Mac ARM64 build report for BioC 3.17 - CHECK results for PDATK on kjohnson2

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson2	macOS 12.6.1 Monterey	arm64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4347
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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/PDATK.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PDATK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PDATK’ version ‘1.8.0’
* 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 ... 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 3.911  0.075   5.814
* 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-3.17-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
** 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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

> 
> test_check("PDATK")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 77 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 77 ]
> 
> proc.time()
   user  system elapsed 
 30.328   5.443  52.383

Example timings

name	user	system	elapsed
CSPC_MAE	0.005	0.002	0.012
ClinicalModel-class	0.103	0.006	0.167
ClinicalModel	0.103	0.005	0.168
CohortList	0.031	0.003	0.054
ConsensusMetaclusteringModel	0.014	0.002	0.028
CoxModel	0.338	0.022	0.524
GeneFuModel	0.122	0.011	0.185
ModelComparison	3.911	0.075	5.814
PCOSP	0.077	0.006	0.107
RandomGeneAssignmentModel	0.078	0.005	0.109
RandomLabelShufflingModel	0.087	0.006	0.118
SurvivalExperiment	0.085	0.004	0.114
SurvivalModel-class	0.040	0.004	0.057
SurvivalModel	0.042	0.004	0.058
assignColDataColumn	0.035	0.001	0.046
assignSubtypes-CohortList-list-method	0.491	0.021	0.724
assignSubtypes-SurvivalExperiment-data.frame-method	0.040	0.007	0.069
assignSubtypes	0.040	0.007	0.064
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	0.883	0.034	1.290
barPlotModelComparison	0.853	0.031	1.332
birnbaum	0.003	0.003	0.007
chen	0.003	0.002	0.007
cohortSubtypeDFs	0.003	0.003	0.006
compareModels-ModelComparison-SurvivalModel-method	0.861	0.031	1.352
compareModels-SurvivalModel-SurvivalModel-method	0.793	0.030	1.207
compareModels	0.775	0.029	1.243
dropNotCensored-CohortList-method	0.555	0.010	0.867
dropNotCensored-SurvivalExperiment-method	0.054	0.004	0.099
dropNotCensored	0.047	0.004	0.077
existingClassifierData	0.003	0.003	0.010
findCommonGenes-CohortList-method	0.025	0.004	0.043
findCommonGenes	0.023	0.004	0.040
findCommonSamples-CohortList-method	0.033	0.003	0.053
findCommonSamples	0.032	0.004	0.050
forestPlot-ModelComparison-method	0.839	0.029	1.340
forestPlot-PCOSP_or_ClinicalModel-method	0.057	0.005	0.098
forestPlot	0.140	0.005	0.229
getModelSeed-SurvivalModel-method	0.008	0.003	0.016
getModelSeed	0.007	0.003	0.016
getTopFeatures-PCOSP-method	0.008	0.003	0.019
getTopFeatures-SummarizedExperiment-method	0.177	0.005	0.278
getTopFeatures	0.007	0.003	0.016
haiderSigScores	0.002	0.003	0.007
hasColDataColumns	0.014	0.001	0.024
merge-SurvivalExperiment-SurvivalExperiment-method	0.152	0.006	0.246
modelParams-set	0.016	0.002	0.030
modelParams	0.017	0.002	0.031
models-SurvivalModel-method	0.007	0.003	0.017
models-set-SurvivalModel-SimpleList-method	0.008	0.003	0.018
models-set	0.015	0.003	0.028
models	0.009	0.002	0.015
normalsMAE	0.002	0.002	0.007
plotROC-PCOSP-method	0.310	0.012	0.510
predictClasses-CohortList-ClinicalModel-method	0.293	0.012	0.468
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	0.369	0.011	0.590
predictClasses-SurvivalExperiment-ClinicalModel-method	0.141	0.008	0.224
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.135	0.009	0.223
predictClasses	0.136	0.009	0.228
rankFeatures-SummarizedExperiment-method	0.170	0.006	0.267
rankFeatures	0.120	0.005	0.193
removeColDataFactorColumns	0.019	0.003	0.032
removeFactorColumns	0.003	0.000	0.008
renameColDataColumns	0.020	0.003	0.034
renameColumns	0.002	0.000	0.003
sampleClinicalModel	0.006	0.003	0.012
sampleCohortList	0.023	0.003	0.034
sampleICGCmicro	0.007	0.003	0.012
samplePCOSPmodel	0.007	0.003	0.015
samplePCOSPpredList	0.030	0.003	0.049
samplePCSIsurvExp	0.005	0.003	0.013
sampleRGAmodel	0.007	0.003	0.011
sampleRLSmodel	0.007	0.003	0.012
sampleTrainedPCOSPmodel	0.008	0.004	0.016
sampleValPCOSPmodel	0.033	0.004	0.054
show-S4Model-method	0.063	0.002	0.098
subset-CohortList-method	0.194	0.005	0.294
trainData-set	0.016	0.003	0.027
trainData	0.009	0.002	0.015
trainModel-ClinicalModel-method	0.052	0.004	0.085
trainModel-PCOSP-method	0.857	0.017	1.324
trainModel-RGAModel-method	0.865	0.010	1.346
trainModel-RLSModel-method	0.795	0.010	1.241
trainModel	0.855	0.011	1.330
validateModel-ClinicalModel-CohortList-method	0.253	0.009	0.402
validateModel-ClinicalModel-SurvivalExperiment-method	0.708	0.043	1.137
validateModel-GeneFuModel-CohortList-method	1.304	0.109	2.159
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	1.273	0.091	2.100
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	1.210	0.074	1.954
validateModel	0.100	0.008	0.171
validationData-SurvivalModel-method	0.009	0.003	0.016
validationData-set-SurvivalModel-CohortList-method	0.007	0.004	0.019
validationData-set	0.008	0.002	0.016
validationData	0.007	0.002	0.015
validationStats-SurvivalModel-method	0.007	0.003	0.015
validationStats-set-SurvivalModel-data.frame-method	0.008	0.003	0.015
validationStats-set	0.008	0.002	0.016
validationStats	0.008	0.002	0.016

CHECK results for PDATK on kjohnson2

Summary

Command output

Installation output

Tests output

Example timings