Multiple platform build/check report for BioC 3.19 - CHECK results for PDATK on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4753
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4518
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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/PDATK.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-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 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 ‘1.12.0’
* 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-3.19-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 ... 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-3.19-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/4.4-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 
 34.529   9.252  40.480

Example timings

name	user	system	elapsed
CSPC_MAE	0.006	0.003	0.008
ClinicalModel-class	0.098	0.005	0.103
ClinicalModel	0.102	0.005	0.107
CohortList	0.030	0.002	0.033
ConsensusMetaclusteringModel	0.014	0.003	0.016
CoxModel	0.322	0.012	0.337
GeneFuModel	0.120	0.003	0.123
ModelComparison	4.640	0.074	4.753
PCOSP	0.123	0.009	0.134
RandomGeneAssignmentModel	0.087	0.006	0.095
RandomLabelShufflingModel	0.080	0.004	0.084
SurvivalExperiment	0.087	0.003	0.090
SurvivalModel-class	0.043	0.003	0.047
SurvivalModel	0.043	0.002	0.045
assignColDataColumn	0.038	0.000	0.040
assignSubtypes-CohortList-list-method	0.525	0.015	0.549
assignSubtypes-SurvivalExperiment-data.frame-method	0.063	0.006	0.070
assignSubtypes	0.036	0.003	0.039
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	0.897	0.030	0.937
barPlotModelComparison	0.835	0.028	0.872
birnbaum	0.003	0.002	0.004
chen	0.002	0.002	0.004
cohortSubtypeDFs	0.002	0.002	0.004
compareModels-ModelComparison-SurvivalModel-method	0.790	0.024	0.819
compareModels-SurvivalModel-SurvivalModel-method	0.739	0.024	0.768
compareModels	0.813	0.025	0.844
dropNotCensored-CohortList-method	0.526	0.008	0.539
dropNotCensored-SurvivalExperiment-method	0.044	0.002	0.046
dropNotCensored	0.048	0.003	0.050
existingClassifierData	0.003	0.002	0.005
findCommonGenes-CohortList-method	0.028	0.002	0.030
findCommonGenes	0.021	0.003	0.024
findCommonSamples-CohortList-method	0.034	0.002	0.036
findCommonSamples	0.032	0.003	0.039
forestPlot-ModelComparison-method	0.870	0.029	0.910
forestPlot-PCOSP_or_ClinicalModel-method	0.061	0.004	0.065
forestPlot	0.157	0.004	0.162
getModelSeed-SurvivalModel-method	0.008	0.001	0.009
getModelSeed	0.007	0.002	0.010
getTopFeatures-PCOSP-method	0.009	0.003	0.012
getTopFeatures-SummarizedExperiment-method	0.163	0.004	0.169
getTopFeatures	0.007	0.002	0.009
haiderSigScores	0.003	0.001	0.004
hasColDataColumns	0.015	0.000	0.015
merge-SurvivalExperiment-SurvivalExperiment-method	0.170	0.004	0.174
modelParams-set	0.015	0.002	0.017
modelParams	0.014	0.002	0.017
models-SurvivalModel-method	0.006	0.002	0.008
models-set-SurvivalModel-SimpleList-method	0.009	0.002	0.011
models-set	0.017	0.002	0.020
models	0.010	0.002	0.013
normalsMAE	0.002	0.003	0.007
plotROC-PCOSP-method	0.290	0.008	0.299
predictClasses-CohortList-ClinicalModel-method	0.283	0.008	0.293
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	0.388	0.012	0.403
predictClasses-SurvivalExperiment-ClinicalModel-method	0.140	0.007	0.147
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.142	0.006	0.149
predictClasses	0.138	0.006	0.146
rankFeatures-SummarizedExperiment-method	0.158	0.004	0.164
rankFeatures	0.122	0.003	0.126
removeColDataFactorColumns	0.019	0.002	0.022
removeFactorColumns	0.003	0.001	0.003
renameColDataColumns	0.021	0.003	0.024
renameColumns	0.001	0.000	0.002
sampleClinicalModel	0.006	0.003	0.008
sampleCohortList	0.027	0.003	0.030
sampleICGCmicro	0.008	0.002	0.010
samplePCOSPmodel	0.007	0.003	0.009
samplePCOSPpredList	0.032	0.002	0.035
samplePCSIsurvExp	0.007	0.003	0.009
sampleRGAmodel	0.008	0.002	0.011
sampleRLSmodel	0.007	0.002	0.008
sampleTrainedPCOSPmodel	0.008	0.003	0.013
sampleValPCOSPmodel	0.036	0.003	0.043
show-S4Model-method	0.085	0.004	0.090
subset-CohortList-method	0.151	0.003	0.154
trainData-set	0.016	0.002	0.020
trainData	0.009	0.002	0.010
trainModel-ClinicalModel-method	0.050	0.003	0.053
trainModel-PCOSP-method	1.070	0.021	1.110
trainModel-RGAModel-method	1.119	0.010	1.137
trainModel-RLSModel-method	1.119	0.011	1.136
trainModel	1.130	0.013	1.151
validateModel-ClinicalModel-CohortList-method	0.244	0.006	0.250
validateModel-ClinicalModel-SurvivalExperiment-method	0.694	0.043	0.743
validateModel-GeneFuModel-CohortList-method	1.264	0.127	1.408
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	1.279	0.073	1.364
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	1.282	0.072	1.366
validateModel	0.098	0.006	0.106
validationData-SurvivalModel-method	0.009	0.003	0.013
validationData-set-SurvivalModel-CohortList-method	0.007	0.003	0.010
validationData-set	0.008	0.003	0.010
validationData	0.009	0.003	0.011
validationStats-SurvivalModel-method	0.007	0.003	0.010
validationStats-set-SurvivalModel-data.frame-method	0.007	0.003	0.011
validationStats-set	0.010	0.002	0.011
validationStats	0.008	0.002	0.010

CHECK results for PDATK on lconway

Summary

Command output

Installation output

Tests output

Example timings