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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:timeOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings timeOmics_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/timeOmics.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘timeOmics/DESCRIPTION’ ... OK
* this is package ‘timeOmics’ version ‘1.16.0’
* 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:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘timeOmics’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* checking code 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
getCluster:
  function(X, user.block, user.cluster)
getCluster.UpDown:
  function(X, user.block, user.cluster, .by, .preserve, ...)

filter:
  function(.data, ..., .by, .preserve)
filter.cluster.df:
  function(.data, user.block, user.cluster)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.mutate_cluster: no visible binding for global variable ‘cluster’
.mutate_cluster: no visible binding for global variable ‘contrib.max’
check_legend.block.name: no visible global function definition for ‘is’
dmatrix.spearman.dissimilarity: no visible global function definition
  for ‘cor’
filter.cluster.df: no visible binding for global variable ‘block’
filter.cluster.df: no visible binding for global variable ‘cluster’
get_MSE: no visible binding for global variable ‘feature’
get_MSE: no visible global function definition for ‘na.omit’
get_MSE: no visible binding for global variable ‘Y_i’
get_MSE: no visible binding for global variable ‘Y_hat’
get_MSE: no visible binding for global variable ‘error’
getCluster.block.pls: no visible binding for global variable ‘block’
getCluster.block.pls: no visible binding for global variable ‘molecule’
getCluster.block.pls: no visible binding for global variable ‘comp’
getCluster.block.spls: no visible binding for global variable ‘block’
getCluster.block.spls: no visible binding for global variable
  ‘molecule’
getCluster.block.spls: no visible binding for global variable ‘comp’
getCluster.mixo_pls: no visible binding for global variable ‘comp’
getCluster.mixo_spls: no visible binding for global variable ‘comp’
getCluster.pca: no visible binding for global variable ‘comp’
getCluster.spca: no visible binding for global variable ‘comp’
getNcomp: no visible global function definition for ‘is’
getUpDownCluster: no visible global function definition for ‘is’
lmms.filter.lines: no visible global function definition for ‘is’
lmms.filter.lines: no visible global function definition for ‘slot’
lmms.filter.lines: no visible binding for global variable ‘feature’
lmms.filter.lines: no visible binding for global variable ‘BP.test’
lmms.filter.lines: no visible binding for global variable ‘MSE’
lmms.filter.lines: no visible binding for global variable ‘val’
lmms.filter.lines: no visible global function definition for ‘all_of’
plot.ncomp.tune.silhouette: no visible global function definition for
  ‘is’
plot.ncomp.tune.silhouette: no visible binding for global variable
  ‘ncomp’
plot.proportionality: no visible binding for global variable ‘cluster1’
plot.proportionality: no visible binding for global variable ‘value’
plot.proportionality: no visible binding for global variable
  ‘insideout’
plot.spca.tune.silhouette: no visible binding for global variable
  ‘comp’
plot.spca.tune.silhouette: no visible binding for global variable ‘X’
plot.spca.tune.silhouette: no visible binding for global variable
  ‘na.omit’
plot.spca.tune.silhouette: no visible binding for global variable
  ‘contrib’
plot.spca.tune.silhouette: no visible binding for global variable
  ‘value’
plotLong: no visible binding for global variable ‘block’
plotLong: no visible binding for global variable ‘new.block’
plotLong: no visible global function definition for ‘is’
plotLong: no visible binding for global variable ‘.’
plotLong: no visible binding for global variable ‘value’
plotLong: no visible binding for global variable ‘molecule’
proportionality: no visible binding for global variable ‘molecule’
proportionality: no visible binding for global variable ‘cluster’
proportionality: no visible binding for global variable ‘.’
proportionality : <anonymous>: no visible binding for global variable
  ‘.’
proportionality: no visible binding for global variable ‘feature1’
proportionality: no visible binding for global variable ‘feature2’
proportionality: no visible binding for global variable ‘cluster1’
proportionality: no visible binding for global variable ‘cluster2’
