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[Bioc-devel] peculiar warning in BiocOncoTK

3 messages · Martin Morgan, Vincent Carey

Vincent Carey
# 
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
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 at r-project.org on behalf of stvjc at 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
    
    -- 
    The information in this e-mail is intended only for the ...{{dropped:18}}
    
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Vincent Carey
# 
On Thu, Dec 19, 2019 at 3:11 PM Martin Morgan <mtmorgan.bioc at gmail.com>
wrote:
yes -- "without" ... I will contact John Fox.

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