Multiple platform build/check report for BioC 3.13 - CHECK results for rexposome on machv2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rexposome.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rexposome_1.14.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/rexposome.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rexposome/DESCRIPTION’ ... OK
* this is package ‘rexposome’ version ‘1.14.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... WARNING
Found the following file with a non-portable file name:
  vignettes/rsconnect/documents/exposome_data_analysis.Rmd/rpubs.com/rpubs/Publish Document.dcf
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Found the following non-portable file path:
  rexposome/vignettes/rsconnect/documents/exposome_data_analysis.Rmd/rpubs.com/rpubs/Publish Document.dcf

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rexposome’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data      2.8Mb
    extdata   2.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  ‘ggridges’ ‘missMDA’ ‘nnet’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
imputeLOD: multiple local function definitions for ‘faux’ with
  different formal arguments
invExWAS,ExposomeSet : <anonymous>: no visible global function
  definition for ‘reformulate’
invExWAS,ExposomeSet : <anonymous>: no visible global function
  definition for ‘terms’
invExWAS,ExposomeSet: no visible global function definition for
  ‘reformulate’
invExWAS,ExposomeSet: no visible global function definition for ‘terms’
plotHistogram,ExposomeSet: no visible binding for global variable
  ‘..density..’
Undefined global functions or variables:
  ..density.. reformulate terms
Consider adding
  importFrom("stats", "reformulate", "terms")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
clustering-methods      26.262  0.115  26.396
invExWAS-methods        14.682  0.173  14.863
plotCorrelation-methods 12.826  0.095  12.933
correlation-methods      6.067  0.104   6.175
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/rexposome.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rexposome
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘rexposome’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rexposome)

Tests output

Example timings

name	user	system	elapsed
classification-methods	0.024	0.005	0.028
clustering-methods	26.262	0.115	26.396
correlation-methods	6.067	0.104	6.175
ex_imp	0.043	0.002	0.045
expo	0.036	0.021	0.057
expo_c	0.016	0.003	0.019
expos-methods	0.318	0.004	0.322
exposureNames-methods	0.027	0.006	0.033
exwas-methods	0.420	0.013	0.434
familyNames-methods	0.021	0.002	0.023
highAndLow-methods	0.787	0.010	0.796
ilod-methods	0.000	0.000	0.001
imputation-methods	0	0	0
imputeLOD	0.000	0.001	0.001
invExWAS-methods	14.682	0.173	14.863
loadExposome	0.053	0.003	0.057
loadExposome_plain	0.053	0.003	0.057
loadImputed	0.018	0.002	0.020
me	0.003	0.002	0.005
mexwas-methods	1.431	0.007	1.440
ndim-methods	0.058	0.001	0.059
normalityTest-methods	0.244	0.007	0.252
pca-methods	0.075	0.001	0.076
phenotypeNames-methods	0.020	0.002	0.022
plotClassification-methods	0.000	0.001	0.001
plotCorrelation-methods	12.826	0.095	12.933
plotEXP-methods	0.239	0.007	0.247
plotEffect-methods	0.744	0.010	0.756
plotExwas-methods	0.487	0.009	0.497
plotFamily-methods	2.382	0.054	2.441
plotHistogram-methods	0.265	0.004	0.270
plotLOD-methods	0.442	0.004	0.448
plotMissings-methods	0.448	0.005	0.454
plotPCA-methods	1.118	0.015	1.135
plotPHE-methods	0.289	0.006	0.295
readExposome	0.048	0.002	0.049
standardize-methods	0.617	0.015	0.634
tableLOD-methods	0.172	0.009	0.184
tableMissings-methods	0.027	0.004	0.032
tef-methods	0.322	0.015	0.337
toES	0.148	0.006	0.154
trans-methods	0.249	0.004	0.254
volcano_plot	0.744	0.015	0.760

CHECK results for rexposome on machv2

Summary

Command output

Installation output

Tests output

Example timings