Multiple platform build/check report for BioC 3.14 - CHECK results for PDATK on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
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: PDATK

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PDATK.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PDATK_1.2.0.tar.gz

StartedAt: 2022-04-13 00:20:29 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 00:28:16 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 466.5 seconds

RetCode: 0

Status: OK

CheckDir: PDATK.Rcheck

Warnings: 0

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PDATK.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PDATK_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/PDATK.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PDATK/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PDATK' version '1.2.0'
* 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 'PDATK' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.calculateMSMthresholds: no visible binding for global variable
  'funContext'
.plotNetwork: no visible global function definition for 'legend'
NCSModel: no visible binding for global variable 'metric'
NCSModel: no visible binding for global variable 'comparison'
NCSModel: no visible binding for global variable 'centroid_K'
NCSModel: no visible binding for global variable 'assay_K'
NetworkCommunitySearchModel: no visible binding for global variable
  'metric'
NetworkCommunitySearchModel: no visible binding for global variable
  'comparison'
NetworkCommunitySearchModel: no visible binding for global variable
  'centroid_K'
NetworkCommunitySearchModel: no visible binding for global variable
  'assay_K'
predictClasses,ConsensusMetaclusteringModel-ANY: no visible global
  function definition for '.error'
predictClasses,NCSModel-ANY: no visible binding for global variable
  'centroid_cohort'
predictClasses,NCSModel-ANY: no visible binding for global variable
  'centroid_K'
predictClasses,NCSModel-ANY: no visible binding for global variable
  'assay_cohort'
predictClasses,NCSModel-ANY: no visible binding for global variable
  'assay_K'
predictClasses,NCSModel-ANY: no visible binding for global variable
  'tmp'
predictClasses,NCSModel-ANY: no visible binding for global variable
  'cluster_label'
rankFeatures,MultiAssayExperiment: no visible binding for global
  variable 'feature'
rankFeatures,MultiAssayExperiment: no visible binding for global
  variable 'missignAssays'
rankFeatures,MultiAssayExperiment: no visible binding for global
  variable 'feature_score'
rankFeatures,MultiAssayExperiment: no visible binding for global
  variable 'feature_rank'
trainModel,ConsensusMetaclusteringModel: no visible global function
  definition for 'pdf'
trainModel,ConsensusMetaclusteringModel: no visible global function
  definition for 'dev.off'
trainModel,NCSModel: no visible binding for global variable
  'ingroup_proportion'
trainModel,NCSModel: no visible binding for global variable
  'cor_threshold'
Undefined global functions or variables:
  .error assay_K assay_cohort centroid_K centroid_cohort cluster_label
  comparison cor_threshold dev.off feature feature_rank feature_score
  funContext ingroup_proportion legend metric missignAssays pdf tmp
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "legend")
to your NAMESPACE file.
* 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 ...
** 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 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/PDATK.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/PDATK_1.2.0.tar.gz && rm -rf PDATK.buildbin-libdir && mkdir PDATK.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PDATK.buildbin-libdir PDATK_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL PDATK_1.2.0.zip && rm PDATK_1.2.0.tar.gz PDATK_1.2.0.zip
###
##############################################################################
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                                 Dload  Upload   Total   Spent    Left  Speed

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100  869k  100  869k    0     0  2064k      0 --:--:-- --:--:-- --:--:-- 2070k

