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This page was generated on 2024-05-04 11:36:57 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1557/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PhenStat 2.40.0  (landing page)
Hamed Haselimashhadi
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/PhenStat
git_branch: RELEASE_3_19
git_last_commit: d560e21
git_last_commit_date: 2024-04-30 10:34:35 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for PhenStat on nebbiolo1


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: 2.40.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings PhenStat_2.40.0.tar.gz
StartedAt: 2024-05-04 02:20:29 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 02:22:41 -0400 (Sat, 04 May 2024)
EllapsedTime: 132.0 seconds
RetCode: 0
Status:   OK  
CheckDir: PhenStat.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings PhenStat_2.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/PhenStat.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/PhenStat.Rcheck/00check.log’
for details.


Installation output

PhenStat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL PhenStat
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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)

Tests output

PhenStat.Rcheck/tests/runTests.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 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.

> 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 -- Sat May  4 02:22:25 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 
  2.983   0.197   3.169 

Example timings

PhenStat.Rcheck/PhenStat-Ex.timings

nameusersystemelapsed
FisherExactTest0.1190.0200.140
JSONOutput0.7510.0200.772
LRDataset0.080.000.08
PhenList-class0.1780.0040.183
PhenList0.1650.0000.165
PhenStatReport0.0420.0000.043
PhenTestResult-class0.6320.0080.640
PhenTestResult0.5400.0000.539
RRTest0.0870.0000.088
TFDataset0.1780.0350.214
analysedDataset0.6070.0550.663
analysisResults0.6090.0050.614
boxplotResidualBatch0.6560.0000.657
boxplotSexGenotype0.0560.0040.060
boxplotSexGenotypeBatch0.1190.0000.118
boxplotSexGenotypeBatchAdjusted0.0590.0000.059
boxplotSexGenotypeResult1.0460.0401.087
boxplotSexGenotypeWeightBatchAdjusted0.0550.0000.055
categoricalBarplot0.1110.0000.110
checkDataset0.0410.0000.040
classificationTag0.5900.0040.594
determiningLambda0.8430.0440.887
dim0.0360.0000.036
finalLRModel0.4770.0200.498
finalModel0.5190.0000.519
finalTFModel0.3760.0200.396
htestPhenStat-class0.0980.0030.102
modelFormula0.0000.0000.001
modelFormulaLR000
parserOutputSummary0.6160.0000.615
parserOutputSummaryLR0.3960.0000.395
parserOutputTFSummary0.0790.0040.083
performReverseTransformation0.0010.0000.000
performTransformation0.0010.0000.000
plot.PhenList2.0820.0312.114
plot.PhenTestResult2.0840.0602.145
plotResidualPredicted0.6180.0080.626
printLROutput0.4230.0010.423
printTabStyle0.0010.0000.000
qqplotGenotype0.6360.0000.636
qqplotRandomEffects0.6200.0040.624
qqplotRotatedResiduals3.9190.0633.983
recommendMethod0.1860.0280.214
scatterplotGenotypeWeight0.140.000.14
scatterplotGenotypeWeightResult0.8190.0040.823
scatterplotSexGenotypeBatch0.0730.0090.080
scatterplotSexGenotypeBatchResult0.7760.0000.776
startLRModel0.3910.0000.391
startModel0.4450.0030.448
startTFModel0.3310.0040.335
summaryOutput0.7230.0280.751
summaryPhenListResult0.9650.0280.993
testDataset2.0110.0282.039
testFinalLRModel0.4090.0000.409
testFinalModel0.7790.0280.807
vectorOutput0.7300.0160.745
vectorOutputMatrices0.1060.0000.106