[Bioc-devel] peculiar warning in BiocOncoTK

[Vincent Carey]

On Thu, Dec 19, 2019 at 3:11 PM Martin Morgan <mtmorgan.bioc using gmail.com>
wrote:

> 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?
>

yes -- "without" ... I will contact John Fox.

The error messaging seemed strange, because there are no problems
loading/checking car on its own


> 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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>
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