install for i386

* installing *source* package 'PDATK' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PDATK'
    finding HTML links ... done
    CSPC_MAE                                html  
    ClinicalModel-class                     html  
    ClinicalModel                           html  
    CohortList-class                        html  
    CohortList                              html  
    ConsensusMetaclusteringModel-class      html  
    ConsensusMetaclusteringModel            html  
    CoxModel-class                          html  
    CoxModel                                html  
    GeneFuModel-class                       html  
    GeneFuModel                             html  
    ModelComparison-class                   html  
    ModelComparison                         html  
    NCSModel-class                          html  
    NetworkCommunitySearchModel             html  
    PCOSP-class                             html  
    PCOSP                                   html  
    PCOSP_or_ClinicalModel-class            html  
    PCOSP_or_RLS_or_RGA-class               html  
    RGAModel-class                          html  
    RLSModel-class                          html  
    RandomGeneAssignmentModel               html  
    RandomLabelShufflingModel               html  
    S4Model-class                           html  
    SurvivalExperiment-class                html  
    SurvivalExperiment                      html  
    SurvivalModel-class                     html  
    SurvivalModel                           html  
    assignColDataColumn                     html  
    assignSubtypes-CohortList-list-method   html  
    assignSubtypes-SurvivalExperiment-data.frame-method
                                            html  
    assignSubtypes                          html  
    barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method
                                            html  
    barPlotModelComparison                  html  
    birnbaum                                html  
    chen                                    html  
    cohortSubtypeDFs                        html  
    compareModels-ModelComparison-SurvivalModel-method
                                            html  
    compareModels-SurvivalModel-SurvivalModel-method
                                            html  
    compareModels                           html  
    densityPlotModelComparison-PCOSP_or_RLS_or_RGA-PCOSP_or_RLS_or_RGA-method
                                            html  
    densityPlotModelComparison              html  
    dot-findAllCohortPairs                  html  
    dot-randomSampleIndex                   html  
    dropNotCensored-CohortList-method       html  
    dropNotCensored-SurvivalExperiment-method
                                            html  
    dropNotCensored                         html  
    existingClassifierData                  html  
    findCommonGenes-CohortList-method       html  
    findCommonGenes-MultiAssayExperiment-method
                                            html  
    findCommonGenes                         html  
    findCommonSamples-CohortList-method     html  
    findCommonSamples                       html  
    forestPlot-ModelComparison-method       html  
    forestPlot-PCOSP_or_ClinicalModel-method
                                            html  
    forestPlot                              html  
    getModelSeed-SurvivalModel-method       html  
    getModelSeed                            html  
    getTopFeatures-MultiAssayExperiment-method
                                            html  
    getTopFeatures-PCOSP-method             html  
    getTopFeatures-SummarizedExperiment-method
                                            html  
    getTopFeatures                          html  
    haiderSigScores                         html  
    hasColDataColumns                       html  
    merge-SurvivalExperiment-SurvivalExperiment-method
                                            html  
    modelParams-S4Model-method              html  
    modelParams-set-S4Model-List_or_list_or_NULL-method
                                            html  
    modelParams-set                         html  
    modelParams                             html  
    models-S4Model-method                   html  
    models-SurvivalModel-method             html  
    models-set-S4Model-List_or_list_or_NULL-method
                                            html  
    models-set-SurvivalModel-SimpleList-method
                                            html  
    models-set                              html  
    models                                  html  
    normalize-DFrame-method                 html  
    normalize-MultiAssayExperiment-method   html  
    normalize-SummarizedExperiment-method   html  
    normalize-data.frame_or_matrix-method   html  
    normalsMAE                              html  
    optimalKMinimizeAmbiguity               html  
    plotNetworkGraph-NCSModel-method        html  
    plotNetworkGraph                        html  
    plotROC-PCOSP-method                    html  
    plotROC                                 html  
    plotSurvivalCurves-CoxModel-method      html  
    plotSurvivalCurves                      html  
    predictClasses-CohortList-ClinicalModel-method
                                            html  
    predictClasses-CohortList-GeneFuModel-method
                                            html  
    predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method
                                            html  
    predictClasses-ConsensusMetaclusteringModel-ANY-method
                                            html  
    predictClasses-NCSModel-ANY-method      html  
    predictClasses-SurvivalExperiment-ClinicalModel-method
                                            html  
    predictClasses-SurvivalExperiment-GeneFuModel-method
                                            html  
    predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method
                                            html  
    predictClasses                          html  
    preprocessCaret                         html  
    rankFeatures-MultiAssayExperiment-method
                                            html  
    rankFeatures-SummarizedExperiment-method
                                            html  
    rankFeatures                            html  
    removeColDataFactorColumns              html  
    removeFactorColumns                     html  
    renameColDataColumns                    html  
    renameColumns                           html  
    runGSEA-PCOSP-data.frame-method         html  
    runGSEA                                 html  
    sampleClinicalModel                     html  
    sampleCohortList                        html  
    sampleICGCmicro                         html  
    samplePCOSPmodel                        html  
    samplePCOSPpredList                     html  
    samplePCSIsurvExp                       html  
    sampleRGAmodel                          html  
    sampleRLSmodel                          html  
    sampleTrainedPCOSPmodel                 html  
    sampleValPCOSPmodel                     html  
    show-S4Model-method                     html  
    subset-CohortList-method                html  
    trainData-S4Model-method                html  
    trainData-set-S4Model-method            html  
    trainData-set                           html  
    trainData                               html  
    trainModel-ClinicalModel-method         html  
    trainModel-ConsensusMetaclusteringModel-method
                                            html  
    trainModel-CoxModel-method              html  
    trainModel-GeneFuModel-method           html  
    trainModel-NCSModel-method              html  
    trainModel-PCOSP-method                 html  
    trainModel-RGAModel-method              html  
    trainModel-RLSModel-method              html  
    trainModel                              html  
    validateModel-ClinicalModel-CohortList-method
                                            html  
    validateModel-ClinicalModel-SurvivalExperiment-method
                                            html  
    validateModel-ConsensusMetaclusteringModel-ConsensusMetaclusteringModel-method
                                            html  
    validateModel-GeneFuModel-CohortList-method
                                            html  
    validateModel-GeneFuModel-SurvivalExperiment-method
                                            html  
    validateModel-PCOSP_or_RLS_or_RGA-CohortList-method
                                            html  
    validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method
                                            html  
    validateModel                           html  
    validationData-S4Model-method           html  
    validationData-SurvivalModel-method     html  
    validationData-set-S4Model-List_or_list_or_NULL-method
                                            html  
    validationData-set-SurvivalModel-CohortList-method
                                            html  
    validationData-set                      html  
    validationData                          html  
    validationStats-S4Model-method          html  
    validationStats-SurvivalModel-method    html  
    validationStats-set-S4Model-DFrame_or_data.frame_data.table_or_NULL-method
                                            html  
    validationStats-set-SurvivalModel-data.frame-method
                                            html  
    validationStats-set                     html  
    validationStats                         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 'PDATK' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PDATK' as PDATK_1.2.0.zip
* DONE (PDATK)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'PDATK' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.

