Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:08:07 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 machv2


To the developers/maintainers of the PDATK package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1388/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PDATK 1.2.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/PDATK
git_branch: RELEASE_3_14
git_last_commit: ecf1881
git_last_commit_date: 2021-10-26 13:07:20 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PDATK
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2022-01-23 16:19:03 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 16:26:42 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 459.0 seconds
RetCode: 0
Status:   OK  
CheckDir: PDATK.Rcheck
Warnings: 0

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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/PDATK.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.2.0’
* 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 ... OK
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-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/4.1/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

PDATK.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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, 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 
 50.140  10.869  54.545 

Example timings

PDATK.Rcheck/PDATK-Ex.timings

nameusersystemelapsed
CSPC_MAE0.0080.0030.011
ClinicalModel-class0.1850.0200.205
ClinicalModel0.2500.0270.278
CohortList0.0380.0060.044
ConsensusMetaclusteringModel0.0210.0040.026
CoxModel0.8320.0790.912
GeneFuModel0.2470.0220.269
ModelComparison3.8380.0783.923
PCOSP0.2050.0180.224
RandomGeneAssignmentModel0.1780.0180.196
RandomLabelShufflingModel0.1770.0170.194
SurvivalExperiment0.3580.0160.375
SurvivalModel-class0.0980.0020.099
SurvivalModel0.0910.0020.092
assignColDataColumn0.0710.0010.072
assignSubtypes-CohortList-list-method0.7450.0060.752
assignSubtypes-SurvivalExperiment-data.frame-method0.0680.0030.072
assignSubtypes0.0770.0050.083
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method1.4990.0151.515
barPlotModelComparison1.6670.0161.684
birnbaum0.0020.0020.004
chen0.0020.0020.004
cohortSubtypeDFs0.0050.0030.008
compareModels-ModelComparison-SurvivalModel-method1.6290.0141.646
compareModels-SurvivalModel-SurvivalModel-method1.5640.0181.583
compareModels1.4640.0181.485
dropNotCensored-CohortList-method1.3100.0041.316
dropNotCensored-SurvivalExperiment-method0.1390.0030.141
dropNotCensored0.1290.0040.133
existingClassifierData0.0040.0030.006
findCommonGenes-CohortList-method0.1100.0030.112
findCommonGenes0.0820.0020.084
findCommonSamples-CohortList-method0.1190.0030.122
findCommonSamples0.1070.0030.110
forestPlot-ModelComparison-method1.5210.0171.540
forestPlot-PCOSP_or_ClinicalModel-method0.0780.0030.081
forestPlot0.2220.0040.226
getModelSeed-SurvivalModel-method0.0120.0030.014
getModelSeed0.0100.0030.013
getTopFeatures-PCOSP-method0.0110.0030.014
getTopFeatures-SummarizedExperiment-method0.4160.0040.420
getTopFeatures0.0100.0030.012
haiderSigScores0.0020.0020.005
hasColDataColumns0.0370.0000.038
merge-SurvivalExperiment-SurvivalExperiment-method0.3000.0030.303
modelParams-set0.0130.0030.016
modelParams0.0120.0030.015
models-SurvivalModel-method0.0110.0020.013
models-set-SurvivalModel-SimpleList-method0.0120.0030.014
models-set0.0080.0020.010
models0.0120.0030.015
normalsMAE0.0020.0030.006
plotROC-PCOSP-method0.2440.0060.250
predictClasses-CohortList-ClinicalModel-method0.7580.0110.771
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method0.7430.0110.755
predictClasses-SurvivalExperiment-ClinicalModel-method0.3300.0090.340
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method0.3080.0070.316
predictClasses0.2850.0060.292
rankFeatures-SummarizedExperiment-method0.4020.0030.406
rankFeatures0.3650.0030.368
removeColDataFactorColumns0.0800.0040.084
removeFactorColumns0.0030.0010.004
renameColDataColumns0.0770.0040.081
renameColumns0.0020.0000.003
sampleClinicalModel0.0080.0030.011
sampleCohortList0.0300.0030.033
sampleICGCmicro0.0080.0020.009
samplePCOSPmodel0.0090.0030.012
samplePCOSPpredList0.0380.0020.039
samplePCSIsurvExp0.0080.0030.011
sampleRGAmodel0.0100.0030.013
sampleRLSmodel0.0100.0020.013
sampleTrainedPCOSPmodel0.0110.0030.013
sampleValPCOSPmodel0.0490.0030.052
show-S4Model-method0.1400.0040.144
subset-CohortList-method0.4450.0060.453
trainData-set0.0130.0030.016
trainData0.0110.0030.013
trainModel-ClinicalModel-method0.0930.0040.097
trainModel-PCOSP-method1.0850.0401.126
trainModel-RGAModel-method1.1310.0111.146
trainModel-RLSModel-method0.9860.0090.999
trainModel1.0740.0111.085
validateModel-ClinicalModel-CohortList-method0.5830.0040.588
validateModel-ClinicalModel-SurvivalExperiment-method1.4170.0371.456
validateModel-GeneFuModel-CohortList-method0.9340.0290.965
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method0.9100.0130.924
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method0.9000.0150.915
validateModel0.1320.0080.140
validationData-SurvivalModel-method0.0120.0030.015
validationData-set-SurvivalModel-CohortList-method0.0100.0030.012
validationData-set0.0120.0030.015
validationData0.0120.0040.015
validationStats-SurvivalModel-method0.0100.0030.012
validationStats-set-SurvivalModel-data.frame-method0.0110.0030.014
validationStats-set0.0120.0030.015
validationStats0.0110.0030.014