Multiple platform build/check report for BioC 3.20 - CHECK results for PDATK on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4679
palomino4	Windows Server 2022 Datacenter	x64	4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"	4414
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4441
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4394
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*

CHECK results for PDATK on kjohnson1

To the developers/maintainers of the PDATK package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PDATK.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: PDATK

Version: 1.13.0

Command: /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_1.13.0.tar.gz

StartedAt: 2024-06-11 04:00:12 -0400 (Tue, 11 Jun 2024)

EndedAt: 2024-06-11 04:06:09 -0400 (Tue, 11 Jun 2024)

EllapsedTime: 356.6 seconds

RetCode: 0

Status: WARNINGS

CheckDir: PDATK.Rcheck

Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PDATK.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-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 Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PDATK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PDATK’ version ‘1.13.0’
* 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-3.20-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-3.20-bioc/meat/PDATK.Rcheck/00check.log’
for details.

Installation output

PDATK.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PDATK
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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

PDATK.Rcheck/tests/testthat.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 
 31.178   6.801  35.448

Example timings

PDATK.Rcheck/PDATK-Ex.timings

name	user	system	elapsed
CSPC_MAE	0.006	0.003	0.008
ClinicalModel-class	0.083	0.004	0.088
ClinicalModel	0.087	0.005	0.092
CohortList	0.029	0.003	0.032
ConsensusMetaclusteringModel	0.013	0.002	0.015
CoxModel	0.285	0.008	0.297
GeneFuModel	0.089	0.002	0.091
ModelComparison	4.868	0.040	4.910
PCOSP	0.099	0.007	0.107
RandomGeneAssignmentModel	0.077	0.005	0.084
RandomLabelShufflingModel	0.075	0.005	0.081
SurvivalExperiment	0.081	0.003	0.085
SurvivalModel-class	0.038	0.003	0.041
SurvivalModel	0.045	0.003	0.048
assignColDataColumn	0.032	0.000	0.032
assignSubtypes-CohortList-list-method	0.445	0.012	0.462
assignSubtypes-SurvivalExperiment-data.frame-method	0.056	0.006	0.063
assignSubtypes	0.036	0.007	0.042
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	0.764	0.024	0.807
barPlotModelComparison	0.737	0.024	0.773
birnbaum	0.003	0.002	0.005
chen	0.002	0.002	0.005
cohortSubtypeDFs	0.003	0.003	0.006
compareModels-ModelComparison-SurvivalModel-method	0.744	0.023	0.778
compareModels-SurvivalModel-SurvivalModel-method	0.679	0.022	0.719
compareModels	0.683	0.022	0.722
dropNotCensored-CohortList-method	0.452	0.005	0.468
dropNotCensored-SurvivalExperiment-method	0.043	0.003	0.049
dropNotCensored	0.042	0.003	0.045
existingClassifierData	0.003	0.003	0.006
findCommonGenes-CohortList-method	0.030	0.003	0.036
findCommonGenes	0.030	0.003	0.033
findCommonSamples-CohortList-method	0.039	0.003	0.041
findCommonSamples	0.036	0.003	0.040
forestPlot-ModelComparison-method	0.733	0.021	0.772
forestPlot-PCOSP_or_ClinicalModel-method	0.059	0.003	0.063
forestPlot	0.130	0.004	0.135
getModelSeed-SurvivalModel-method	0.009	0.003	0.013
getModelSeed	0.009	0.002	0.012
getTopFeatures-PCOSP-method	0.009	0.002	0.013
getTopFeatures-SummarizedExperiment-method	0.141	0.004	0.149
getTopFeatures	0.008	0.003	0.012
haiderSigScores	0.003	0.003	0.008
hasColDataColumns	0.014	0.001	0.015
merge-SurvivalExperiment-SurvivalExperiment-method	0.141	0.004	0.146
modelParams-set	0.015	0.003	0.018
modelParams	0.017	0.003	0.019
models-SurvivalModel-method	0.010	0.003	0.013
models-set-SurvivalModel-SimpleList-method	0.011	0.002	0.014
models-set	0.016	0.003	0.019
models	0.009	0.002	0.011
normalsMAE	0.002	0.003	0.006
plotROC-PCOSP-method	0.281	0.008	0.293
predictClasses-CohortList-ClinicalModel-method	0.259	0.008	0.271
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	0.353	0.011	0.369
predictClasses-SurvivalExperiment-ClinicalModel-method	0.124	0.007	0.134
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.123	0.007	0.138
predictClasses	0.129	0.007	0.137
rankFeatures-SummarizedExperiment-method	0.137	0.004	0.143
rankFeatures	0.099	0.003	0.103
removeColDataFactorColumns	0.021	0.003	0.025
removeFactorColumns	0.003	0.000	0.004
renameColDataColumns	0.020	0.004	0.024
renameColumns	0.002	0.000	0.001
sampleClinicalModel	0.007	0.002	0.010
sampleCohortList	0.030	0.003	0.034
sampleICGCmicro	0.010	0.003	0.012
samplePCOSPmodel	0.008	0.003	0.011
samplePCOSPpredList	0.037	0.003	0.040
samplePCSIsurvExp	0.007	0.003	0.010
sampleRGAmodel	0.008	0.003	0.011
sampleRLSmodel	0.009	0.003	0.012
sampleTrainedPCOSPmodel	0.008	0.003	0.011
sampleValPCOSPmodel	0.039	0.003	0.043
show-S4Model-method	0.075	0.004	0.080
subset-CohortList-method	0.144	0.004	0.151
trainData-set	0.016	0.003	0.022
trainData	0.009	0.002	0.011
trainModel-ClinicalModel-method	0.046	0.003	0.049
trainModel-PCOSP-method	1.195	0.014	1.241
trainModel-RGAModel-method	1.229	0.008	1.262
trainModel-RLSModel-method	1.145	0.005	1.151
trainModel	1.150	0.005	1.156
validateModel-ClinicalModel-CohortList-method	0.202	0.006	0.208
validateModel-ClinicalModel-SurvivalExperiment-method	0.558	0.032	0.591
validateModel-GeneFuModel-CohortList-method	1.053	0.088	1.141
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	0.988	0.052	1.044
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	0.984	0.046	1.034
validateModel	0.093	0.006	0.100
validationData-SurvivalModel-method	0.011	0.003	0.014
validationData-set-SurvivalModel-CohortList-method	0.009	0.002	0.011
validationData-set	0.009	0.003	0.012
validationData	0.008	0.003	0.011
validationStats-SurvivalModel-method	0.009	0.003	0.011
validationStats-set-SurvivalModel-data.frame-method	0.010	0.003	0.012
validationStats-set	0.008	0.003	0.012
validationStats	0.008	0.003	0.010