Multiple platform build/check report for BioC 3.18 - CHECK results for PDATK on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4669
palomino4	Windows Server 2022 Datacenter	x64	4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"	4404
merida1	macOS 12.7.1 Monterey	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4427
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/meat/PDATK.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-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 12.7.1
* 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/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 5.722  0.121   5.996
* 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/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-x86_64/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: x86_64-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 
 55.792  12.648  66.910

Example timings

name	user	system	elapsed
CSPC_MAE	0.008	0.004	0.012
ClinicalModel-class	0.211	0.010	0.261
ClinicalModel	0.187	0.006	0.209
CohortList	0.052	0.005	0.060
ConsensusMetaclusteringModel	0.023	0.003	0.032
CoxModel	0.583	0.014	0.738
GeneFuModel	0.213	0.003	0.225
ModelComparison	5.722	0.121	5.996
PCOSP	0.152	0.025	0.180
RandomGeneAssignmentModel	0.159	0.026	0.188
RandomLabelShufflingModel	0.152	0.027	0.186
SurvivalExperiment	0.171	0.028	0.200
SurvivalModel-class	0.078	0.013	0.098
SurvivalModel	0.078	0.015	0.100
assignColDataColumn	0.066	0.009	0.082
assignSubtypes-CohortList-list-method	0.950	0.112	1.150
assignSubtypes-SurvivalExperiment-data.frame-method	0.069	0.008	0.084
assignSubtypes	0.068	0.007	0.081
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	1.542	0.038	1.678
barPlotModelComparison	1.500	0.037	1.660
birnbaum	0.004	0.004	0.008
chen	0.004	0.003	0.007
cohortSubtypeDFs	0.006	0.003	0.011
compareModels-ModelComparison-SurvivalModel-method	1.527	0.039	1.703
compareModels-SurvivalModel-SurvivalModel-method	1.394	0.036	1.565
compareModels	1.386	0.035	1.560
dropNotCensored-CohortList-method	0.974	0.009	1.075
dropNotCensored-SurvivalExperiment-method	0.087	0.004	0.095
dropNotCensored	0.087	0.004	0.100
existingClassifierData	0.004	0.004	0.010
findCommonGenes-CohortList-method	0.038	0.005	0.043
findCommonGenes	0.038	0.005	0.045
findCommonSamples-CohortList-method	0.054	0.004	0.062
findCommonSamples	0.052	0.004	0.059
forestPlot-ModelComparison-method	1.450	0.033	1.563
forestPlot-PCOSP_or_ClinicalModel-method	0.091	0.004	0.098
forestPlot	0.252	0.006	0.271
getModelSeed-SurvivalModel-method	0.012	0.005	0.017
getModelSeed	0.010	0.004	0.017
getTopFeatures-PCOSP-method	0.012	0.004	0.017
getTopFeatures-SummarizedExperiment-method	0.258	0.006	0.281
getTopFeatures	0.010	0.004	0.014
haiderSigScores	0.004	0.004	0.008
hasColDataColumns	0.025	0.001	0.026
merge-SurvivalExperiment-SurvivalExperiment-method	0.266	0.008	0.303
modelParams-set	0.026	0.006	0.038
modelParams	0.024	0.005	0.033
models-SurvivalModel-method	0.012	0.004	0.015
models-set-SurvivalModel-SimpleList-method	0.012	0.003	0.017
models-set	0.025	0.005	0.032
models	0.015	0.004	0.020
normalsMAE	0.002	0.004	0.007
plotROC-PCOSP-method	0.544	0.013	0.623
predictClasses-CohortList-ClinicalModel-method	0.537	0.013	0.631
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	0.656	0.017	0.757
predictClasses-SurvivalExperiment-ClinicalModel-method	0.266	0.014	0.313
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.253	0.014	0.298
predictClasses	0.285	0.011	0.325
rankFeatures-SummarizedExperiment-method	0.270	0.006	0.305
rankFeatures	0.206	0.005	0.235
removeColDataFactorColumns	0.033	0.005	0.043
removeFactorColumns	0.005	0.001	0.007
renameColDataColumns	0.035	0.005	0.044
renameColumns	0.003	0.001	0.004
sampleClinicalModel	0.008	0.003	0.013
sampleCohortList	0.037	0.004	0.046
sampleICGCmicro	0.010	0.004	0.016
samplePCOSPmodel	0.011	0.004	0.016
samplePCOSPpredList	0.050	0.004	0.056
samplePCSIsurvExp	0.008	0.003	0.013
sampleRGAmodel	0.011	0.004	0.014
sampleRLSmodel	0.011	0.004	0.015
sampleTrainedPCOSPmodel	0.011	0.003	0.015
sampleValPCOSPmodel	0.054	0.004	0.066
show-S4Model-method	0.116	0.005	0.138
subset-CohortList-method	0.298	0.006	0.336
trainData-set	0.025	0.004	0.032
trainData	0.012	0.004	0.019
trainModel-ClinicalModel-method	0.092	0.005	0.105
trainModel-PCOSP-method	1.269	0.016	1.400
trainModel-RGAModel-method	1.346	0.040	1.585
trainModel-RLSModel-method	1.167	0.010	1.291
trainModel	1.297	0.012	1.404
validateModel-ClinicalModel-CohortList-method	0.468	0.011	0.500
validateModel-ClinicalModel-SurvivalExperiment-method	1.285	0.035	1.441
validateModel-GeneFuModel-CohortList-method	2.374	0.152	2.824
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	2.298	0.088	2.632
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	2.191	0.080	2.535
validateModel	0.17	0.01	0.20
validationData-SurvivalModel-method	0.013	0.004	0.020
validationData-set-SurvivalModel-CohortList-method	0.011	0.004	0.017
validationData-set	0.014	0.004	0.022
validationData	0.014	0.005	0.018
validationStats-SurvivalModel-method	0.010	0.004	0.017
validationStats-set-SurvivalModel-data.frame-method	0.013	0.004	0.021
validationStats-set	0.014	0.004	0.020
validationStats	0.013	0.004	0.021

CHECK results for PDATK on merida1

Summary

Command output

Installation output

Tests output

Example timings