Multiple platform build/check report for BioC 3.12 - CHECK report for PhenStat on tokay1

Package: PhenStat

Version: 2.26.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PhenStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings PhenStat_2.26.0.tar.gz

StartedAt: 2021-05-06 05:31:11 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 05:35:10 -0400 (Thu, 06 May 2021)

EllapsedTime: 239.2 seconds

RetCode: 0

Status: OK

CheckDir: PhenStat.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PhenStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings PhenStat_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/PhenStat.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PhenStat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PhenStat' version '2.26.0'
* 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 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/PhenStat.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/PhenStat_2.26.0.tar.gz && rm -rf PhenStat.buildbin-libdir && mkdir PhenStat.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PhenStat.buildbin-libdir PhenStat_2.26.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL PhenStat_2.26.0.zip && rm PhenStat_2.26.0.tar.gz PhenStat_2.26.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  734k  100  734k    0     0  26.7M      0 --:--:-- --:--:-- --:--:-- 26.5M

install for i386

* installing *source* package 'PhenStat' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PhenStat'
    finding HTML links ... done
    FisherExactTest                         html  
    JSONOutput                              html  
    LRDataset                               html  
    LargeDataObject-class                   html  
    PhenList-class                          html  
    PhenList                                html  
    PhenStatReport                          html  
    PhenTestResult-class                    html  
    PhenTestResult                          html  
    RRTest                                  html  
    TFDataset                               html  
    analysedDataset                         html  
    analysedDatasetPhenList                 html  
    analysedSubset                          html  
    analysisResults                         html  
    batchIn                                 html  
    boxplotResidualBatch                    html  
    boxplotSexGenotype                      html  
    boxplotSexGenotypeBatch                 html  
    boxplotSexGenotypeBatchAdjusted         html  
    boxplotSexGenotypeResult                html  
    boxplotSexGenotypeWeightBatchAdjusted   html  
    categoricalBarplot                      html  
    checkDataset                            html  
    classificationTag                       html  
    columnChecks                            html  
    columnLevels                            html  
    comparison                              html  
    dataset                                 html  
    determiningLambda                       html  
    dim                                     html  
    finalLRModel                            html  
    finalModel                              html  
    finalTFModel                            html  
    formulaDeterminingLambda                html  
    generateGraphs                          html  
    getColumn                               html  
    getColumnBatchAdjusted                  html  
    getColumnView                           html  
    getColumnWeightBatchAdjusted            html  
    getCountMatrices                        html  
    getDataset                              html  
    getGenotypeEffect                       html  
    getMatrix                               html  
    getPercentageMatrix                     html  
    getStat                                 html  
    getVariable                             html  
    getVariables                            html  
    hemiGenotype                            html  
    htest-class                             html  
    htestPhenStat-class                     html  
    matrixCount                             html  
    method                                  html  
    methodText                              html  
    modelFormula                            html  
    modelFormulaLR                          html  
    multipleBatches                         html  
    noSexes                                 html  
    parameters                              html  
    parserOutputSummary                     html  
    parserOutputSummaryLR                   html  
    parserOutputTFSummary                   html  
    performReverseTransformation            html  
    performTransformation                   html  
    plot.PhenList                           html  
    plot.PhenTestResult                     html  
    plotResidualPredicted                   html  
    printLROutput                           html  
    printTabStyle                           html  
    pvalue                                  html  
    qqplotGenotype                          html  
    qqplotRandomEffects                     html  
    qqplotRotatedResiduals                  html  
    recommendMethod                         html  
    refGenotype                             html  
    scatterplotGenotypeWeight               html  
    scatterplotGenotypeWeightResult         html  
    scatterplotSexGenotypeBatch             html  
    scatterplotSexGenotypeBatchResult       html  
    setBatch                                html  
    setGenotype                             html  
    setMissingValue                         html  
    setSex                                  html  
    setWeight                               html  
    startLRModel                            html  
    startModel                              html  
    startTFModel                            html  
    subsetText                              html  
    summaryOutput                           html  
    summaryPhenListResult                   html  
    testDataset                             html  
    testFinalLRModel                        html  
    testFinalModel                          html  
    testGenotype                            html  
    transformation                          html  
    transformationJSON                      html  
    transformationText                      html  
    vectorOutput                            html  
    vectorOutputMatrices                    html  
    weightIn                                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

install for x64

* installing *source* package 'PhenStat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PhenStat' as PhenStat_2.26.0.zip
* DONE (PhenStat)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'PhenStat' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.

> 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 -- Thu May 06 05:34:58 2021 
*********************************************** 
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 
   4.62    0.29    4.89


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.

> 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 -- Thu May 06 05:35:02 2021 
*********************************************** 
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 
   3.78    0.31    4.07

name	user	system	elapsed
FisherExactTest	0.21	0.01	0.28
JSONOutput	0.92	0.02	0.94
LRDataset	0.07	0.00	0.10
PhenList-class	0.20	0.00	0.23
PhenList	0.23	0.00	0.23
PhenStatReport	0.05	0.00	0.05
PhenTestResult-class	0.63	0.00	0.63
PhenTestResult	0.85	0.00	0.86
RRTest	0.15	0.00	0.14
TFDataset	0.42	0.02	0.44
analysedDataset	1.06	0.00	1.06
analysisResults	0.67	0.01	0.69
boxplotResidualBatch	0.69	0.00	0.69
boxplotSexGenotype	0.08	0.02	0.09
boxplotSexGenotypeBatch	0.15	0.00	0.16
boxplotSexGenotypeBatchAdjusted	0.07	0.02	0.08
boxplotSexGenotypeResult	0.86	0.00	0.85
boxplotSexGenotypeWeightBatchAdjusted	0.07	0.00	0.08
categoricalBarplot	0.13	0.00	0.13
checkDataset	0.05	0.01	0.06
classificationTag	0.76	0.00	0.77
determiningLambda	1.2	0.0	1.2
dim	0.04	0.00	0.03
finalLRModel	0.71	0.00	0.72
finalModel	0.54	0.00	0.53
finalTFModel	0.45	0.00	0.45
htestPhenStat-class	0.12	0.00	0.13
modelFormula	0	0	0
modelFormulaLR	0	0	0
parserOutputSummary	0.63	0.00	0.62
parserOutputSummaryLR	0.92	0.00	0.93
parserOutputTFSummary	0.17	0.00	0.17
performReverseTransformation	0.02	0.00	0.01
performTransformation	0	0	0
plot.PhenList	2.94	0.02	2.96
plot.PhenTestResult	2.14	0.01	2.15
plotResidualPredicted	0.67	0.00	0.67
printLROutput	0.68	0.00	0.67
printTabStyle	0	0	0
qqplotGenotype	0.98	0.00	0.99
qqplotRandomEffects	1.02	0.02	1.03
qqplotRotatedResiduals	4.85	0.01	4.87
recommendMethod	0.36	0.00	0.36
scatterplotGenotypeWeight	0.25	0.00	0.25
scatterplotGenotypeWeightResult	1.33	0.00	1.33
scatterplotSexGenotypeBatch	0.16	0.00	0.16
scatterplotSexGenotypeBatchResult	1.31	0.00	1.31
startLRModel	0.88	0.00	0.87
startModel	0.75	0.00	0.75
startTFModel	0.48	0.00	0.49
summaryOutput	0.77	0.00	0.76
summaryPhenListResult	0.76	0.03	0.80
testDataset	2.80	0.07	2.86
testFinalLRModel	0.69	0.00	0.69
testFinalModel	0.78	0.00	0.78
vectorOutput	0.81	0.00	0.81
vectorOutputMatrices	0.14	0.00	0.14

name	user	system	elapsed
FisherExactTest	0.17	0.02	0.19
JSONOutput	1.28	0.00	1.28
LRDataset	0.09	0.00	0.10
PhenList-class	0.28	0.00	0.28
PhenList	0.28	0.00	0.28
PhenStatReport	0.06	0.00	0.06
PhenTestResult-class	1.35	0.00	1.34
PhenTestResult	0.77	0.00	0.76
RRTest	0.15	0.00	0.16
TFDataset	0.47	0.01	0.48
analysedDataset	0.96	0.00	0.96
analysisResults	0.93	0.00	0.94
boxplotResidualBatch	1.03	0.00	1.03
boxplotSexGenotype	0.11	0.02	0.12
boxplotSexGenotypeBatch	0.22	0.01	0.24
boxplotSexGenotypeBatchAdjusted	0.09	0.00	0.10
boxplotSexGenotypeResult	1.14	0.00	1.14
boxplotSexGenotypeWeightBatchAdjusted	0.06	0.00	0.06
categoricalBarplot	0.19	0.00	0.19
checkDataset	0.08	0.00	0.08
classificationTag	0.98	0.00	0.98
determiningLambda	1.09	0.05	1.14
dim	0.07	0.00	0.07
finalLRModel	1.01	0.00	1.01
finalModel	0.80	0.02	0.82
finalTFModel	0.78	0.00	0.78
htestPhenStat-class	0.14	0.00	0.14
modelFormula	0	0	0
modelFormulaLR	0	0	0
parserOutputSummary	0.78	0.00	0.78
parserOutputSummaryLR	0.98	0.00	0.98
parserOutputTFSummary	0.17	0.00	0.18
performReverseTransformation	0	0	0
performTransformation	0	0	0
plot.PhenList	3.11	0.05	3.15
plot.PhenTestResult	2.18	0.00	2.17
plotResidualPredicted	0.67	0.00	0.68
printLROutput	0.61	0.00	0.61
printTabStyle	0	0	0
qqplotGenotype	0.7	0.0	0.7
qqplotRandomEffects	0.67	0.00	0.67
qqplotRotatedResiduals	3.28	0.01	3.30
recommendMethod	0.25	0.00	0.25
scatterplotGenotypeWeight	0.17	0.00	0.17
scatterplotGenotypeWeightResult	1.04	0.00	1.03
scatterplotSexGenotypeBatch	0.11	0.00	0.11
scatterplotSexGenotypeBatchResult	0.87	0.00	0.87
startLRModel	0.72	0.00	0.72
startModel	0.60	0.00	0.59
startTFModel	0.73	0.00	0.74
summaryOutput	0.82	0.00	0.81
summaryPhenListResult	1.31	0.00	1.31
testDataset	2.62	0.02	2.64
testFinalLRModel	0.96	0.00	0.96
testFinalModel	1.12	0.00	1.12
vectorOutput	1.08	0.02	1.09
vectorOutputMatrices	0.20	0.00	0.21

CHECK report for PhenStat on tokay1

Summary

Command output

Installation output

Tests output

Example timings