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This page was generated on 2025-04-22 13:18 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1572/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhenStat 2.44.0  (landing page)
Hamed Haselimashhadi
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/PhenStat
git_branch: RELEASE_3_21
git_last_commit: 2aa17ff
git_last_commit_date: 2025-04-15 10:28:01 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for PhenStat on kjohnson3

To the developers/maintainers of the PhenStat package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PhenStat.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: PhenStat
Version: 2.44.0
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_2.44.0.tar.gz
StartedAt: 2025-04-21 20:54:01 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 20:54:53 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 51.6 seconds
RetCode: 0
Status:   OK  
CheckDir: PhenStat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_2.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/PhenStat.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 ‘PhenStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhenStat’ version ‘2.44.0’
* 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
* 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-3.21-bioc/meat/PhenStat.Rcheck/00check.log’
for details.


Installation output

PhenStat.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘PhenStat’ ...
** this is package ‘PhenStat’ version ‘2.44.0’
** 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)

Tests output

PhenStat.Rcheck/tests/runTests.Rout


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.

> 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 -- Mon Apr 21 20:54:48 2025 
*********************************************** 
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 
  1.027   0.073   1.095 

Example timings

PhenStat.Rcheck/PhenStat-Ex.timings

nameusersystemelapsed
FisherExactTest0.0450.0040.050
JSONOutput0.3210.0130.335
LRDataset0.0160.0010.018
PhenList-class0.0550.0040.058
PhenList0.0560.0020.060
PhenStatReport0.0100.0010.011
PhenTestResult-class0.2880.0060.294
PhenTestResult0.2410.0030.245
RRTest0.0330.0030.035
TFDataset0.0650.0060.071
analysedDataset0.2700.0050.274
analysisResults0.2650.0020.267
boxplotResidualBatch0.2910.0050.295
boxplotSexGenotype0.0210.0020.023
boxplotSexGenotypeBatch0.0380.0020.041
boxplotSexGenotypeBatchAdjusted0.0200.0010.021
boxplotSexGenotypeResult0.3370.0090.349
boxplotSexGenotypeWeightBatchAdjusted0.0190.0010.020
categoricalBarplot0.1860.0030.190
checkDataset0.0110.0010.011
classificationTag0.2630.0060.272
determiningLambda0.4270.1400.573
dim0.0120.0000.012
finalLRModel0.1580.0080.165
finalModel0.2430.0100.253
finalTFModel0.1310.0070.139
htestPhenStat-class0.0370.0030.040
modelFormula000
modelFormulaLR0.0000.0000.001
parserOutputSummary0.2710.0090.279
parserOutputSummaryLR0.1380.0080.146
parserOutputTFSummary0.030.000.03
performReverseTransformation0.0000.0000.001
performTransformation000
plot.PhenList0.8720.0360.910
plot.PhenTestResult0.8620.0270.890
plotResidualPredicted0.2820.0090.292
printLROutput0.1440.0040.149
printTabStyle000
qqplotGenotype0.2780.0070.285
qqplotRandomEffects0.2760.0070.282
qqplotRotatedResiduals1.5380.0141.556
recommendMethod0.0640.0020.066
scatterplotGenotypeWeight0.0560.0020.059
scatterplotGenotypeWeightResult0.3410.0140.355
scatterplotSexGenotypeBatch0.0270.0030.030
scatterplotSexGenotypeBatchResult0.3280.0100.338
startLRModel0.1450.0060.151
startModel0.2290.0030.233
startTFModel0.1200.0030.123
summaryOutput0.3170.0090.327
summaryPhenListResult0.3130.0210.333
testDataset0.8500.0340.883
testFinalLRModel0.1400.0080.148
testFinalModel0.3320.0070.339
vectorOutput0.3030.0090.312
vectorOutputMatrices0.0410.0040.044