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### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PathoStat.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings PathoStat_1.21.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/PathoStat.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PathoStat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PathoStat' version '1.21.0'
* 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 whether package 'PathoStat' 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 ... 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 ... NOTE
Namespaces in Imports field not imported from:
  'ComplexHeatmap' 'RColorBrewer'
  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 ... OK
* 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 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
Bootstrap_LOOCV_LR_AUC         15.21   0.14   15.36
getSignatureFromMultipleGlmnet  8.25   0.01    8.26
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/PathoStat.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL PathoStat
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'PathoStat' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PathoStat'
    finding HTML links ... done
    Bootstrap_LOOCV_LR_AUC                  html  
    Chisq_Test_Pam                          html  
    Fisher_Test_Pam                         html  
    GET_PAM                                 html  
    LOOAUC_simple_multiple_noplot_one_df    html  
    LOOAUC_simple_multiple_one_df           html  
    PathoStat-class                         html  
    TranslateIdToTaxLevel                   html  
    Wilcox_Test_df                          html  
    findRAfromCount                         html  
    findTaxonMat                            html  
    findTaxonomy                            html  
    findTaxonomy300                         html  
    formatTaxTable                          html  
    getShinyInput                           html  
    getShinyInputCombat                     html  
    getShinyInputOrig                       html  
    getSignatureFromMultipleGlmnet          html  
    grepTid                                 html  
    loadPathoscopeReports                   html  
    loadPstat                               html  
    log2CPM                                 html  
    percent                                 html  
    phyloseq_to_edgeR                       html  
    plotPCAPlotly                           html  
    plotPCoAPlotly                          html  
    pstat_data                              html  
    readPathoscopeData                      html  
    runPathoStat                            html  
    savePstat                               html  
    setShinyInput                           html  
    setShinyInputCombat                     html  
    setShinyInputOrig                       html  
    summarizeTable                          html  
** 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 (PathoStat)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'tRanslatome' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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(PathoStat)
> 
> test_check("PathoStat")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
   8.07    0.76    8.82