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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:omXplore.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings omXplore_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/omXplore.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘omXplore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘omXplore’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘omXplore’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘bs4Dash::box’ by ‘graphics::box’ when loading ‘omXplore’
  Warning: replacing previous import ‘bs4Dash::column’ by ‘shiny::column’ when loading ‘omXplore’
  Warning: replacing previous import ‘bs4Dash::actionButton’ by ‘shiny::actionButton’ when loading ‘omXplore’
  Warning: replacing previous import ‘bs4Dash::tabsetPanel’ by ‘shiny::tabsetPanel’ when loading ‘omXplore’
  Warning: replacing previous import ‘bs4Dash::insertTab’ by ‘shiny::insertTab’ when loading ‘omXplore’
  Warning: replacing previous import ‘bs4Dash::navbarMenu’ by ‘shiny::navbarMenu’ when loading ‘omXplore’
  Warning: replacing previous import ‘bs4Dash::removePopover’ by ‘shinyBS::removePopover’ when loading ‘omXplore’
  Warning: replacing previous import ‘bs4Dash::addPopover’ by ‘shinyBS::addPopover’ when loading ‘omXplore’
  Warning: replacing previous import ‘bs4Dash::addTooltip’ by ‘shinyBS::addTooltip’ when loading ‘omXplore’
  Warning: replacing previous import ‘bs4Dash::createAlert’ by ‘shinyBS::createAlert’ when loading ‘omXplore’
  Warning: replacing previous import ‘bs4Dash::closeAlert’ by ‘shinyBS::closeAlert’ when loading ‘omXplore’
  Warning: replacing previous import ‘bs4Dash::removeTooltip’ by ‘shinyBS::removeTooltip’ when loading ‘omXplore’
  Warning: replacing previous import ‘shiny::dataTableOutput’ by ‘DT::dataTableOutput’ when loading ‘omXplore’
  Warning: replacing previous import ‘shiny::renderDataTable’ by ‘DT::renderDataTable’ when loading ‘omXplore’
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/omXplore.Rcheck/00install.out’ for details.
* 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 ... OK
* 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Build_X_CC: no visible global function definition for ‘metadata’
Build_X_CC: no visible global function definition for ‘metadata<-’
Check_MSnSet_Consistency : <anonymous>: no visible global function
  definition for ‘experimentData’
MAE_Compatibility_with_Prostar_1x : <anonymous>: no visible binding for
  global variable ‘.colData’
SE_Compatibility_with_Prostar_1.x: no visible global function
  definition for ‘experimentData’
SE_Compatibility_with_Prostar_1.x: no visible global function
  definition for ‘metadata’
SE_Compatibility_with_Prostar_1.x: no visible global function
  definition for ‘metadata<-’
Undefined global functions or variables:
  .colData experimentData metadata metadata<-
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  density-plot.Rd: RColorBrewer
  intensity-plots.Rd: RColorBrewer
  palette.Rd: RColorBrewer
  plot-variance.Rd: RColorBrewer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 data for ASCII and uncompressed saves ... 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/omXplore.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL omXplore
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘omXplore’ ...
** this is package ‘omXplore’ version ‘1.2.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘bs4Dash::box’ by ‘graphics::box’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::column’ by ‘shiny::column’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::actionButton’ by ‘shiny::actionButton’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::tabsetPanel’ by ‘shiny::tabsetPanel’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::insertTab’ by ‘shiny::insertTab’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::navbarMenu’ by ‘shiny::navbarMenu’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::removePopover’ by ‘shinyBS::removePopover’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::addPopover’ by ‘shinyBS::addPopover’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::addTooltip’ by ‘shinyBS::addTooltip’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::createAlert’ by ‘shinyBS::createAlert’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::closeAlert’ by ‘shinyBS::closeAlert’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::removeTooltip’ by ‘shinyBS::removeTooltip’ when loading ‘omXplore’
Warning: replacing previous import ‘shiny::dataTableOutput’ by ‘DT::dataTableOutput’ when loading ‘omXplore’
Warning: replacing previous import ‘shiny::renderDataTable’ by ‘DT::renderDataTable’ when loading ‘omXplore’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘bs4Dash::box’ by ‘graphics::box’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::column’ by ‘shiny::column’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::actionButton’ by ‘shiny::actionButton’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::tabsetPanel’ by ‘shiny::tabsetPanel’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::insertTab’ by ‘shiny::insertTab’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::navbarMenu’ by ‘shiny::navbarMenu’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::removePopover’ by ‘shinyBS::removePopover’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::addPopover’ by ‘shinyBS::addPopover’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::addTooltip’ by ‘shinyBS::addTooltip’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::createAlert’ by ‘shinyBS::createAlert’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::closeAlert’ by ‘shinyBS::closeAlert’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::removeTooltip’ by ‘shinyBS::removeTooltip’ when loading ‘omXplore’
Warning: replacing previous import ‘shiny::dataTableOutput’ by ‘DT::dataTableOutput’ when loading ‘omXplore’
Warning: replacing previous import ‘shiny::renderDataTable’ by ‘DT::renderDataTable’ when loading ‘omXplore’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘bs4Dash::box’ by ‘graphics::box’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::column’ by ‘shiny::column’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::actionButton’ by ‘shiny::actionButton’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::tabsetPanel’ by ‘shiny::tabsetPanel’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::insertTab’ by ‘shiny::insertTab’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::navbarMenu’ by ‘shiny::navbarMenu’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::removePopover’ by ‘shinyBS::removePopover’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::addPopover’ by ‘shinyBS::addPopover’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::addTooltip’ by ‘shinyBS::addTooltip’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::createAlert’ by ‘shinyBS::createAlert’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::closeAlert’ by ‘shinyBS::closeAlert’ when loading ‘omXplore’
Warning: replacing previous import ‘bs4Dash::removeTooltip’ by ‘shinyBS::removeTooltip’ when loading ‘omXplore’
Warning: replacing previous import ‘shiny::dataTableOutput’ by ‘DT::dataTableOutput’ when loading ‘omXplore’
Warning: replacing previous import ‘shiny::renderDataTable’ by ‘DT::renderDataTable’ when loading ‘omXplore’
** testing if installed package keeps a record of temporary installation path
* DONE (omXplore)

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 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)
> 
> test_check("omXplore")
Loading required package: omXplore
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 0 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 0 ]
There were 14 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
  5.520   0.334   5.872