Mac ARM64 build report for BioC 3.18 - CHECK results for PDATK on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.1 Ventura	arm64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4376
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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/PDATK.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PDATK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PDATK’ version ‘1.10.0’
* 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-3.18-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 ... 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 ... WARNING
Missing link or links in documentation object '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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
ModelComparison 5.076   0.05   5.129
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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, 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, sort, 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 
 32.918   8.135  38.227

Example timings

name	user	system	elapsed
CSPC_MAE	0.007	0.003	0.011
ClinicalModel-class	0.126	0.005	0.132
ClinicalModel	0.096	0.005	0.104
CohortList	0.031	0.003	0.034
ConsensusMetaclusteringModel	0.014	0.003	0.017
CoxModel	0.294	0.009	0.307
GeneFuModel	0.096	0.002	0.098
ModelComparison	5.076	0.050	5.129
PCOSP	0.073	0.009	0.082
RandomGeneAssignmentModel	0.072	0.009	0.081
RandomLabelShufflingModel	0.075	0.009	0.085
SurvivalExperiment	0.076	0.009	0.085
SurvivalModel-class	0.040	0.005	0.045
SurvivalModel	0.040	0.005	0.046
assignColDataColumn	0.034	0.002	0.038
assignSubtypes-CohortList-list-method	0.401	0.032	0.433
assignSubtypes-SurvivalExperiment-data.frame-method	0.034	0.005	0.039
assignSubtypes	0.033	0.005	0.039
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	0.695	0.020	0.715
barPlotModelComparison	0.726	0.026	0.758
birnbaum	0.003	0.003	0.005
chen	0.003	0.002	0.007
cohortSubtypeDFs	0.004	0.003	0.006
compareModels-ModelComparison-SurvivalModel-method	0.759	0.024	0.811
compareModels-SurvivalModel-SurvivalModel-method	0.690	0.024	0.753
compareModels	0.679	0.022	0.730
dropNotCensored-CohortList-method	0.481	0.006	0.497
dropNotCensored-SurvivalExperiment-method	0.045	0.003	0.051
dropNotCensored	0.049	0.003	0.054
existingClassifierData	0.003	0.002	0.006
findCommonGenes-CohortList-method	0.032	0.003	0.035
findCommonGenes	0.031	0.004	0.035
findCommonSamples-CohortList-method	0.042	0.003	0.049
findCommonSamples	0.039	0.003	0.042
forestPlot-ModelComparison-method	0.750	0.023	0.797
forestPlot-PCOSP_or_ClinicalModel-method	0.064	0.003	0.071
forestPlot	0.126	0.004	0.133
getModelSeed-SurvivalModel-method	0.010	0.003	0.016
getModelSeed	0.010	0.002	0.014
getTopFeatures-PCOSP-method	0.011	0.003	0.015
getTopFeatures-SummarizedExperiment-method	0.161	0.004	0.171
getTopFeatures	0.009	0.002	0.013
haiderSigScores	0.003	0.003	0.006
hasColDataColumns	0.013	0.001	0.015
merge-SurvivalExperiment-SurvivalExperiment-method	0.128	0.004	0.136
modelParams-set	0.015	0.003	0.019
modelParams	0.018	0.003	0.023
models-SurvivalModel-method	0.008	0.003	0.011
models-set-SurvivalModel-SimpleList-method	0.010	0.002	0.013
models-set	0.014	0.003	0.019
models	0.009	0.003	0.011
normalsMAE	0.002	0.003	0.008
plotROC-PCOSP-method	0.293	0.008	0.311
predictClasses-CohortList-ClinicalModel-method	0.281	0.009	0.303
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	0.351	0.011	0.369
predictClasses-SurvivalExperiment-ClinicalModel-method	0.125	0.008	0.135
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.120	0.008	0.133
predictClasses	0.148	0.006	0.159
rankFeatures-SummarizedExperiment-method	0.138	0.004	0.146
rankFeatures	0.102	0.003	0.108
removeColDataFactorColumns	0.020	0.003	0.024
removeFactorColumns	0.003	0.001	0.004
renameColDataColumns	0.019	0.003	0.024
renameColumns	0.002	0.001	0.001
sampleClinicalModel	0.006	0.003	0.010
sampleCohortList	0.032	0.003	0.034
sampleICGCmicro	0.010	0.003	0.012
samplePCOSPmodel	0.008	0.003	0.012
samplePCOSPpredList	0.041	0.003	0.045
samplePCSIsurvExp	0.007	0.003	0.010
sampleRGAmodel	0.008	0.003	0.011
sampleRLSmodel	0.010	0.002	0.012
sampleTrainedPCOSPmodel	0.009	0.002	0.013
sampleValPCOSPmodel	0.043	0.003	0.048
show-S4Model-method	0.056	0.003	0.064
subset-CohortList-method	0.189	0.004	0.198
trainData-set	0.017	0.004	0.021
trainData	0.009	0.003	0.011
trainModel-ClinicalModel-method	0.046	0.003	0.050
trainModel-PCOSP-method	1.266	0.012	1.321
trainModel-RGAModel-method	1.283	0.024	1.363
trainModel-RLSModel-method	1.161	0.007	1.207
trainModel	1.153	0.007	1.162
validateModel-ClinicalModel-CohortList-method	0.201	0.007	0.208
validateModel-ClinicalModel-SurvivalExperiment-method	0.606	0.025	0.631
validateModel-GeneFuModel-CohortList-method	1.067	0.075	1.143
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	1.031	0.051	1.083
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	1.018	0.047	1.066
validateModel	0.099	0.007	0.106
validationData-SurvivalModel-method	0.011	0.003	0.014
validationData-set-SurvivalModel-CohortList-method	0.010	0.003	0.012
validationData-set	0.009	0.003	0.012
validationData	0.009	0.003	0.011
validationStats-SurvivalModel-method	0.009	0.002	0.012
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