Multiple platform build/check report for BioC 3.16 - CHECK results for PDATK on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4502
palomino4	Windows Server 2022 Datacenter	x64	4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"	4282
lconway	macOS 12.5.1 Monterey	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4310
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*

##############################################################################
##############################################################################
###
### 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/PDATK.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PDATK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PDATK’ version ‘1.6.0’
* 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 ... OK
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/PDATK.Rcheck/00check.log’
for details.

Installation output

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘PDATK’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PDATK)

Tests output


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 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

> 
> test_check("PDATK")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 77 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 77 ]
> 
> proc.time()
   user  system elapsed 
 28.565   9.825  32.656

Example timings

name	user	system	elapsed
CSPC_MAE	0.005	0.002	0.007
ClinicalModel-class	0.085	0.004	0.089
ClinicalModel	0.085	0.004	0.089
CohortList	0.027	0.002	0.028
ConsensusMetaclusteringModel	0.015	0.001	0.016
CoxModel	0.292	0.017	0.310
GeneFuModel	0.129	0.009	0.139
ModelComparison	2.459	0.038	2.503
PCOSP	0.062	0.003	0.065
RandomGeneAssignmentModel	0.063	0.003	0.066
RandomLabelShufflingModel	0.074	0.004	0.078
SurvivalExperiment	0.075	0.004	0.082
SurvivalModel-class	0.027	0.002	0.029
SurvivalModel	0.031	0.002	0.033
assignColDataColumn	0.025	0.001	0.027
assignSubtypes-CohortList-list-method	0.302	0.007	0.309
assignSubtypes-SurvivalExperiment-data.frame-method	0.026	0.003	0.029
assignSubtypes	0.036	0.004	0.040
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method	0.771	0.019	0.791
barPlotModelComparison	0.604	0.014	0.619
birnbaum	0.002	0.002	0.004
chen	0.002	0.001	0.004
cohortSubtypeDFs	0.002	0.001	0.004
compareModels-ModelComparison-SurvivalModel-method	0.574	0.014	0.588
compareModels-SurvivalModel-SurvivalModel-method	0.563	0.015	0.579
compareModels	0.515	0.012	0.528
dropNotCensored-CohortList-method	0.456	0.004	0.461
dropNotCensored-SurvivalExperiment-method	0.042	0.001	0.044
dropNotCensored	0.040	0.002	0.042
existingClassifierData	0.002	0.001	0.003
findCommonGenes-CohortList-method	0.018	0.001	0.019
findCommonGenes	0.020	0.002	0.022
findCommonSamples-CohortList-method	0.023	0.002	0.024
findCommonSamples	0.026	0.002	0.029
forestPlot-ModelComparison-method	0.776	0.019	0.798
forestPlot-PCOSP_or_ClinicalModel-method	0.054	0.002	0.056
forestPlot	0.122	0.003	0.126
getModelSeed-SurvivalModel-method	0.007	0.002	0.009
getModelSeed	0.007	0.002	0.009
getTopFeatures-PCOSP-method	0.006	0.001	0.007
getTopFeatures-SummarizedExperiment-method	0.132	0.001	0.134
getTopFeatures	0.007	0.002	0.008
haiderSigScores	0.003	0.001	0.004
hasColDataColumns	0.012	0.000	0.012
merge-SurvivalExperiment-SurvivalExperiment-method	0.119	0.003	0.123
modelParams-set	0.015	0.003	0.017
modelParams	0.012	0.002	0.014
models-SurvivalModel-method	0.005	0.001	0.006
models-set-SurvivalModel-SimpleList-method	0.006	0.001	0.008
models-set	0.013	0.003	0.016
models	0.009	0.002	0.011
normalsMAE	0.001	0.002	0.003
plotROC-PCOSP-method	0.265	0.007	0.273
predictClasses-CohortList-ClinicalModel-method	0.254	0.005	0.264
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method	0.310	0.006	0.318
predictClasses-SurvivalExperiment-ClinicalModel-method	0.115	0.004	0.119
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method	0.134	0.006	0.141
predictClasses	0.093	0.003	0.095
rankFeatures-SummarizedExperiment-method	0.120	0.002	0.122
rankFeatures	0.105	0.002	0.108
removeColDataFactorColumns	0.016	0.002	0.019
removeFactorColumns	0.002	0.000	0.003
renameColDataColumns	0.015	0.002	0.016
renameColumns	0.001	0.000	0.001
sampleClinicalModel	0.004	0.001	0.006
sampleCohortList	0.018	0.002	0.019
sampleICGCmicro	0.005	0.001	0.006
samplePCOSPmodel	0.005	0.001	0.006
samplePCOSPpredList	0.029	0.002	0.031
samplePCSIsurvExp	0.006	0.002	0.007
sampleRGAmodel	0.008	0.002	0.009
sampleRLSmodel	0.006	0.001	0.009
sampleTrainedPCOSPmodel	0.006	0.001	0.007
sampleValPCOSPmodel	0.023	0.001	0.025
show-S4Model-method	0.041	0.002	0.043
subset-CohortList-method	0.132	0.003	0.134
trainData-set	0.011	0.002	0.012
trainData	0.008	0.002	0.010
trainModel-ClinicalModel-method	0.036	0.002	0.038
trainModel-PCOSP-method	0.923	0.007	0.932
trainModel-RGAModel-method	0.961	0.004	0.967
trainModel-RLSModel-method	0.791	0.003	0.796
trainModel	0.856	0.006	0.866
validateModel-ClinicalModel-CohortList-method	0.211	0.003	0.215
validateModel-ClinicalModel-SurvivalExperiment-method	0.527	0.014	0.541
validateModel-GeneFuModel-CohortList-method	0.903	0.046	0.952
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method	0.799	0.039	0.841
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method	0.955	0.045	1.002
validateModel	0.082	0.004	0.087
validationData-SurvivalModel-method	0.007	0.002	0.010
validationData-set-SurvivalModel-CohortList-method	0.005	0.001	0.007
validationData-set	0.008	0.002	0.010
validationData	0.006	0.002	0.008
validationStats-SurvivalModel-method	0.007	0.002	0.009
validationStats-set-SurvivalModel-data.frame-method	0.006	0.001	0.008
validationStats-set	0.007	0.002	0.009
validationStats	0.006	0.001	0.008

CHECK results for PDATK on lconway

Summary

Command output

Installation output

Tests output

Example timings