Multiple platform build/check report for BioC 3.18 - CHECK results for PDATK on nebbiolo2

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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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:PDATK.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings PDATK_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/PDATK.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 ‘/home/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 loading without being on the library search path ... 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 ...
  ‘PCOSP_model_analysis.Rmd’ using ‘UTF-8’... OK
  ‘PDATK_introduction.rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/PDATK.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL PDATK
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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-pc-linux-gnu (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 12 | SKIP 0 | PASS 77 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 77 ]
> 
> proc.time()
   user  system elapsed 
 29.997   7.565  33.606

Example timings

name	user	system	elapsed
CSPC_MAE	0.005	0.000	0.005
ClinicalModel-class	0.113	0.028	0.142
ClinicalModel	0.092	0.004	0.096
CohortList	0.027	0.000	0.026
ConsensusMetaclusteringModel	0.011	0.000	0.011
CoxModel	0.279	0.012	0.291
GeneFuModel	0.081	0.020	0.100
ModelComparison	4.389	0.276	4.665
PCOSP	0.072	0.004	0.076
RandomGeneAssignmentModel	0.063	0.016	0.079
RandomLabelShufflingModel	0.074	0.004	0.078
SurvivalExperiment	0.072	0.012	0.085
SurvivalModel-class	0.036	0.004	0.041
SurvivalModel	0.036	0.004	0.041
assignColDataColumn	0.036	0.000	0.035
assignSubtypes-CohortList-list-method	0.393	0.060	0.452
assignSubtypes-SurvivalExperiment-data.frame-method	0.031	0.000	0.031
assignSubtypes	0.027	0.004	0.031
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	0.665	0.032	0.696
barPlotModelComparison	0.666	0.040	0.707
birnbaum	0.002	0.000	0.003
chen	0.000	0.003	0.003
cohortSubtypeDFs	0.001	0.001	0.003
compareModels-ModelComparison-SurvivalModel-method	0.726	0.032	0.758
compareModels-SurvivalModel-SurvivalModel-method	0.660	0.028	0.688
compareModels	0.587	0.028	0.616
dropNotCensored-CohortList-method	0.457	0.004	0.461
dropNotCensored-SurvivalExperiment-method	0.036	0.008	0.044
dropNotCensored	0.037	0.000	0.038
existingClassifierData	0.002	0.000	0.002
findCommonGenes-CohortList-method	0.023	0.000	0.023
findCommonGenes	0.023	0.000	0.023
findCommonSamples-CohortList-method	0.03	0.00	0.03
findCommonSamples	0.026	0.004	0.029
forestPlot-ModelComparison-method	0.707	0.028	0.735
forestPlot-PCOSP_or_ClinicalModel-method	0.051	0.000	0.051
forestPlot	0.103	0.020	0.124
getModelSeed-SurvivalModel-method	0.007	0.000	0.007
getModelSeed	0.003	0.004	0.007
getTopFeatures-PCOSP-method	0.007	0.000	0.008
getTopFeatures-SummarizedExperiment-method	0.114	0.012	0.126
getTopFeatures	0.007	0.000	0.007
haiderSigScores	0.000	0.003	0.002
hasColDataColumns	0.009	0.005	0.013
merge-SurvivalExperiment-SurvivalExperiment-method	0.120	0.004	0.124
modelParams-set	0.014	0.000	0.014
modelParams	0.011	0.004	0.015
models-SurvivalModel-method	0.007	0.000	0.007
models-set-SurvivalModel-SimpleList-method	0.008	0.000	0.008
models-set	0.013	0.000	0.013
models	0.007	0.000	0.007
normalsMAE	0.002	0.000	0.002
plotROC-PCOSP-method	0.250	0.016	0.266
predictClasses-CohortList-ClinicalModel-method	0.237	0.016	0.254
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	0.296	0.024	0.320
predictClasses-SurvivalExperiment-ClinicalModel-method	0.105	0.016	0.121
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.134	0.004	0.138
predictClasses	0.114	0.004	0.118
rankFeatures-SummarizedExperiment-method	0.120	0.004	0.124
rankFeatures	0.088	0.008	0.096
removeColDataFactorColumns	0.018	0.000	0.018
removeFactorColumns	0.003	0.000	0.003
renameColDataColumns	0.019	0.000	0.018
renameColumns	0.002	0.000	0.002
sampleClinicalModel	0.006	0.000	0.006
sampleCohortList	0.022	0.000	0.022
sampleICGCmicro	0.007	0.000	0.007
samplePCOSPmodel	0.002	0.004	0.007
samplePCOSPpredList	0.024	0.004	0.028
samplePCSIsurvExp	0.005	0.000	0.005
sampleRGAmodel	0.007	0.000	0.007
sampleRLSmodel	0.007	0.000	0.006
sampleTrainedPCOSPmodel	0.007	0.000	0.007
sampleValPCOSPmodel	0.027	0.004	0.030
show-S4Model-method	0.065	0.000	0.065
subset-CohortList-method	0.176	0.000	0.176
trainData-set	0.012	0.004	0.017
trainData	0.006	0.000	0.006
trainModel-ClinicalModel-method	0.034	0.008	0.042
trainModel-PCOSP-method	1.081	0.120	1.201
trainModel-RGAModel-method	1.067	0.036	1.103
trainModel-RLSModel-method	1.010	0.012	1.022
trainModel	1.054	0.004	1.058
validateModel-ClinicalModel-CohortList-method	0.203	0.000	0.204
validateModel-ClinicalModel-SurvivalExperiment-method	0.574	0.024	0.599
validateModel-GeneFuModel-CohortList-method	1.115	0.032	1.147
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	1.096	0.032	1.128
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	1.025	0.032	1.058
validateModel	0.084	0.000	0.084
validationData-SurvivalModel-method	0.008	0.000	0.008
validationData-set-SurvivalModel-CohortList-method	0.006	0.000	0.006
validationData-set	0.008	0.000	0.008
validationData	0.007	0.000	0.007
validationStats-SurvivalModel-method	0.007	0.000	0.006
validationStats-set-SurvivalModel-data.frame-method	0.004	0.004	0.007
validationStats-set	0.004	0.004	0.007
validationStats	0.007	0.000	0.007

CHECK results for PDATK on nebbiolo2

Summary

Command output

Installation output

Tests output

Example timings