Multiple platform build/check report for BioC 3.13 - CHECK results for PDATK on machv2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PDATK.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PDATK_1.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/PDATK.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PDATK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PDATK’ version ‘1.0.2’
* 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 for sufficient/correct file permissions ... 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
* 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 ... WARNING
Undocumented code objects:
  ‘optimalKMinimizeAmbiguity’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/PDATK.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PDATK
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘PDATK’ ...
** using staged installation
** R
** data
** 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 (PDATK)

Tests output


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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
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 ]
> 
> proc.time()
   user  system elapsed 
 49.332  14.242  50.523

Example timings

name	user	system	elapsed
CSPC_MAE	0.005	0.002	0.007
ClinicalModel-class	0.145	0.003	0.147
ClinicalModel	0.207	0.004	0.211
CohortList	0.024	0.002	0.026
ConsensusMetaclusteringModel	0.016	0.003	0.018
CoxModel	1.082	0.009	1.092
GeneFuModel	0.206	0.016	0.222
ModelComparison	3.590	0.091	3.688
PCOSP	0.187	0.002	0.190
RandomGeneAssignmentModel	0.164	0.003	0.167
RandomLabelShufflingModel	0.183	0.002	0.185
SurvivalExperiment	0.296	0.003	0.299
SurvivalModel-class	0.090	0.002	0.092
SurvivalModel	0.073	0.002	0.075
assignColDataColumn	0.061	0.001	0.062
assignSubtypes-CohortList-list-method	0.729	0.033	0.762
assignSubtypes-SurvivalExperiment-data.frame-method	0.072	0.010	0.081
assignSubtypes	0.077	0.011	0.089
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	1.668	0.053	1.721
barPlotModelComparison	1.505	0.015	1.521
birnbaum	0.004	0.002	0.007
chen	0.003	0.003	0.007
cohortSubtypeDFs	0.005	0.002	0.007
compareModels-ModelComparison-SurvivalModel-method	1.842	0.017	1.859
compareModels-SurvivalModel-SurvivalModel-method	1.510	0.014	1.524
compareModels	1.543	0.015	1.559
dropNotCensored-CohortList-method	1.338	0.004	1.342
dropNotCensored-SurvivalExperiment-method	0.150	0.002	0.153
dropNotCensored	0.123	0.002	0.127
findCommonGenes-CohortList-method	0.098	0.003	0.101
findCommonGenes	0.098	0.003	0.101
findCommonSamples-CohortList-method	0.105	0.003	0.108
findCommonSamples	0.099	0.002	0.101
forestPlot-ModelComparison-method	1.745	0.018	1.764
forestPlot-PCOSP_or_ClinicalModel-method	0.075	0.003	0.079
forestPlot	0.216	0.003	0.219
getModelSeed-SurvivalModel-method	0.011	0.002	0.013
getModelSeed	0.009	0.002	0.011
getTopFeatures-PCOSP-method	0.011	0.001	0.012
getTopFeatures-SummarizedExperiment-method	0.328	0.005	0.333
getTopFeatures	0.011	0.003	0.014
haiderSigScores	0.003	0.002	0.007
hasColDataColumns	0.03	0.00	0.03
merge-SurvivalExperiment-SurvivalExperiment-method	0.307	0.003	0.311
modelParams-set	0.013	0.003	0.015
modelParams	0.019	0.002	0.020
models-SurvivalModel-method	0.010	0.003	0.013
models-set-SurvivalModel-SimpleList-method	0.012	0.003	0.015
models	0.012	0.003	0.015
normalsMAE	0.002	0.002	0.004
plotROC-PCOSP-method	0.157	0.004	0.161
predictClasses-CohortList-ClinicalModel-method	0.891	0.008	0.901
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	1.205	0.038	1.244
predictClasses-SurvivalExperiment-ClinicalModel-method	0.280	0.005	0.286
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.346	0.005	0.350
predictClasses	0.445	0.007	0.471
rankFeatures-SummarizedExperiment-method	0.344	0.004	0.349
rankFeatures	0.313	0.004	0.317
removeColDataFactorColumns	0.074	0.004	0.078
removeFactorColumns	0.004	0.000	0.004
renameColDataColumns	0.084	0.005	0.088
renameColumns	0.002	0.000	0.003
sampleClinicalModel	0.005	0.001	0.007
sampleCohortList	0.029	0.002	0.031
sampleICGCmicro	0.007	0.001	0.009
samplePCOSPmodel	0.008	0.003	0.011
samplePCOSPpredList	0.041	0.003	0.044
samplePCSIsurvExp	0.008	0.002	0.010
sampleRGAmodel	0.010	0.003	0.014
sampleRLSmodel	0.010	0.003	0.013
sampleTrainedPCOSPmodel	0.007	0.001	0.010
sampleValPCOSPmodel	0.048	0.003	0.050
show-S4Model-method	0.126	0.004	0.131
subset-CohortList-method	0.36	0.01	0.37
trainData-set	0.010	0.002	0.012
trainData	0.007	0.002	0.010
trainModel-ClinicalModel-method	0.095	0.006	0.101
trainModel-PCOSP-method	1.081	0.014	1.096
trainModel-RGAModel-method	1.056	0.004	1.061
trainModel-RLSModel-method	1.014	0.008	1.023
trainModel	2.087	0.016	2.107
validateModel-ClinicalModel-CohortList-method	0.542	0.006	0.548
validateModel-ClinicalModel-SurvivalExperiment-method	1.598	0.019	1.618
validateModel-GeneFuModel-CohortList-method	1.000	0.014	1.013
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	0.799	0.010	0.809
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	0.825	0.017	0.843
validateModel	0.109	0.006	0.115
validationData-SurvivalModel-method	0.012	0.003	0.015
validationData-set-SurvivalModel-CohortList-method	0.009	0.003	0.012
validationData-set	0.009	0.002	0.011
validationData	0.009	0.003	0.012
validationStats-SurvivalModel-method	0.008	0.003	0.011
validationStats-set-SurvivalModel-data.frame-method	0.009	0.003	0.012
validationStats-set	0.011	0.003	0.013
validationStats	0.009	0.003	0.012

CHECK results for PDATK on machv2

Summary

Command output

Installation output

Tests output

Example timings