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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RUCova.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RUCova_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RUCova.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘RUCova/DESCRIPTION’ ... OK
* this is package ‘RUCova’ version ‘1.0.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RUCova’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘magrittr’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calc_mean_BC: no visible binding for global variable ‘quantile’
calc_mean_BC: no visible global function definition for ‘head’
calc_mean_DNA: no visible binding for global variable ‘quantile’
compare_corr: no visible global function definition for ‘cor’
rucova: no visible global function definition for ‘setNames’
rucova : <anonymous>: no visible global function definition for
  ‘reformulate’
rucova : <anonymous>: no visible global function definition for ‘lm’
rucova: no visible binding for global variable ‘coef’
rucova: no visible global function definition for ‘coef’
rucova: no visible binding for global variable ‘resid’
rucova: no visible global function definition for ‘resid’
rucova : <anonymous>: no visible global function definition for
  ‘residuals’
rucova : <anonymous>: no visible global function definition for ‘coef’
rucova: no visible global function definition for ‘reformulate’
rucova: no visible binding for global variable ‘marker’
rucova: no visible binding for global variable ‘coef_key’
rucova: no visible binding for global variable ‘surrogate’
rucova: no visible binding for global variable ‘value’
rucova: no visible binding for global variable ‘sd’
rucova: no visible binding for global variable ‘eff_value’
rucova: no visible binding for global variable ‘sd_x’
rucova: no visible binding for global variable ‘sd_y’
Undefined global functions or variables:
  coef coef_key cor eff_value head lm marker quantile reformulate resid
  residuals sd sd_x sd_y setNames surrogate value
Consider adding
  importFrom("stats", "coef", "cor", "lm", "quantile", "reformulate",
             "resid", "residuals", "sd", "setNames")
  importFrom("utils", "head")
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
heatmap_compare_corr 6.337  0.258   6.595
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/RUCova.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL RUCova
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘RUCova’ ...
** this is package ‘RUCova’ version ‘1.0.0’
** 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 (RUCova)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(RUCova)
> 
> test_check("RUCova")
Fitting pH3
Fitting IdU
Fitting Cyclin_D1
Fitting Cyclin_B1
Fitting Ki.67
Fitting pRb
Fitting pH2A.X
Fitting p.p53
Fitting p.p38
Fitting pChk2
Fitting pCDC25c
Fitting cCasp3
Fitting cPARP
Fitting pAkt
Fitting pAkt_T308
Fitting pMEK1.2
Fitting pERK1.2
Fitting pS6
Fitting p4e.BP1
Fitting pSmad1.8
Fitting pSmad2.3
Fitting pNFkB
Fitting IkBa
Fitting CXCL1
Fitting Lamin_B1
Fitting pStat1
Fitting pStat3
Fitting YAP
Fitting NICD
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 11.569   0.729  12.299