Mac ARM64 build report for BioC 3.20 - CHECK results for PDATK on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4378
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_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/PDATK.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PDATK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PDATK’ version ‘1.13.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘survival::brier’ by ‘verification::brier’ when loading ‘PDATK’
See ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/PDATK.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 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 ... WARNING
Missing link or links in Rd file 'rankFeatures-MultiAssayExperiment-method.Rd':
  ‘[dplyr:ranking]{dplyr::dense_rank}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 'dot-randomSampleIndex.Rd':
  ‘numSamples’

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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
ModelComparison 4.944  0.047    5.06
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/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/4.4-arm64/Resources/library’
* installing *source* package ‘PDATK’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘survival::brier’ by ‘verification::brier’ when loading ‘PDATK’
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘survival::brier’ by ‘verification::brier’ when loading ‘PDATK’
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘survival::brier’ by ‘verification::brier’ when loading ‘PDATK’
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
** testing if installed package keeps a record of temporary installation path
* DONE (PDATK)

Tests output


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, aperm, 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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

Warning messages:
1: replacing previous import 'survival::brier' by 'verification::brier' when loading 'PDATK' 
2: replacing previous import 'limma::logsumexp' by 'mclust::logsumexp' when loading 'genefu' 
> 
> test_check("PDATK")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 77 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 77 ]
> 
> proc.time()
   user  system elapsed 
 31.035   6.629  35.175

Example timings

name	user	system	elapsed
CSPC_MAE	0.005	0.002	0.008
ClinicalModel-class	0.085	0.004	0.089
ClinicalModel	0.086	0.004	0.090
CohortList	0.028	0.003	0.031
ConsensusMetaclusteringModel	0.012	0.003	0.014
CoxModel	0.285	0.009	0.295
GeneFuModel	0.094	0.003	0.096
ModelComparison	4.944	0.047	5.060
PCOSP	0.109	0.007	0.117
RandomGeneAssignmentModel	0.078	0.005	0.086
RandomLabelShufflingModel	0.077	0.005	0.083
SurvivalExperiment	0.078	0.004	0.085
SurvivalModel-class	0.038	0.004	0.042
SurvivalModel	0.038	0.004	0.043
assignColDataColumn	0.034	0.001	0.035
assignSubtypes-CohortList-list-method	0.465	0.014	0.484
assignSubtypes-SurvivalExperiment-data.frame-method	0.053	0.006	0.060
assignSubtypes	0.036	0.005	0.042
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	0.768	0.024	0.801
barPlotModelComparison	0.764	0.024	0.800
birnbaum	0.003	0.003	0.006
chen	0.002	0.002	0.005
cohortSubtypeDFs	0.003	0.002	0.005
compareModels-ModelComparison-SurvivalModel-method	0.719	0.021	0.747
compareModels-SurvivalModel-SurvivalModel-method	0.668	0.022	0.702
compareModels	0.684	0.021	0.714
dropNotCensored-CohortList-method	0.451	0.006	0.488
dropNotCensored-SurvivalExperiment-method	0.043	0.003	0.048
dropNotCensored	0.044	0.003	0.048
existingClassifierData	0.003	0.002	0.006
findCommonGenes-CohortList-method	0.031	0.002	0.034
findCommonGenes	0.030	0.003	0.034
findCommonSamples-CohortList-method	0.037	0.003	0.040
findCommonSamples	0.036	0.003	0.040
forestPlot-ModelComparison-method	0.736	0.022	0.766
forestPlot-PCOSP_or_ClinicalModel-method	0.058	0.004	0.065
forestPlot	0.128	0.004	0.133
getModelSeed-SurvivalModel-method	0.010	0.003	0.014
getModelSeed	0.008	0.002	0.011
getTopFeatures-PCOSP-method	0.010	0.002	0.013
getTopFeatures-SummarizedExperiment-method	0.141	0.004	0.148
getTopFeatures	0.010	0.003	0.013
haiderSigScores	0.003	0.003	0.006
hasColDataColumns	0.012	0.001	0.012
merge-SurvivalExperiment-SurvivalExperiment-method	0.145	0.005	0.152
modelParams-set	0.015	0.003	0.018
modelParams	0.017	0.002	0.021
models-SurvivalModel-method	0.009	0.003	0.013
models-set-SurvivalModel-SimpleList-method	0.011	0.003	0.013
models-set	0.013	0.004	0.017
models	0.010	0.003	0.012
normalsMAE	0.002	0.003	0.006
plotROC-PCOSP-method	0.286	0.007	0.298
predictClasses-CohortList-ClinicalModel-method	0.240	0.008	0.248
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	0.315	0.009	0.325
predictClasses-SurvivalExperiment-ClinicalModel-method	0.110	0.006	0.116
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.107	0.006	0.113
predictClasses	0.108	0.006	0.115
rankFeatures-SummarizedExperiment-method	0.114	0.003	0.117
rankFeatures	0.090	0.003	0.093
removeColDataFactorColumns	0.019	0.003	0.023
removeFactorColumns	0.003	0.000	0.003
renameColDataColumns	0.020	0.003	0.023
renameColumns	0.002	0.001	0.001
sampleClinicalModel	0.007	0.003	0.010
sampleCohortList	0.031	0.003	0.034
sampleICGCmicro	0.009	0.003	0.011
samplePCOSPmodel	0.009	0.002	0.011
samplePCOSPpredList	0.037	0.002	0.040
samplePCSIsurvExp	0.007	0.002	0.010
sampleRGAmodel	0.009	0.002	0.011
sampleRLSmodel	0.009	0.002	0.011
sampleTrainedPCOSPmodel	0.009	0.002	0.012
sampleValPCOSPmodel	0.040	0.003	0.043
show-S4Model-method	0.060	0.003	0.063
subset-CohortList-method	0.122	0.003	0.125
trainData-set	0.014	0.003	0.016
trainData	0.008	0.002	0.011
trainModel-ClinicalModel-method	0.042	0.003	0.045
trainModel-PCOSP-method	1.192	0.010	1.204
trainModel-RGAModel-method	1.209	0.006	1.259
trainModel-RLSModel-method	1.155	0.006	1.179
trainModel	1.191	0.006	1.197
validateModel-ClinicalModel-CohortList-method	0.194	0.006	0.201
validateModel-ClinicalModel-SurvivalExperiment-method	0.562	0.035	0.597
validateModel-GeneFuModel-CohortList-method	1.067	0.089	1.156
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	0.966	0.044	1.011
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	0.939	0.039	0.978
validateModel	0.092	0.006	0.097
validationData-SurvivalModel-method	0.011	0.002	0.013
validationData-set-SurvivalModel-CohortList-method	0.009	0.002	0.011
validationData-set	0.009	0.003	0.011
validationData	0.008	0.003	0.011
validationStats-SurvivalModel-method	0.009	0.002	0.011
validationStats-set-SurvivalModel-data.frame-method	0.010	0.002	0.012
validationStats-set	0.009	0.003	0.012
validationStats	0.008	0.004	0.018

CHECK results for PDATK on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings