly ... OK
    
    * checking dependencies in R code ... OK
    
    * checking S3 generic/method consistency ... OK
    
    * checking replacement functions ... OK
    
    * checking foreign function calls ... OK
    
    * checking R code for possible problems ... NOTE
    
    Error in globalVariables(".groups") :
    
      could not find function "globalVariables"
    
    Error: unable to load R code in package ‘car’
    
    Execution halted
    
    
    R Under development (unstable) (2019-11-01 r77355)
    
    Platform: x86_64-apple-darwin15.6.0 (64-bit)
    
    Running under: macOS Mojave 10.14.6
    
    
    Matrix products: default
    
    BLAS:
    /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.0.dylib
    
    LAPACK:
    /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
    
    
    locale:
    
    [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
    
    
    attached base packages:
    
    [1] stats     graphics  grDevices utils     datasets  methods   base
    
    
    other attached packages:
    
    [1] rmarkdown_2.0
    
    
    loaded via a namespace (and not attached):
    
     [1] Rcpp_1.0.3        knitr_1.26        magrittr_1.5      rcmdcheck_1.3.3
    
     [5] R6_2.4.1          rlang_0.4.2       fansi_0.4.0       tools_4.0.0
    
     [9] pkgbuild_1.0.6    xopen_1.0.0       xfun_0.11         cli_2.0.0
    
    [13] withr_2.1.2       htmltools_0.4.0   digest_0.6.23     assertthat_0.2.1
    
    [17] rprojroot_1.3-2   crayon_1.3.4      processx_3.4.1    startup_0.14.0
    
    [21] callr_3.4.0       ps_1.3.0          codetools_0.2-16  glue_1.3.1
    
    [25] evaluate_0.14     compiler_4.0.0    desc_1.2.0        backports_1.1.5
    
    [29] prettyunits_1.0.2
    
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