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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"	4692
palomino4	Windows Server 2022 Datacenter	x64	4.3.2 (2023-10-31 ucrt) -- "Eye Holes"	4445
lconway	macOS 12.7.1 Monterey	x86_64	4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"	4466
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 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    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
* 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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 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 
 34.313   8.701  39.898

Example timings

name	user	system	elapsed
CSPC_MAE	0.004	0.001	0.006
ClinicalModel-class	0.120	0.006	0.127
ClinicalModel	0.087	0.003	0.091
CohortList	0.028	0.002	0.030
ConsensusMetaclusteringModel	0.013	0.001	0.014
CoxModel	0.337	0.011	0.351
GeneFuModel	0.129	0.005	0.136
ModelComparison	4.463	0.083	4.580
PCOSP	0.070	0.008	0.078
RandomGeneAssignmentModel	0.074	0.009	0.083
RandomLabelShufflingModel	0.082	0.012	0.096
SurvivalExperiment	0.095	0.012	0.108
SurvivalModel-class	0.045	0.007	0.053
SurvivalModel	0.042	0.006	0.048
assignColDataColumn	0.039	0.004	0.043
assignSubtypes-CohortList-list-method	0.512	0.049	0.566
assignSubtypes-SurvivalExperiment-data.frame-method	0.032	0.004	0.035
assignSubtypes	0.034	0.003	0.037
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	0.822	0.025	0.853
barPlotModelComparison	0.857	0.025	0.887
birnbaum	0.003	0.001	0.004
chen	0.002	0.001	0.004
cohortSubtypeDFs	0.004	0.002	0.006
compareModels-ModelComparison-SurvivalModel-method	0.814	0.024	0.845
compareModels-SurvivalModel-SurvivalModel-method	0.760	0.025	0.790
compareModels	0.747	0.024	0.774
dropNotCensored-CohortList-method	0.518	0.005	0.525
dropNotCensored-SurvivalExperiment-method	0.051	0.003	0.054
dropNotCensored	0.050	0.002	0.052
existingClassifierData	0.002	0.002	0.004
findCommonGenes-CohortList-method	0.024	0.003	0.026
findCommonGenes	0.023	0.003	0.026
findCommonSamples-CohortList-method	0.035	0.003	0.038
findCommonSamples	0.033	0.003	0.036
forestPlot-ModelComparison-method	0.822	0.023	0.851
forestPlot-PCOSP_or_ClinicalModel-method	0.050	0.002	0.052
forestPlot	0.138	0.003	0.141
getModelSeed-SurvivalModel-method	0.008	0.002	0.011
getModelSeed	0.006	0.002	0.008
getTopFeatures-PCOSP-method	0.008	0.002	0.011
getTopFeatures-SummarizedExperiment-method	0.151	0.003	0.155
getTopFeatures	0.009	0.002	0.012
haiderSigScores	0.003	0.001	0.003
hasColDataColumns	0.016	0.001	0.017
merge-SurvivalExperiment-SurvivalExperiment-method	0.145	0.004	0.149
modelParams-set	0.016	0.002	0.019
modelParams	0.015	0.002	0.018
models-SurvivalModel-method	0.008	0.002	0.010
models-set-SurvivalModel-SimpleList-method	0.009	0.002	0.012
models-set	0.016	0.003	0.021
models	0.008	0.002	0.011
normalsMAE	0.002	0.002	0.004
plotROC-PCOSP-method	0.313	0.008	0.323
predictClasses-CohortList-ClinicalModel-method	0.313	0.008	0.323
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	0.400	0.010	0.414
predictClasses-SurvivalExperiment-ClinicalModel-method	0.154	0.007	0.163
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.137	0.007	0.146
predictClasses	0.160	0.006	0.167
rankFeatures-SummarizedExperiment-method	0.150	0.003	0.154
rankFeatures	0.111	0.003	0.114
removeColDataFactorColumns	0.019	0.002	0.021
removeFactorColumns	0.004	0.000	0.004
renameColDataColumns	0.018	0.002	0.021
renameColumns	0.002	0.000	0.002
sampleClinicalModel	0.006	0.002	0.008
sampleCohortList	0.023	0.002	0.025
sampleICGCmicro	0.007	0.003	0.009
samplePCOSPmodel	0.008	0.002	0.010
samplePCOSPpredList	0.031	0.002	0.034
samplePCSIsurvExp	0.006	0.002	0.008
sampleRGAmodel	0.008	0.002	0.010
sampleRLSmodel	0.007	0.002	0.010
sampleTrainedPCOSPmodel	0.008	0.002	0.010
sampleValPCOSPmodel	0.035	0.003	0.039
show-S4Model-method	0.065	0.003	0.069
subset-CohortList-method	0.167	0.004	0.173
trainData-set	0.015	0.002	0.018
trainData	0.009	0.002	0.011
trainModel-ClinicalModel-method	0.053	0.003	0.057
trainModel-PCOSP-method	1.051	0.015	1.074
trainModel-RGAModel-method	1.118	0.025	1.150
trainModel-RLSModel-method	0.967	0.009	0.980
trainModel	0.974	0.009	0.986
validateModel-ClinicalModel-CohortList-method	0.232	0.007	0.240
validateModel-ClinicalModel-SurvivalExperiment-method	0.621	0.024	0.646
validateModel-GeneFuModel-CohortList-method	1.204	0.088	1.302
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	1.194	0.067	1.270
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	1.175	0.069	1.252
validateModel	0.091	0.005	0.097
validationData-SurvivalModel-method	0.009	0.002	0.011
validationData-set-SurvivalModel-CohortList-method	0.006	0.002	0.008
validationData-set	0.009	0.002	0.011
validationData	0.009	0.002	0.010
validationStats-SurvivalModel-method	0.006	0.001	0.008
validationStats-set-SurvivalModel-data.frame-method	0.006	0.001	0.008
validationStats-set	0.009	0.002	0.012
validationStats	0.009	0.002	0.010

CHECK results for PDATK on lconway

Summary

Command output

Installation output

Tests output

Example timings