proportionality: no visible global function definition for ‘na.omit’
remove.low.cv: no visible global function definition for ‘is’
remove.low.cv : <anonymous>: no visible global function definition for
  ‘sd’
sd_new: no visible global function definition for ‘sd’
silhouette: no visible binding for global variable ‘silhouette.coef’
stat_median: no visible binding for global variable ‘cluster1’
stat_median: no visible binding for global variable ‘cluster2’
stat_median: no visible binding for global variable ‘value’
stat_median: no visible global function definition for ‘median’
stat_median: no visible binding for global variable ‘Pvalue’
stat_median: no visible binding for global variable ‘na.omit’
to_lr2phs: no visible global function definition for ‘var’
tune.silhouette.get_choice_keepX: no visible binding for global
  variable ‘comp’
tune.silhouette.get_choice_keepX: no visible binding for global
  variable ‘direction’
tune.silhouette.get_choice_keepX: no visible binding for global
  variable ‘Pval.pos’
tune.silhouette.get_choice_keepX: no visible binding for global
  variable ‘Pval.neg’
tune.silhouette.get_choice_keepX: no visible binding for global
  variable ‘distance_from_origin’
tune.silhouette.get_choice_keepX: no visible binding for global
  variable ‘Pval.dir’
tune.silhouette.get_choice_keepX: no visible binding for global
  variable ‘Pval.value’
tune.silhouette.get_choice_keepX: no visible global function definition
  for ‘na.omit’
tune.silhouette.get_choice_keepX : <anonymous>: no visible binding for
  global variable ‘Pval.value’
tune.silhouette.get_choice_keepX : <anonymous>: no visible binding for
  global variable ‘distance_from_origin’
tune.silhouette.get_choice_keepX : <anonymous>: no visible binding for
  global variable ‘.’
tune.silhouette.get_slopes: no visible global function definition for
  ‘is’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘origin’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘destination’
tune.silhouette.get_slopes: no visible binding for global variable ‘.’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘comp’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘direction’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘slope.pos’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘slope.neg’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘Z_score.pos’
tune.silhouette.get_slopes: no visible global function definition for
  ‘pnorm’
tune.silhouette.get_slopes: no visible binding for global variable
  ‘Z_score.neg’
tuneCluster.block.spls: no visible binding for global variable
  ‘silhouette.coef’
tuneCluster.spca: no visible binding for global variable
  ‘silhouette.coef’
tuneCluster.spls: no visible binding for global variable
  ‘silhouette.coef’
unscale: no visible global function definition for ‘is’
Undefined global functions or variables:
  . all_of block BP.test cluster cluster1 cluster2 comp contrib
  contrib.max cor destination direction distance_from_origin error
  feature feature1 feature2 insideout is median molecule MSE na.omit
  ncomp new.block origin pnorm Pval.dir Pval.neg Pval.pos Pval.value
  Pvalue sd silhouette.coef slope.neg slope.pos slot val value var X
  Y_hat Y_i Z_score.neg Z_score.pos
Consider adding
  importFrom("methods", "is", "slot")
  importFrom("stats", "cor", "median", "na.omit", "pnorm", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘timeOmics.simdata’
Undocumented data sets:
  ‘timeOmics.simdata’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc-mac-arm64/meat/timeOmics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL timeOmics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘timeOmics’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '*' 
** help
*** installing help indices
*** copying figures
** 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 (timeOmics)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(timeOmics)
Loading required package: mixOmics
Loading required package: MASS
Loading required package: lattice
Loading required package: ggplot2

Loaded mixOmics 6.28.0
Thank you for using mixOmics!
Tutorials: http://mixomics.org
Bookdown vignette: https://mixomicsteam.github.io/Bookdown
Questions, issues: Follow the prompts at http://mixomics.org/contact-us
Cite us:  citation('mixOmics')

> 
> test_check("timeOmics")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 263 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 263 ]
> 
> proc.time()
   user  system elapsed 
 17.567   0.196  17.772