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"	4381
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
* 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 
 31.223   6.758  35.500

Example timings

name	user	system	elapsed
CSPC_MAE	0.005	0.002	0.008
ClinicalModel-class	0.085	0.004	0.090
ClinicalModel	0.091	0.005	0.096
CohortList	0.030	0.003	0.032
ConsensusMetaclusteringModel	0.014	0.003	0.017
CoxModel	0.290	0.009	0.301
GeneFuModel	0.088	0.002	0.090
ModelComparison	4.879	0.037	4.922
PCOSP	0.103	0.007	0.109
RandomGeneAssignmentModel	0.071	0.005	0.076
RandomLabelShufflingModel	0.068	0.005	0.073
SurvivalExperiment	0.073	0.004	0.077
SurvivalModel-class	0.038	0.004	0.042
SurvivalModel	0.038	0.004	0.041
assignColDataColumn	0.030	0.001	0.030
assignSubtypes-CohortList-list-method	0.421	0.013	0.434
assignSubtypes-SurvivalExperiment-data.frame-method	0.049	0.006	0.056
assignSubtypes	0.034	0.005	0.039
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	0.695	0.020	0.715
barPlotModelComparison	0.668	0.018	0.686
birnbaum	0.003	0.003	0.006
chen	0.003	0.002	0.005
cohortSubtypeDFs	0.003	0.002	0.005
compareModels-ModelComparison-SurvivalModel-method	0.722	0.022	0.748
compareModels-SurvivalModel-SurvivalModel-method	0.678	0.023	0.709
compareModels	0.688	0.023	0.721
dropNotCensored-CohortList-method	0.453	0.005	0.464
dropNotCensored-SurvivalExperiment-method	0.043	0.003	0.046
dropNotCensored	0.045	0.003	0.048
existingClassifierData	0.003	0.003	0.005
findCommonGenes-CohortList-method	0.030	0.003	0.033
findCommonGenes	0.030	0.003	0.033
findCommonSamples-CohortList-method	0.039	0.003	0.046
findCommonSamples	0.037	0.003	0.041
forestPlot-ModelComparison-method	0.720	0.021	0.766
forestPlot-PCOSP_or_ClinicalModel-method	0.060	0.003	0.063
forestPlot	0.129	0.004	0.135
getModelSeed-SurvivalModel-method	0.008	0.002	0.010
getModelSeed	0.010	0.002	0.012
getTopFeatures-PCOSP-method	0.011	0.003	0.014
getTopFeatures-SummarizedExperiment-method	0.141	0.004	0.147
getTopFeatures	0.008	0.003	0.011
haiderSigScores	0.003	0.003	0.005
hasColDataColumns	0.013	0.001	0.014
merge-SurvivalExperiment-SurvivalExperiment-method	0.147	0.005	0.153
modelParams-set	0.015	0.004	0.019
modelParams	0.017	0.004	0.020
models-SurvivalModel-method	0.008	0.003	0.011
models-set-SurvivalModel-SimpleList-method	0.010	0.003	0.013
models-set	0.015	0.004	0.019
models	0.008	0.003	0.012
normalsMAE	0.002	0.003	0.008
plotROC-PCOSP-method	0.297	0.009	0.366
predictClasses-CohortList-ClinicalModel-method	0.274	0.009	0.287
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	0.356	0.009	0.369
predictClasses-SurvivalExperiment-ClinicalModel-method	0.121	0.007	0.129
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.118	0.007	0.125
predictClasses	0.119	0.007	0.128
rankFeatures-SummarizedExperiment-method	0.124	0.004	0.130
rankFeatures	0.101	0.004	0.106
removeColDataFactorColumns	0.020	0.003	0.025
removeFactorColumns	0.003	0.000	0.003
renameColDataColumns	0.022	0.003	0.025
renameColumns	0.002	0.000	0.002
sampleClinicalModel	0.008	0.003	0.010
sampleCohortList	0.031	0.003	0.034
sampleICGCmicro	0.007	0.003	0.011
samplePCOSPmodel	0.010	0.003	0.011
samplePCOSPpredList	0.036	0.003	0.040
samplePCSIsurvExp	0.006	0.003	0.009
sampleRGAmodel	0.009	0.002	0.012
sampleRLSmodel	0.009	0.003	0.012
sampleTrainedPCOSPmodel	0.009	0.003	0.013
sampleValPCOSPmodel	0.039	0.003	0.042
show-S4Model-method	0.070	0.004	0.075
subset-CohortList-method	0.144	0.004	0.149
trainData-set	0.015	0.004	0.018
trainData	0.009	0.004	0.012
trainModel-ClinicalModel-method	0.045	0.004	0.049
trainModel-PCOSP-method	1.263	0.013	1.294
trainModel-RGAModel-method	1.219	0.008	1.244
trainModel-RLSModel-method	1.160	0.009	1.181
trainModel	1.182	0.011	1.210
validateModel-ClinicalModel-CohortList-method	0.196	0.007	0.202
validateModel-ClinicalModel-SurvivalExperiment-method	0.556	0.035	0.602
validateModel-GeneFuModel-CohortList-method	1.086	0.078	1.206
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	1.020	0.050	1.072
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	1.006	0.047	1.053
validateModel	0.095	0.006	0.101
validationData-SurvivalModel-method	0.011	0.003	0.014
validationData-set-SurvivalModel-CohortList-method	0.009	0.003	0.011
validationData-set	0.009	0.003	0.013
validationData	0.008	0.003	0.011
validationStats-SurvivalModel-method	0.009	0.003	0.011
validationStats-set-SurvivalModel-data.frame-method	0.010	0.003	0.013
validationStats-set	0.009	0.003	0.012
validationStats	0.009	0.003	0.011

CHECK results for PDATK on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings