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This page was generated on 2022-05-20 12:08:31 -0400 (Fri, 20 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4155
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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:
- 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? 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 1426/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PDATK 1.4.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2022-05-19 13:55:15 -0400 (Thu, 19 May 2022)
git_url: https://git.bioconductor.org/packages/PDATK
git_branch: RELEASE_3_15
git_last_commit: e8151e0
git_last_commit_date: 2022-04-26 12:13:17 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PDATK
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2022-05-20 05:44:23 -0400 (Fri, 20 May 2022)
EndedAt: 2022-05-20 05:53:36 -0400 (Fri, 20 May 2022)
EllapsedTime: 552.2 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/PDATK.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.4.0’
* 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-3.15-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/4.2/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

PDATK.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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 
 54.366  12.277  60.826 

Example timings

PDATK.Rcheck/PDATK-Ex.timings

nameusersystemelapsed
CSPC_MAE0.0080.0020.010
ClinicalModel-class0.1560.0040.161
ClinicalModel0.1640.0030.167
CohortList0.0800.0040.086
ConsensusMetaclusteringModel0.0240.0030.027
CoxModel0.5700.0060.577
GeneFuModel0.1820.0000.183
ModelComparison3.6870.0873.790
PCOSP0.1320.0150.148
RandomGeneAssignmentModel0.1540.0110.165
RandomLabelShufflingModel0.1230.0030.127
SurvivalExperiment0.1500.0030.154
SurvivalModel-class0.0630.0030.065
SurvivalModel0.0640.0030.067
assignColDataColumn0.0590.0010.060
assignSubtypes-CohortList-list-method0.7890.0080.800
assignSubtypes-SurvivalExperiment-data.frame-method0.0660.0050.073
assignSubtypes0.0670.0060.073
barPlotModelComparison-ClinicalModel-PCOSP_or_RLS_or_RGA-method1.6100.0161.641
barPlotModelComparison1.4990.0131.521
birnbaum0.0040.0020.005
chen0.0030.0020.005
cohortSubtypeDFs0.0040.0020.006
compareModels-ModelComparison-SurvivalModel-method1.3980.0121.413
compareModels-SurvivalModel-SurvivalModel-method1.3030.0131.322
compareModels1.3410.0121.355
dropNotCensored-CohortList-method1.0040.0051.011
dropNotCensored-SurvivalExperiment-method0.1000.0030.103
dropNotCensored0.0950.0030.098
existingClassifierData0.0040.0030.006
findCommonGenes-CohortList-method0.0390.0040.042
findCommonGenes0.0340.0030.038
findCommonSamples-CohortList-method0.0540.0020.057
findCommonSamples0.0540.0030.056
forestPlot-ModelComparison-method1.3710.0121.386
forestPlot-PCOSP_or_ClinicalModel-method0.0830.0030.086
forestPlot0.2300.0030.235
getModelSeed-SurvivalModel-method0.0120.0030.014
getModelSeed0.0110.0030.013
getTopFeatures-PCOSP-method0.0120.0030.014
getTopFeatures-SummarizedExperiment-method0.2790.0030.283
getTopFeatures0.0110.0030.014
haiderSigScores0.0040.0020.007
hasColDataColumns0.0240.0000.024
merge-SurvivalExperiment-SurvivalExperiment-method0.2440.0040.247
modelParams-set0.0210.0030.024
modelParams0.0230.0020.026
models-SurvivalModel-method0.0110.0020.014
models-set-SurvivalModel-SimpleList-method0.0130.0020.015
models-set0.0210.0030.024
models0.0150.0030.018
normalsMAE0.0030.0030.006
plotROC-PCOSP-method0.2370.0060.244
predictClasses-CohortList-ClinicalModel-method0.5440.0070.552
predictClasses-CohortList-PCOSP_or_RLS_or_RGA-method0.6490.0090.660
predictClasses-SurvivalExperiment-ClinicalModel-method0.2640.0050.269
predictClasses-SurvivalExperiment-PCOSP_or_RLS_or_RGA-method0.2530.0060.260
predictClasses0.2550.0070.263
rankFeatures-SummarizedExperiment-method0.3090.0030.313
rankFeatures0.2160.0020.219
removeColDataFactorColumns0.0300.0020.033
removeFactorColumns0.0050.0000.005
renameColDataColumns0.0350.0020.038
renameColumns0.0030.0000.003
sampleClinicalModel0.0090.0020.011
sampleCohortList0.0350.0020.038
sampleICGCmicro0.0080.0020.011
samplePCOSPmodel0.0100.0030.013
samplePCOSPpredList0.0460.0030.049
samplePCSIsurvExp0.0080.0020.011
sampleRGAmodel0.0110.0020.013
sampleRLSmodel0.0100.0030.013
sampleTrainedPCOSPmodel0.0110.0020.013
sampleValPCOSPmodel0.0500.0020.053
show-S4Model-method0.1140.0030.118
subset-CohortList-method0.2970.0030.302
trainData-set0.0220.0030.025
trainData0.0130.0030.016
trainModel-ClinicalModel-method0.0940.0030.100
trainModel-PCOSP-method1.1950.0151.214
trainModel-RGAModel-method1.2010.0061.210
trainModel-RLSModel-method1.0200.0061.027
trainModel1.2120.0071.221
validateModel-ClinicalModel-CohortList-method0.4790.0070.487
validateModel-ClinicalModel-SurvivalExperiment-method1.2680.0301.359
validateModel-GeneFuModel-CohortList-method1.8260.0121.938
validateModel-PCOSP_or_RLS_or_RGA-CohortList-method1.6940.0111.759
validateModel-PCOSP_or_RLS_or_RGA-SurvivalExperiment-method1.6730.0111.689
validateModel0.1560.0060.162
validationData-SurvivalModel-method0.0130.0020.015
validationData-set-SurvivalModel-CohortList-method0.0100.0030.013
validationData-set0.0130.0030.015
validationData0.0120.0030.015
validationStats-SurvivalModel-method0.0110.0030.014
validationStats-set-SurvivalModel-data.frame-method0.0120.0030.015
validationStats-set0.0130.0020.016
validationStats0.0120.0020.014