Multiple platform build/check report for BioC 3.14 - CHECK results for PDATK on machv2

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*

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PDATK.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PDATK_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/PDATK.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.2.0’
* 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 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 ... 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 ... 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/PDATK.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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

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
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 
 54.064  12.020  58.980

Example timings

name	user	system	elapsed
CSPC_MAE	0.009	0.003	0.010
ClinicalModel-class	0.186	0.018	0.205
ClinicalModel	0.207	0.020	0.228
CohortList	0.040	0.005	0.046
ConsensusMetaclusteringModel	0.022	0.004	0.027
CoxModel	0.901	0.090	0.992
GeneFuModel	0.280	0.025	0.306
ModelComparison	3.509	0.091	3.609
PCOSP	0.216	0.018	0.234
RandomGeneAssignmentModel	0.203	0.018	0.222
RandomLabelShufflingModel	0.202	0.015	0.217
SurvivalExperiment	0.354	0.014	0.369
SurvivalModel-class	0.118	0.004	0.122
SurvivalModel	0.116	0.002	0.118
assignColDataColumn	0.087	0.001	0.088
assignSubtypes-CohortList-list-method	0.910	0.006	0.918
assignSubtypes-SurvivalExperiment-data.frame-method	0.048	0.004	0.053
assignSubtypes	0.074	0.003	0.077
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	1.880	0.019	1.900
barPlotModelComparison	1.829	0.016	1.847
birnbaum	0.003	0.002	0.006
chen	0.004	0.002	0.006
cohortSubtypeDFs	0.005	0.003	0.008
compareModels-ModelComparison-SurvivalModel-method	1.426	0.017	1.445
compareModels-SurvivalModel-SurvivalModel-method	1.457	0.019	1.479
compareModels	1.360	0.016	1.377
dropNotCensored-CohortList-method	1.413	0.006	1.420
dropNotCensored-SurvivalExperiment-method	0.128	0.003	0.131
dropNotCensored	0.124	0.002	0.127
existingClassifierData	0.004	0.002	0.006
findCommonGenes-CohortList-method	0.066	0.003	0.069
findCommonGenes	0.067	0.001	0.070
findCommonSamples-CohortList-method	0.104	0.002	0.106
findCommonSamples	0.086	0.004	0.089
forestPlot-ModelComparison-method	1.590	0.022	1.615
forestPlot-PCOSP_or_ClinicalModel-method	0.103	0.004	0.108
forestPlot	0.200	0.004	0.205
getModelSeed-SurvivalModel-method	0.011	0.002	0.013
getModelSeed	0.010	0.002	0.012
getTopFeatures-PCOSP-method	0.010	0.002	0.012
getTopFeatures-SummarizedExperiment-method	0.371	0.002	0.374
getTopFeatures	0.011	0.003	0.014
haiderSigScores	0.004	0.003	0.006
hasColDataColumns	0.025	0.001	0.026
merge-SurvivalExperiment-SurvivalExperiment-method	0.284	0.004	0.289
modelParams-set	0.021	0.003	0.023
modelParams	0.018	0.003	0.020
models-SurvivalModel-method	0.010	0.003	0.013
models-set-SurvivalModel-SimpleList-method	0.011	0.003	0.014
models-set	0.020	0.003	0.023
models	0.009	0.001	0.010
normalsMAE	0.002	0.003	0.006
plotROC-PCOSP-method	0.243	0.005	0.248
predictClasses-CohortList-ClinicalModel-method	0.737	0.008	0.746
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	0.763	0.012	0.776
predictClasses-SurvivalExperiment-ClinicalModel-method	0.370	0.009	0.379
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.288	0.007	0.296
predictClasses	0.289	0.007	0.296
rankFeatures-SummarizedExperiment-method	0.359	0.003	0.361
rankFeatures	0.275	0.003	0.279
removeColDataFactorColumns	0.069	0.003	0.072
removeFactorColumns	0.005	0.001	0.006
renameColDataColumns	0.076	0.003	0.079
renameColumns	0.003	0.000	0.003
sampleClinicalModel	0.008	0.003	0.012
sampleCohortList	0.034	0.003	0.037
sampleICGCmicro	0.009	0.002	0.011
samplePCOSPmodel	0.009	0.003	0.012
samplePCOSPpredList	0.039	0.003	0.041
samplePCSIsurvExp	0.005	0.002	0.006
sampleRGAmodel	0.009	0.002	0.010
sampleRLSmodel	0.009	0.002	0.012
sampleTrainedPCOSPmodel	0.010	0.002	0.012
sampleValPCOSPmodel	0.047	0.003	0.051
show-S4Model-method	0.122	0.004	0.126
subset-CohortList-method	0.371	0.004	0.375
trainData-set	0.021	0.003	0.023
trainData	0.011	0.003	0.014
trainModel-ClinicalModel-method	0.092	0.002	0.095
trainModel-PCOSP-method	0.964	0.027	0.992
trainModel-RGAModel-method	0.974	0.006	0.980
trainModel-RLSModel-method	0.917	0.008	0.925
trainModel	1.039	0.013	1.052
validateModel-ClinicalModel-CohortList-method	0.675	0.007	0.682
validateModel-ClinicalModel-SurvivalExperiment-method	1.496	0.033	1.530
validateModel-GeneFuModel-CohortList-method	1.325	0.027	1.353
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	1.139	0.017	1.157
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	1.023	0.015	1.041
validateModel	0.103	0.006	0.109
validationData-SurvivalModel-method	0.012	0.003	0.015
validationData-set-SurvivalModel-CohortList-method	0.010	0.003	0.014
validationData-set	0.010	0.003	0.013
validationData	0.013	0.003	0.015
validationStats-SurvivalModel-method	0.006	0.002	0.008
validationStats-set-SurvivalModel-data.frame-method	0.010	0.003	0.013
validationStats-set	0.013	0.003	0.015
validationStats	0.012	0.003	0.015

CHECK results for PDATK on machv2

Summary

Command output

Installation output

Tests output

Example timings