> library(testthat)
> library(PDATK)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("PDATK")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 77 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 77 ]
> 
> proc.time()
   user  system elapsed 
  25.26    1.71   26.96


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(PDATK)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("PDATK")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 77 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 77 ]
> 
> proc.time()
   user  system elapsed 
  31.90    0.92   32.82

name	user	system	elapsed
CSPC_MAE	0.00	0.01	0.01
ClinicalModel-class	0.14	0.02	0.16
ClinicalModel	0.15	0.00	0.15
CohortList	0.04	0.00	0.03
ConsensusMetaclusteringModel	0.00	0.02	0.02
CoxModel	0.51	0.00	0.52
GeneFuModel	0.14	0.00	0.14
ModelComparison	2.15	0.42	2.75
PCOSP	0.24	0.08	0.31
RandomGeneAssignmentModel	0.15	0.10	0.27
RandomLabelShufflingModel	0.22	0.07	0.28
SurvivalExperiment	0.24	0.02	0.25
SurvivalModel-class	0.06	0.01	0.08
SurvivalModel	0.06	0.00	0.06
assignColDataColumn	0.07	0.00	0.06
assignSubtypes-CohortList-list-method	0.50	0.02	0.52
assignSubtypes-SurvivalExperiment-data.frame-method	0.03	0.03	0.06
assignSubtypes	0.06	0.00	0.06
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	1.03	0.02	1.05
barPlotModelComparison	0.91	0.03	0.94
birnbaum	0	0	0
chen	0.01	0.00	0.01
cohortSubtypeDFs	0.02	0.00	0.02
compareModels-ModelComparison-SurvivalModel-method	0.87	0.01	0.89
compareModels-SurvivalModel-SurvivalModel-method	0.88	0.00	0.87
compareModels	0.84	0.02	0.86
dropNotCensored-CohortList-method	0.81	0.00	0.81
dropNotCensored-SurvivalExperiment-method	0.05	0.00	0.06
dropNotCensored	0.07	0.00	0.08
existingClassifierData	0.02	0.00	0.01
findCommonGenes-CohortList-method	0.08	0.02	0.10
findCommonGenes	0.11	0.00	0.10
findCommonSamples-CohortList-method	0.11	0.00	0.11
findCommonSamples	0.07	0.00	0.06
forestPlot-ModelComparison-method	0.9	0.0	0.9
forestPlot-PCOSP_or_ClinicalModel-method	0.04	0.00	0.05
forestPlot	0.14	0.00	0.14
getModelSeed-SurvivalModel-method	0.02	0.00	0.01
getModelSeed	0.02	0.00	0.02
getTopFeatures-PCOSP-method	0.01	0.00	0.01
getTopFeatures-SummarizedExperiment-method	0.20	0.00	0.21
getTopFeatures	0.02	0.00	0.01
haiderSigScores	0	0	0
hasColDataColumns	0.03	0.00	0.03
merge-SurvivalExperiment-SurvivalExperiment-method	0.16	0.00	0.16
modelParams-set	0.01	0.00	0.02
modelParams	0.02	0.00	0.01
models-SurvivalModel-method	0.01	0.00	0.02
models-set-SurvivalModel-SimpleList-method	0.02	0.00	0.01
models-set	0.02	0.00	0.02
models	0	0	0
normalsMAE	0.00	0.01	0.01
plotROC-PCOSP-method	0.14	0.03	0.18
predictClasses-CohortList-ClinicalModel-method	0.53	0.07	0.59
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	0.47	0.07	0.55
predictClasses-SurvivalExperiment-ClinicalModel-method	0.22	0.00	0.22
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.18	0.00	0.19
predictClasses	0.17	0.01	0.19
rankFeatures-SummarizedExperiment-method	0.23	0.00	0.24
rankFeatures	0.19	0.00	0.18
removeColDataFactorColumns	0.05	0.02	0.07
removeFactorColumns	0	0	0
renameColDataColumns	0.05	0.00	0.04
renameColumns	0	0	0
sampleClinicalModel	0.00	0.02	0.02
sampleCohortList	0.03	0.00	0.03
sampleICGCmicro	0.00	0.01	0.02
samplePCOSPmodel	0.03	0.00	0.03
samplePCOSPpredList	0.08	0.00	0.07
samplePCSIsurvExp	0.01	0.02	0.04
sampleRGAmodel	0.02	0.01	0.03
sampleRLSmodel	0.01	0.00	0.01
sampleTrainedPCOSPmodel	0.03	0.00	0.03
sampleValPCOSPmodel	0.07	0.02	0.08
show-S4Model-method	0.08	0.01	0.10
subset-CohortList-method	0.32	0.00	0.32
trainData-set	0.02	0.00	0.02
trainData	0.01	0.00	0.02
trainModel-ClinicalModel-method	0.07	0.00	0.06
trainModel-PCOSP-method	0.84	0.04	0.87
trainModel-RGAModel-method	0.75	0.00	0.75
trainModel-RLSModel-method	0.67	0.00	0.67
trainModel	0.78	0.02	0.79
validateModel-ClinicalModel-CohortList-method	0.34	0.00	0.35
validateModel-ClinicalModel-SurvivalExperiment-method	0.77	0.01	0.78
validateModel-GeneFuModel-CohortList-method	0.76	0.00	0.76
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	0.83	0.00	0.85
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	0.86	0.03	0.89
validateModel	0.10	0.02	0.11
validationData-SurvivalModel-method	0.01	0.00	0.01
validationData-set-SurvivalModel-CohortList-method	0.00	0.01	0.02
validationData-set	0.00	0.02	0.01
validationData	0.00	0.02	0.02
validationStats-SurvivalModel-method	0.00	0.01	0.02
validationStats-set-SurvivalModel-data.frame-method	0.00	0.02	0.01
validationStats-set	0.00	0.01	0.02
validationStats	0.00	0.02	0.01

name	user	system	elapsed
CSPC_MAE	0	0	0
ClinicalModel-class	0.11	0.02	0.12
ClinicalModel	0.17	0.01	0.19
CohortList	0.03	0.00	0.03
ConsensusMetaclusteringModel	0.01	0.00	0.02
CoxModel	0.52	0.03	0.54
GeneFuModel	0.16	0.02	0.18
ModelComparison	2.23	0.02	2.40
PCOSP	0.13	0.00	0.12
RandomGeneAssignmentModel	0.12	0.00	0.13
RandomLabelShufflingModel	0.13	0.00	0.12
SurvivalExperiment	0.18	0.00	0.19
SurvivalModel-class	0.07	0.00	0.06
SurvivalModel	0.06	0.02	0.08
assignColDataColumn	0.06	0.00	0.06
assignSubtypes-CohortList-list-method	0.55	0.01	0.57
assignSubtypes-SurvivalExperiment-data.frame-method	0.03	0.03	0.06
assignSubtypes	0.08	0.02	0.09
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	1.26	0.01	1.28
barPlotModelComparison	1.03	0.00	1.03
birnbaum	0	0	0
chen	0	0	0
cohortSubtypeDFs	0	0	0
compareModels-ModelComparison-SurvivalModel-method	1.01	0.00	1.01
compareModels-SurvivalModel-SurvivalModel-method	0.95	0.00	0.95
compareModels	0.91	0.02	0.93
dropNotCensored-CohortList-method	0.86	0.00	0.86
dropNotCensored-SurvivalExperiment-method	0.06	0.02	0.07
dropNotCensored	0.08	0.00	0.08
existingClassifierData	0	0	0
findCommonGenes-CohortList-method	0.06	0.00	0.06
findCommonGenes	0.05	0.01	0.07
findCommonSamples-CohortList-method	0.06	0.02	0.07
findCommonSamples	0.06	0.00	0.07
forestPlot-ModelComparison-method	0.96	0.00	0.95
forestPlot-PCOSP_or_ClinicalModel-method	0.04	0.01	0.06
forestPlot	0.11	0.00	0.11
getModelSeed-SurvivalModel-method	0	0	0
getModelSeed	0.00	0.01	0.01
getTopFeatures-PCOSP-method	0.02	0.00	0.02
getTopFeatures-SummarizedExperiment-method	0.22	0.00	0.22
getTopFeatures	0.01	0.00	0.01
haiderSigScores	0	0	0
hasColDataColumns	0.02	0.00	0.01
merge-SurvivalExperiment-SurvivalExperiment-method	0.17	0.00	0.18
modelParams-set	0.01	0.00	0.01
modelParams	0.02	0.00	0.02
models-SurvivalModel-method	0.01	0.00	0.01
models-set-SurvivalModel-SimpleList-method	0	0	0
models-set	0.02	0.00	0.02
models	0.00	0.02	0.01
normalsMAE	0.02	0.00	0.02
plotROC-PCOSP-method	0.15	0.00	0.16
predictClasses-CohortList-ClinicalModel-method	0.45	0.02	0.47
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	0.47	0.00	0.46
predictClasses-SurvivalExperiment-ClinicalModel-method	0.22	0.00	0.22
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.19	0.00	0.19
predictClasses	0.25	0.00	0.25
rankFeatures-SummarizedExperiment-method	0.28	0.00	0.28
rankFeatures	0.2	0.0	0.2
removeColDataFactorColumns	0.05	0.00	0.05
removeFactorColumns	0	0	0
renameColDataColumns	0.05	0.00	0.04
renameColumns	0	0	0
sampleClinicalModel	0.01	0.00	0.02
sampleCohortList	0.03	0.00	0.03
sampleICGCmicro	0	0	0
samplePCOSPmodel	0.00	0.02	0.02
samplePCOSPpredList	0.03	0.01	0.05
samplePCSIsurvExp	0.00	0.02	0.01
sampleRGAmodel	0.00	0.01	0.02
sampleRLSmodel	0.01	0.00	0.01
sampleTrainedPCOSPmodel	0.02	0.00	0.02
sampleValPCOSPmodel	0.05	0.02	0.06
show-S4Model-method	0.14	0.00	0.14
subset-CohortList-method	0.36	0.01	0.38
trainData-set	0.01	0.00	0.01
trainData	0.00	0.02	0.02
trainModel-ClinicalModel-method	0.06	0.02	0.07
trainModel-PCOSP-method	1.13	0.00	1.13
trainModel-RGAModel-method	1.05	0.00	1.04
trainModel-RLSModel-method	0.91	0.00	0.91
trainModel	0.93	0.00	0.94
validateModel-ClinicalModel-CohortList-method	0.36	0.00	0.36
validateModel-ClinicalModel-SurvivalExperiment-method	0.85	0.01	0.85
validateModel-GeneFuModel-CohortList-method	0.79	0.02	0.82
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	0.86	0.00	0.86
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	0.82	0.00	0.81
validateModel	0.06	0.01	0.08
validationData-SurvivalModel-method	0.01	0.00	0.01
validationData-set-SurvivalModel-CohortList-method	0.02	0.00	0.02
validationData-set	0.02	0.00	0.01
validationData	0	0	0
validationStats-SurvivalModel-method	0.00	0.02	0.02
validationStats-set-SurvivalModel-data.frame-method	0.00	0.01	0.02
validationStats-set	0.01	0.00	0.01
validationStats	0.02	0.00	0.02

CHECK results for PDATK on tokay2

Summary

Command output

Installation output

Tests output

Example timings