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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PhenStat_2.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/PhenStat.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhenStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhenStat’ version ‘2.40.0’
* 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 ‘PhenStat’ 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 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 ... NOTE
Namespace in Imports field not imported from: ‘SmoothWin’
  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 ... NOTE
checkRd: (-1) plot.PhenList.Rd:49-53: Lost braces
    49 |       \item boxplotSexGenotype. See documentations for {
       |                                                        ^
checkRd: (-1) plot.PhenList.Rd:54-58: Lost braces
    54 |       \item boxplotSexGenotypeBatchAdjusted. See documentations for {
       |                                                                     ^
checkRd: (-1) plot.PhenList.Rd:59-63: Lost braces
    59 |       \item boxplotSexGenotypeWeightBatchAdjusted. See documentations for {
       |                                                                           ^
checkRd: (-1) plot.PhenList.Rd:64-68: Lost braces
    64 |       \item scatterplotSexGenotypeBatch. See documentations for {
       |                                                                 ^
checkRd: (-1) plot.PhenList.Rd:69-73: Lost braces
    69 |       \item scatterplotGenotypeWeight. See documentations for {
       |                                                               ^
checkRd: (-1) plot.PhenList.Rd:74-78: Lost braces
    74 |       \item boxplotSexGenotypeBatch. See documentations for {
       |                                                             ^
checkRd: (-1) plot.PhenTestResult.Rd:41-45: Lost braces
    41 |       \item boxplotSexGenotypeResult. See documentations for {
       |                                                              ^
checkRd: (-1) plot.PhenTestResult.Rd:46-50: Lost braces
    46 |       \item scatterplotSexGenotypeBatchResult. See documentations for {
       |                                                                       ^
checkRd: (-1) plot.PhenTestResult.Rd:51-55: Lost braces
    51 |       \item scatterplotGenotypeWeightResult. See documentations for {
       |                                                                     ^
checkRd: (-1) plot.PhenTestResult.Rd:56-60: Lost braces
    56 |       \item plotResidualPredicted. See documentations for {
       |                                                           ^
checkRd: (-1) plot.PhenTestResult.Rd:61-65: Lost braces
    61 |       \item qqplotRandomEffects. See documentations for {
       |                                                         ^
checkRd: (-1) plot.PhenTestResult.Rd:66-70: Lost braces
    66 |       \item boxplotResidualBatch. See documentations for {
       |                                                          ^
checkRd: (-1) plot.PhenTestResult.Rd:71-75: Lost braces
    71 |       \item qqplotRotatedResiduals. See documentations for {
       |                                                            ^
checkRd: (-1) plot.PhenTestResult.Rd:76-80: Lost braces
    76 |       \item qqplotGenotype. See documentations for {
       |                                                    ^
checkRd: (-1) plot.PhenTestResult.Rd:81-85: Lost braces
    81 |       \item categoricalBarplot. See documentations for {
       |                                                        ^
checkRd: (-1) qqplotRotatedResiduals.Rd:18: Lost braces
    18 |     Houseman, E. A., Ryan, L. M., Coull, B. A. (2004): Cholesky residuals for assessing normal errors in a linear model with correlated outcomes. \emph{Journal of the American Statistical Association} \bold{99}{466}: pg 383-394. Doi 10.1198
       |                                                                                                                                                                                                                   ^
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'printLROutput.Rd':
  ‘effectValues’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... NOTE
Argument items with no description in Rd file 'plot.PhenList.Rd':
  ‘\dots’
Argument items with no description in Rd file 'plot.PhenTestResult.Rd':
  ‘\dots’
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
qqplotRotatedResiduals 5.577  0.068    5.74
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/PhenStat.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PhenStat
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘PhenStat’ ...
** using staged installation
** R
** 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 (PhenStat)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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.

> BiocGenerics:::testPackage("PhenStat")

 >=========================================================================<
 This version of PhenStat includes *FEWER* functions than the previous ones 
 You *still* can use the previous functions by using `:::`. For example :   
 PhenStat:::boxplotSexGenotype   or   PhenStat:::FisherExactTest            
 *** Want to know what is new in this version? run PhenStat:::WhatIsNew()   
 >=========================================================================<


RUNIT TEST PROTOCOL -- Fri Oct 18 07:27:43 2024 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
PhenStat RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  3.734   0.293   4.062