Multiple platform build/check report for BioC 3.20 - CHECK results for PDATK on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4769
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4504
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4527
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4480
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4416
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 merida1

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: 1.14.0

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_1.14.0.tar.gz

StartedAt: 2025-03-04 07:58:25 -0500 (Tue, 04 Mar 2025)

EndedAt: 2025-03-04 08:21:42 -0500 (Tue, 04 Mar 2025)

EllapsedTime: 1397.1 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/PDATK.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PDATK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PDATK’ version ‘1.14.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
trainModel-PCOSP-method 0.825  0.009   7.538
CoxModel                0.306  0.008   9.152
* 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-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

PDATK.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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, saveRDS, 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 
 32.123   6.765  36.415

Example timings

PDATK.Rcheck/PDATK-Ex.timings

name	user	system	elapsed
CSPC_MAE	0.004	0.002	0.006
ClinicalModel-class	0.095	0.004	0.099
ClinicalModel	0.105	0.004	0.109
CohortList	0.028	0.003	0.031
ConsensusMetaclusteringModel	0.013	0.002	0.015
CoxModel	0.306	0.008	9.152
GeneFuModel	0.133	0.004	0.137
ModelComparison	3.510	0.043	4.046
PCOSP	0.101	0.008	0.109
RandomGeneAssignmentModel	0.084	0.004	0.087
RandomLabelShufflingModel	0.082	0.004	0.085
SurvivalExperiment	0.142	0.006	0.155
SurvivalModel-class	0.077	0.006	0.101
SurvivalModel	0.049	0.005	0.055
assignColDataColumn	0.037	0.001	0.039
assignSubtypes-CohortList-list-method	0.529	0.010	0.540
assignSubtypes-SurvivalExperiment-data.frame-method	0.047	0.004	0.050
assignSubtypes	0.038	0.004	0.042
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	0.855	0.020	0.876
barPlotModelComparison	0.804	0.019	0.823
birnbaum	0.002	0.001	0.004
chen	0.003	0.002	0.004
cohortSubtypeDFs	0.003	0.002	0.004
compareModels-ModelComparison-SurvivalModel-method	0.827	0.019	0.848
compareModels-SurvivalModel-SurvivalModel-method	0.780	0.021	0.804
compareModels	0.753	0.017	0.770
dropNotCensored-CohortList-method	0.487	0.003	0.490
dropNotCensored-SurvivalExperiment-method	0.043	0.002	0.045
dropNotCensored	0.046	0.002	0.048
existingClassifierData	0.002	0.002	0.004
findCommonGenes-CohortList-method	0.022	0.002	0.024
findCommonGenes	0.022	0.002	0.023
findCommonSamples-CohortList-method	0.030	0.002	0.033
findCommonSamples	0.030	0.002	0.033
forestPlot-ModelComparison-method	0.808	0.016	0.823
forestPlot-PCOSP_or_ClinicalModel-method	0.051	0.002	0.053
forestPlot	0.139	0.002	0.141
getModelSeed-SurvivalModel-method	0.007	0.002	0.009
getModelSeed	0.006	0.002	0.008
getTopFeatures-PCOSP-method	0.007	0.002	0.009
getTopFeatures-SummarizedExperiment-method	0.139	0.003	0.142
getTopFeatures	0.007	0.002	0.009
haiderSigScores	0.002	0.001	0.004
hasColDataColumns	0.014	0.000	0.014
merge-SurvivalExperiment-SurvivalExperiment-method	0.155	0.003	0.157
modelParams-set	0.014	0.003	0.017
modelParams	0.013	0.002	0.015
models-SurvivalModel-method	0.007	0.002	0.009
models-set-SurvivalModel-SimpleList-method	0.008	0.002	0.009
models-set	0.014	0.002	0.015
models	0.008	0.002	0.010
normalsMAE	0.002	0.002	0.003
plotROC-PCOSP-method	0.288	0.007	0.295
predictClasses-CohortList-ClinicalModel-method	0.276	0.006	0.282
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	0.368	0.007	1.058
predictClasses-SurvivalExperiment-ClinicalModel-method	0.144	0.005	0.150
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.129	0.004	0.133
predictClasses	0.133	0.004	0.136
rankFeatures-SummarizedExperiment-method	0.153	0.003	0.156
rankFeatures	0.115	0.002	0.118
removeColDataFactorColumns	0.021	0.003	0.024
removeFactorColumns	0.004	0.000	0.005
renameColDataColumns	0.019	0.002	0.022
renameColumns	0.002	0.001	0.002
sampleClinicalModel	0.005	0.002	0.007
sampleCohortList	0.021	0.002	0.022
sampleICGCmicro	0.006	0.001	0.008
samplePCOSPmodel	0.006	0.002	0.008
samplePCOSPpredList	0.027	0.002	0.029
samplePCSIsurvExp	0.005	0.002	0.007
sampleRGAmodel	0.006	0.001	0.007
sampleRLSmodel	0.006	0.002	0.008
sampleTrainedPCOSPmodel	0.006	0.002	0.009
sampleValPCOSPmodel	0.029	0.002	0.031
show-S4Model-method	0.095	0.005	0.102
subset-CohortList-method	0.159	0.002	0.161
trainData-set	0.013	0.002	0.016
trainData	0.007	0.001	0.009
trainModel-ClinicalModel-method	0.051	0.003	0.054
trainModel-PCOSP-method	0.825	0.009	7.538
trainModel-RGAModel-method	0.829	0.004	0.833
trainModel-RLSModel-method	0.724	0.003	0.728
trainModel	0.810	0.007	0.817
validateModel-ClinicalModel-CohortList-method	0.249	0.005	0.253
validateModel-ClinicalModel-SurvivalExperiment-method	0.676	0.042	0.717
validateModel-GeneFuModel-CohortList-method	1.291	0.124	1.415
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	1.165	0.044	1.209
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	1.214	0.044	1.260
validateModel	0.091	0.005	0.095
validationData-SurvivalModel-method	0.008	0.002	0.010
validationData-set-SurvivalModel-CohortList-method	0.006	0.002	0.008
validationData-set	0.008	0.003	0.010
validationData	0.008	0.002	0.010
validationStats-SurvivalModel-method	0.006	0.001	0.008
validationStats-set-SurvivalModel-data.frame-method	0.007	0.002	0.009
validationStats-set	0.008	0.002	0.010
validationStats	0.007	0.002	0.009