Multiple platform build/check report for BioC 3.21 - CHECK results for PDATK on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4716
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4478
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4489
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4442
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 lconway

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: 1.15.0

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_1.15.0.tar.gz

StartedAt: 2025-02-03 22:22:11 -0500 (Mon, 03 Feb 2025)

EndedAt: 2025-02-03 22:28:17 -0500 (Mon, 03 Feb 2025)

EllapsedTime: 365.4 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_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/PDATK.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PDATK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PDATK’ version ‘1.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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-3.21-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(s) 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-3.21-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/4.5-x86_64/Resources/library’
* installing *source* package ‘PDATK’ ...
** this is package ‘PDATK’ version ‘1.15.0’
** 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 Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"
Copyright (C) 2025 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
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 
 33.946   7.779  38.662

Example timings

PDATK.Rcheck/PDATK-Ex.timings

name	user	system	elapsed
CSPC_MAE	0.006	0.003	0.009
ClinicalModel-class	0.122	0.006	0.129
ClinicalModel	0.102	0.004	0.105
CohortList	0.030	0.002	0.033
ConsensusMetaclusteringModel	0.013	0.002	0.016
CoxModel	0.315	0.007	0.325
GeneFuModel	0.114	0.003	0.117
ModelComparison	4.241	0.058	4.322
PCOSP	0.087	0.011	0.098
RandomGeneAssignmentModel	0.083	0.011	0.094
RandomLabelShufflingModel	0.078	0.012	0.090
SurvivalExperiment	0.086	0.011	0.100
SurvivalModel-class	0.039	0.006	0.044
SurvivalModel	0.043	0.006	0.050
assignColDataColumn	0.034	0.003	0.037
assignSubtypes-CohortList-list-method	0.504	0.042	0.549
assignSubtypes-SurvivalExperiment-data.frame-method	0.034	0.005	0.040
assignSubtypes	0.034	0.005	0.039
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	0.740	0.021	0.765
barPlotModelComparison	0.718	0.022	0.745
birnbaum	0.002	0.002	0.005
chen	0.002	0.002	0.004
cohortSubtypeDFs	0.002	0.001	0.003
compareModels-ModelComparison-SurvivalModel-method	0.711	0.020	0.735
compareModels-SurvivalModel-SurvivalModel-method	0.671	0.022	0.697
compareModels	0.700	0.023	0.727
dropNotCensored-CohortList-method	0.482	0.005	0.491
dropNotCensored-SurvivalExperiment-method	0.050	0.002	0.053
dropNotCensored	0.045	0.002	0.047
existingClassifierData	0.001	0.002	0.003
findCommonGenes-CohortList-method	0.019	0.002	0.021
findCommonGenes	0.017	0.002	0.019
findCommonSamples-CohortList-method	0.027	0.003	0.030
findCommonSamples	0.026	0.002	0.028
forestPlot-ModelComparison-method	0.700	0.022	0.726
forestPlot-PCOSP_or_ClinicalModel-method	0.039	0.003	0.041
forestPlot	0.105	0.002	0.109
getModelSeed-SurvivalModel-method	0.006	0.002	0.007
getModelSeed	0.005	0.002	0.007
getTopFeatures-PCOSP-method	0.008	0.002	0.010
getTopFeatures-SummarizedExperiment-method	0.120	0.002	0.123
getTopFeatures	0.006	0.003	0.008
haiderSigScores	0.002	0.003	0.004
hasColDataColumns	0.012	0.000	0.014
merge-SurvivalExperiment-SurvivalExperiment-method	0.113	0.003	0.116
modelParams-set	0.013	0.002	0.016
modelParams	0.013	0.002	0.015
models-SurvivalModel-method	0.004	0.002	0.006
models-set-SurvivalModel-SimpleList-method	0.006	0.002	0.007
models-set	0.013	0.002	0.016
models	0.008	0.002	0.010
normalsMAE	0.002	0.001	0.004
plotROC-PCOSP-method	0.280	0.008	0.291
predictClasses-CohortList-ClinicalModel-method	0.270	0.007	0.282
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	0.318	0.009	0.329
predictClasses-SurvivalExperiment-ClinicalModel-method	0.113	0.005	0.120
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.115	0.004	0.119
predictClasses	0.123	0.005	0.128
rankFeatures-SummarizedExperiment-method	0.129	0.002	0.132
rankFeatures	0.103	0.002	0.105
removeColDataFactorColumns	0.018	0.003	0.021
removeFactorColumns	0.003	0.001	0.003
renameColDataColumns	0.019	0.003	0.022
renameColumns	0.001	0.001	0.002
sampleClinicalModel	0.005	0.002	0.006
sampleCohortList	0.019	0.002	0.022
sampleICGCmicro	0.005	0.002	0.007
samplePCOSPmodel	0.005	0.002	0.006
samplePCOSPpredList	0.024	0.003	0.027
samplePCSIsurvExp	0.004	0.002	0.006
sampleRGAmodel	0.007	0.002	0.009
sampleRLSmodel	0.005	0.002	0.007
sampleTrainedPCOSPmodel	0.005	0.001	0.010
sampleValPCOSPmodel	0.029	0.002	0.032
show-S4Model-method	0.049	0.002	0.052
subset-CohortList-method	0.166	0.003	0.170
trainData-set	0.014	0.003	0.017
trainData	0.007	0.002	0.009
trainModel-ClinicalModel-method	0.044	0.002	0.046
trainModel-PCOSP-method	1.100	0.013	1.120
trainModel-RGAModel-method	1.064	0.022	1.092
trainModel-RLSModel-method	1.029	0.009	1.044
trainModel	1.089	0.009	1.104
validateModel-ClinicalModel-CohortList-method	0.223	0.007	0.232
validateModel-ClinicalModel-SurvivalExperiment-method	0.618	0.021	0.641
validateModel-GeneFuModel-CohortList-method	1.159	0.071	1.236
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	1.157	0.060	1.227
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	1.115	0.060	1.184
validateModel	0.082	0.005	0.088
validationData-SurvivalModel-method	0.006	0.002	0.008
validationData-set-SurvivalModel-CohortList-method	0.005	0.001	0.006
validationData-set	0.007	0.002	0.009
validationData	0.007	0.002	0.009
validationStats-SurvivalModel-method	0.006	0.002	0.008
validationStats-set-SurvivalModel-data.frame-method	0.007	0.003	0.009
validationStats-set	0.008	0.002	0.010
validationStats	0.009	0.001	0.011